research title about plants and animals

Plant–animal communication: past, present and future

• Published: 30 January 2017
• Volume 31 , pages 143–151, ( 2017 )

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• Anne S. Leonard   ORCID: orcid.org/0000-0003-4464-269X 1 &
• Jacob S. Francis 1  

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Communication between plants and their animal partners underlies some of the planet’s most ecologically and economically important mutualisms. Study of communication in this context offers many opportunities to address fundamental questions about the costs and benefits of signal production, signal honesty, and receiver cognition. In this special issue, contributors highlight several key areas of current research, including how multiple receivers affect floral signaling, and how signaling may be related across different phases of reproduction. Visual signals are a particular emphasis, including how learning can mediate pollinator preferences, and the evolution of conspicuousness. In light of these focal areas, we summarize current trends towards the study of greater complexity both in terms of floral phenotypes and signaling/interaction networks.

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Acknowledgements

This work was supported by the National Science Foundation (Grant IOS-1257762 to A.S.L.; Graduate Research Fellowship to J.S.F). Thank you to D. Picklum, D.L. Moseley and F. Muth for comments.

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Department of Biology, University of Nevada, Reno, NV, 89557, USA

Anne S. Leonard & Jacob S. Francis

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Leonard, A.S., Francis, J.S. Plant–animal communication: past, present and future. Evol Ecol 31 , 143–151 (2017). https://doi.org/10.1007/s10682-017-9884-5

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Received : 16 December 2016

Accepted : 07 January 2017

Published : 30 January 2017

Issue Date : April 2017

DOI : https://doi.org/10.1007/s10682-017-9884-5

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Plant-Animal Communication

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Communication is an essential factor underpinning the interactions between species and the structure of their communities. Plant–animal interactions are particularly diverse due to the complex nature of their mutualistic and antagonistic relationships. However the evolution of communication and the underlying mechanisms responsible remain poorly understood. This book is a timely summary of the latest research and ideas on the ecological and evolutionary foundations of communication between plants and animals, including discussions of fundamental concepts such as deception, reliability, and camouflage. It introduces how the sensory world of animals shapes the various modes of communication employed, laying out the basics of vision, scent, acoustic, and gustatory communication. Subsequent chapters discuss how plants communicate in these sensory modes to attract animals to facilitate seed dispersal, pollination, and carnivory, and how they communicate to defend themselves against herbivores. Potential avenues for productive theoretical and empirical research are clearly identified, and suggestions for novel empirical approaches to the study of communication in general are outlined.

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Trees as a metaphor to understand relationships in biology

* E-mail: [email protected]

Affiliation Public Library of Science, San Francisco, California, United States of America and Cambridge, United Kingdom

¶ ‡ The PLOS Biology staff editors are Ines Alvarez-Garcia, Joanna Clarke, Richard Hodge, Nonia Pariente, Roland Roberts, Christian Schnell, Lucas Smith and Melissa Vazquez Hernandez

• Roland G. Roberts, 
• on behalf of PLOS Biology staff editors

Published: May 28, 2024

• https://doi.org/10.1371/journal.pbio.3002681
• Reader Comments

The phylogenetic tree has been a core conceptual tool for evolutionary biology for nearly 200 years. This editorial explores the role of the tree as a metaphor, discussing two new PLOS Biology Essays that look to the future.

Citation: Roberts RG, on behalf of PLOS Biology staff editors (2024) Trees as a metaphor to understand relationships in biology. PLoS Biol 22(5): e3002681. https://doi.org/10.1371/journal.pbio.3002681

Copyright: © 2024 Roberts, on behalf of PLOS Biology staff editors. This is an open access article distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Funding: The author received no specific funding for this work.

Competing interests: I have read the journal’s policy and the authors of this manuscript have the following competing interests: The authors are paid employees of PLOS.

We all know what trees look like; a single sturdy trunk, splitting into progressively thinner branches that end in a thousand leaf-bearing twigs. We also have some idea of the process by which they arise from their single origin, via linear growth through time, ramified by a series of simple forks.

Many branching organs arise in biology through related processes, and some of these bear the name “tree” to reflect this fact, whether in English (“bronchial tree”) or other languages—“dendritic arbor” manages to incorporate both Greek and Latin words for tree.

But there are other aspects of life on Earth where the tree has taken a more metaphorical turn. With its own roots in family trees and taxonomic trees, the phylogenetic tree first appears in a now-famous 1837 notebook jotting by Charles Darwin ( Fig 1A ), with more literally tree-like representations by scientists such as Ernst Haeckel ( Fig 1B ).

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A. The iconic page from Charles Darwin’s 1837 notebook. B. Ernst Haeckel’s very literal and anthropocentric phylogenetic tree from his 1879 book “The evolution of man.” C. Steenwyk and King’s depiction [ 1 ] of the use of synteny arguments by Schultz et al. to probe the deep evolutionary history of animals [ 2 ]. D. Church et al . propose intersecting multiple trees to generate a tree of cellular life. Images are from Wikimedia Commons (A and B, public domain), pbio.3002632, pbio.3002632, respectively.

https://doi.org/10.1371/journal.pbio.3002681.g001

Darwin’s conceptual leap was that this tree did not represent a mere rigid taxonomy, categorising a fait accompli creation in hierarchical form, but rather that it arose by a process of genotypic and phenotypic variation over enormous tracts of time and serial division through speciation. The metaphor works at the level of the process, as well as the form.

Nearly 190 years later, our journals are full of phylogenetic trees of staggering complexity, and they remain a central tool of evolutionary biology. However, there are some aspects in which the tree metaphor has its limitations; phylogenetic trees have been heavily pruned by extinction, branch points can be knotted and reticular rather than neat and binary, and branches can fuse and exchange material. We need to ensure that the metaphor serves us without constraining us, but on the whole, it largely holds water.

The types of character data that are used to infer the relationship between the branch-tips have moved with the technology, starting with gross anatomical features and progressing via antigen cross-reactivity and gene sequences to entire genomes. As higher-quality, chromosome-level genome assemblies become more widely available, some researchers are using synteny data (roughly speaking, chromosomal gene order) to tease apart particularly tricky branches in the Tree of Life. As Steenwyk and King describe in this issue of PLOS Biology [ 1 ], the benefit of synteny data is the rarity and specificity of the changes that are studied. The assumption that the observed changes in synteny are unique reduces the chances of confusing convergence for genuine relatedness. Steenwyk and King use two particularly thorny phylogenetic problems (the base of the animal tree [ 2 ], Fig 1C , and the relationship between major groups of teleost fish [ 3 ]) as case studies of how recent consideration of synteny has allowed us to disentangle relationships that had previously been challenging to disambiguate.

By contrast, Church et al . consider an orthogonal tree that is present in multicellular organisms [ 4 ]—the series of binary divisions that generate the trillions of cells in our own bodies from a single zygotic cell, including the generation of distinct cell types through differentiation. They recognise that the cellular trees of different animals could be combined with species and gene phylogenetic trees to generate an overarching tree of cellular life ( Fig 1D ). Thus, to use a Shakesperean example, a newt’s eyeball and a frog’s toe are both derived from a single ancestral cell (the zygote of their last common ancestor) by processes of speciation and differentiation. Again, technological advance is in the driving seat, as Church et al . propose that this could be formalized by leveraging the copious single-cell transcriptome (scRNA-seq) datasets that are increasingly available. The use of phylogenetic methods to explore comparative scRNA-seq data promises a new level of resolution in evolutionary developmental biology.

Both of the enabling technologies (widespread availability of chromosome-level genome assemblies and scRNA-seq data) have arisen very recently, so who knows what will we be doing with trees in another 200 years…?

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Plant physiology articles from across Nature Portfolio

Plant physiology is a sub-discipline of botany concerned with the physical, chemical and biological functioning of plants.

Latest Research and Reviews

Central transcriptional regulator controls photosynthetic growth and carbon storage in response to high light

Researchers identify unique transcriptional regulation that controls photosynthetic response, growth and biochemical carbon storage in high light for two variants of the same algae species, offering a glimpse into diel control of plant and crop yields.

• Seth Steichen
• Arnav Deshpande
• Lieve M. L. Laurens

Biosynthesis of copper nanoparticles using Solenostemma argel and their effect on enhancing salt tolerance in barley plants

• Hassan O. Shaikhaldein
• Fahad Al-Qurainy
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Thiourea improves yield and quality traits of Brassica napus L. by upregulating the antioxidant defense system under high temperature stress

• Muhammad Ahmad
• Ejaz Ahmad Waraich
• Mohamed S. Elshikh

High temperature and nib acidification during cacao-controlled fermentation improve cadmium transfer from nibs to testa and the liquor’s flavor

• Ivan D. Camargo
• Lucero G. Rodriguez-Silva
• Lucas F. Quintana-Fuentes

Exclusion-zone water inside and outside of plant xylem vessels

• Gerald H. Pollack

Osmosensor-mediated control of Ca 2+ spiking in pollen germination

Screening in Escherichia coli and biochemical experiments show that in Arabidopsis thaliana , OSCA2.1 and OSCA2.2 function as plant sensors of hypo-osmolarity, utilize Ca 2+ oscillations as second messengers and have crucial roles in pollen germination.

News and Comment

The importance of early human choices of wild plants in determining crop physiology

Leaf ecophysiological traits of crops are primarily inherited from their wild progenitors, challenging the conventional assumption that the origins of fast physiology lie only in early domestication and modern breeding.

How to establish a GAPLESS Casparian strip

To control the movement of water and nutrients, vascular plants seal the paracellular space between adjacent endodermal cells with a tight junction-like complex comprising the Casparian strip and Casparian strip membrane domain. In rice, GAPLESS proteins mediate the attachment of these two components and enable nutrient homeostasis.

• Milica Nenadić
• Joop E. M. Vermeer

Opening the gates

A new study reveals that epigenetic mechanism mediates temperature control of callose synthase expression to regulate opening of plasmodesmata and facilitate bud sprouting in lilies.

• Rishikesh P. Bhalerao

The glycerate transporter NPF8.4 links photorespiration and nitrogen flux in plants

Photorespiration is known to be involved in carbon flux in plants, enabling the carbon lost during RuBisCO oxygenation to be recovered. We show that NPF8.4 is a transporter responsible for sequestering the photorespiratory carbon intermediate glycerate into vacuoles during nitrogen depletion, elucidating a novel function for photorespiration in nitrogen flux.

Two bHLH transcription factors affect sprouting by regulating the level of ABA

For plants, the decision to germinate is a gamble on their subsequent survival. Xu et al. have now discovered a mechanism that determines the choice between germination and dormancy by regulating the level of ABA.

• Hideki Yoshida
• Makoto Matsuoka

Two nitrate sensors, how many more?

Nitrate is a nutrient and a signal. Membrane protein NRT1.1 reflects this duality as both a nitrate transporter and sensor. A new perception mechanism has just been discovered: transcription factor NLP7 is also a nitrate sensor. Thus, two distinct but interacting systems perceive nitrate. Are there others?

• Jordan Courrèges-Clercq
• Gabriel Krouk

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23 Ideas for Science Experiments Using Plants

ThoughtCo / Hilary Allison

• Cell Biology
• Weather & Climate
• B.A., Biology, Emory University
• A.S., Nursing, Chattahoochee Technical College

Plants are tremendously crucial to life on earth. They are the foundation of food chains in almost every ecosystem. Plants also play a significant role in the environment by influencing climate and producing life-giving oxygen. Plant project studies allow us to learn about plant biology and potential usage for plants in other fields such as medicine, agriculture, and biotechnology. The following plant project ideas provide suggestions for topics that can be explored through experimentation.

Plant Project Ideas

• Do magnetic fields affect plant growth?
• Do different colors of light affect the direction of plant growth?
• Do sounds (music, noise, etc.) affect plant growth?
• Do different colors of light affect the rate of photosynthesis ?
• What are the effects of acid rain on plant growth?
• Do household detergents affect plant growth?
• Can plants conduct electricity?
• Does cigarette smoke affect plant growth?
• Does soil temperature affect root growth?
• Does caffeine affect plant growth?
• Does water salinity affect plant growth?
• Does artificial gravity affect seed germination?
• Does freezing affect seed germination?
• Does burned soil affect seed germination?
• Does seed size affect plant height?
• Does fruit size affect the number of seeds in the fruit?
• Do vitamins or fertilizers promote plant growth?
• Do fertilizers extend plant life during a drought?
• Does leaf size affect plant transpiration rates?
• Can plant spices inhibit bacterial growth ?
• Do different types of artificial light affect plant growth?
• Does soil pH affect plant growth?
• Do carnivorous plants prefer certain insects?
• 8th Grade Science Fair Project Ideas
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• Science Fair Experiment Ideas: Food and Cooking Chemistry

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Muddy mangrove in Brazil, near mouth of the Amazon

Clear water mangrove on Twin Cays archipelago, Belize

Dwarf Rhizophora  in Paynes Creek National Park, Belize

Avicennia encroaching on Spartina  marsh at Port Fouchon, LA

Tall Ceriops  forest along the Hinchinbrook Channel, QLD

Rhizophora  on the beach at Cape Tribulation, QLD

Avicennia  and succulent marsh at Tinchi Tamba Wetlands, QLD

Mangrove at Waikopua Estuary near Aukland, NZ

Quiet mangrove creek at Bocas del Toro, Panama

Extensive dwarf mangrove forests in Zapata Swamp, Cuba

Dwarf Avicennia  forest at Whangapoua, New Zealand

Mangrove sunset at Twin Cays, Belize

Dwarf Avicennia  forest at KAUST along the Red Sea, SA

Mangroves Matter

Camel browsed Avicennia marina  along Red Sea

Mangroves on Cape Cleveland QLD, near AIMS

Vast cyanobacteria mat in the mangrove at Port Douglas, QLD

Dwarf Ceriops  forest along Hinchinbrook Channel, QLD

Overview of the mangrove forests along the Hinchinbrook Channel, QLD

Setting up mangrove experiments at GTMNERRS, Florida

Mangroves and eucalypts along the Clyde River, NSW

Inside the mangrove forest along the Clyde River, NWS

Dwarf Laguncularia with prop roots, Merritt Island, Florida

Sloth in a mangrove forest at Bocas del Toro, Panama

Dwarf Pelliciera and Rhizophora , Peninsula Valiente, Panama

Rainy flight over dwarf mangroves, Atlantico Sur, Nicaragua

Propagule of Pelliciera rhizophorae , Bocas del Toro, Panama

Mangroves at Giralia along the Great Sandy Desert, WA

Pelliciera at Peninsula Valiente, Bocas del Toro, Panama

Flower of  Pelliciera rhizophorae , Bocas del Toro, Panama

Smithsonian Marine Field Station on Carrie Bow Cay, Belize

Dinosaurs in the mangrove?

Experiments in the mangrove-saltmarsh ecotone, MINWR, FL

Magnificent frigate birds in the mangrove canopy, Belize

Measuring dwarf mangrove leaf area index, Fort Pierce, Fla.

Dwarf Rhizophora at Hidden Lake, Twin Cays, Belize

Mangroves at Carrie Bow, Twin, and South Water Cays, Belize

Northernmost Avicennia germinans , GTMNERRS, Florida

Arid land mangroves in Baja CA, Mexico

Strange little elephants in the mangrove, too?

Cormorant calling in the mangrove at Merritt Island, FL

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Principal Investigator

Our research focuses on animal-plant interactions in forested ecosystems. We study the interactions of plants and insects in temperate forests and tropical forested wetlands, with a keen interest in the ecological roles of herbivores in forested ecosystems and how they affect and are affected by resource availability.

For the past 25 years, we have been studying the effects of nutrient availability on animal-plant dynamics, nutrient cycling, and patterns of nutrient conservation in mangrove ecosystems in the Neotropics. We also have been attempting to determine the role of wood borers and other endophytic herbivores on plant architecture, growth, reproduction, sex expression, nutrient cycling, and community structure in forested ecosystems.

Animal-plant interactions are critical components of many ecological processes in forests, such as seed dispersal, pollination, or community structure.  In both temperate and tropical ecosystems, herbivores play important ecological roles in nutrient cycling, gap formation, and succession, and influence the composition and hydrology of forests.

By primary consumption (i.e., herbivory), animals can cause structural and functional disruption of primary and secondary growth of trees and shrubs. Herbivores can prune, weaken, or kill trees, reducing the timber quality of commercially important species. Forests of trees weakened by drought, nutrient deficiencies, air pollution, and other environmental stresses become more susceptible to outbreaks of insect herbivores. Herbivores that attack apical meristems affect plant architecture, growth, reproduction, and sex expression.  

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Wildlife conservation.

Wildlife conservation aims to protect plant and animal species as the human population encroaches on their resources.

Biology, Ecology, Conservation, Storytelling, Photography

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Wildlife conservation is the practice of protecting plant and animal species and their habitats . Wildlife is integral to the world’s ecosystems , providing balance and stability to nature’s processes. The goal of wildlife conservation is to ensure the survival of these species, and to educate people on living sustainably with other species. The human population has grown exponentially over the past 200 years, to more than eight billion humans as of November 2022, and it continues to rapidly grow. This means natural resources are being consumed faster than ever by the billions of people on the planet. This growth and development also endangers the habitats and existence of various types of wildlife around the world, particularly animals and plants that may be displaced for land development, or used for food or other human purposes. Other threats to wildlife include the introduction of invasive species from other parts of the world, climate change, pollution, hunting, fishing, and poaching. National and international organizations like the World Wildlife Fund, Conservation International, the Wildlife Conservation Society, the United Nations, and National Geographic, itself, work to support global animal and habitat conservation efforts on many different fronts. They work with the government to establish and protect public lands, like national parks and wildlife refuges . They help write legislation, such as the Endangered Species Act (ESA) of 1973 in the United States, to protect various species. They work with law enforcement to prosecute wildlife crimes, like wildlife trafficking and illegal hunting (poaching). They also promote biodiversity to support the growing human population while preserving existing species and habitats. National Geographic Explorers, like conservation biologist Charudutt Mishra and conservation technologist Rebecca Ryakitimbo, are working to slow the extinction of global species and to protect global biodiversity and habitats. Environmental filmmakers and photographers, like Thomas P. Peschak and Joel Sartore, are essential to conservation efforts as well, documenting and bringing attention to endangered wildlife all over the world.

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New study reveals shocking lack of conservation efforts for most threatened plants and animals

• Media release
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A new study from our top-rated Biosciences department, Princeton University, Williams College and Yale University has uncovered a dramatic lack of conservation actions being implemented for thousands of the world's most endangered species.

Despite biodiversity falling into crisis, the majority of endangered plants and animals are being left to fend for themselves with no evidence of targeted actions in place to recover their populations from threats like habitat loss, overexploitation, and invasive pests.

Very concerning findings

The study findings are deeply concerning as without intensified, strategic conservation efforts, we're headed towards a mass extinction catastrophe.

This study is the first comprehensive global assessment of how conservation efforts are being allocated across nearly 6,000 terrestrial species listed as threatened on the International Union for Conservation of Nature (IUCN) Red List of Threatened Species.

What the researchers found was an alarming intervention shortage:

• For over half (58%) of highly threatened species, they could not find any evidence of key conservation actions being implemented like habitat protections, invasive species control, or regulations on international trade.
• Just 9% of species threatened by habitat loss have minimally sufficiently amounts of habitat safeguarded in protected areas.
• Only 24% of species endangered by invasive species like rats, cats, and deadly fungi have documented programmes in place to control these problematic invaders.

While the overall findings are bleak, the study did uncover some bright spots demonstrating that conservation can be greatly effective when efforts are made.

Call for conservation scale-up

The researchers argue the number of seriously neglected threatened species indicates a major deficit in global interventions that must be urgently prioritised and funded, especially in biodiversity-rich developing nations.

They call on all parties to the Kunming-Montreal Global Biodiversity Framework to greatly accelerate strategic and well-funded conservation programmes to meet agreed upon goals for limiting extinction rates.

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Opportunities in Biology.

• Hardcopy Version at National Academies Press

11 Plant Biology and Agriculture

• Plants Constitute the Only Renewable Source of Energy

The enormous quantity of energy from the sun that is captured by the earth every day becomes available for life processes only through the photosynthetic activities of plants, algae, and a few kinds of bacteria. These activities have resulted in the characteristics of the atmosphere that we breathe and have altered our atmosphere's chemical makeup so that it is hospitable to animal life; prolonged over hundreds of millions of years, these activities have given rise to the fossil fuels that power our civilization. At the same time, photosynthesis constitutes the only renewable source of energy that is available to us for the future: a source of energy that is clean and potentially inexhaustible. Since plants directly or indirectly provide for our fuel and fiber needs in addition to being our primary source of food, they are exceedingly important to us from every point of view. Understanding their characteristics is of vital importance for the advance of biological knowledge and for human prosperity as well.

Vegetation plays a major role in maintaining the earth-atmosphere system in a habitable state. Except for the polar icecaps, snow- and ice-covered mountains, and certain of the earth's deserts, all land masses are covered with vegetation. This vegetation contributes to global energy and water budgets through modification of the solar energy, water, carbon dioxide, and nitrogen exchanges at the earth's surface. In short, not the atmosphere, nor the soil, nor any of the other conspicuous features of the earth's surface would exist in their present condition if it were not for the existence of photosynthesis, a process that we now believe to have evolved among the cyanobacteria (blue-green algae) at least 3.5 billion years ago—at least 2 billion years before the origin of any photosynthetic eukaryotes and more than 3 billion years before that of plants.

The solar energy metabolically fixed through photosynthesis constitutes about 0.3 percent of the total solar radiation that reaches the surface of the earth. In addition, a substantial fraction of the solar radiation that reaches the earth is converted into latent heat that leaves the earth's surface through plant transpiration. Some 75 trillion tons of water evaporate each year from the vegetation to the atmosphere. Agricultural vegetation is responsible for about one-third of this water flux and also, because of the coupling of these two processes, for one-third of the total photosynthetic energy fixation. Natural tree ecosystems in the tropical and subtropical zones constitute the major vegetation mediating global water and carbon dioxide exchanges.

The greater part of our food is produced by a few species of annual crop plants, mostly in the temperate and semihumid to semiarid middle latitudes. In food production, accumulation of dry matter is the process of greatest importance. Most of the weight in dry matter comes from the 175 billion tons of carbon dioxide that agricultural plants fix annually through photosynthesis.

In addition to the more obvious activities of plants that occur above ground, extensive activity in modifying the characteristics of the soil is a role of the roots. The amount of water passing through a plant in its transpiration stream is many times the amount required to supply its internal needs. All of this water, together with the inorganic nutrients that plants require for growth, enters plants by way of their roots. Plants accomplish this through physical forces and highly specific transport systems. Interactions between plants and soil microorganisms are of critical importance for certain assimilatory processes: for example, Rhizobium, Frankia , and certain free-living bacteria for obtaining nitrogen, and mycorrhizal fungi, regularly associated with the roots of approximately 80 percent of all plant species, for phosphorus uptake. In addition, roots produce hormones that are important in directing the characteristics of shoot growth.

• Plants and Their Environment

Through Evolution, Plants Have Developed Characteristics to Cope with Their Environment

One group of unicellular eukaryotes, the green algae (Chlorophyta), consists of organisms that share a number of biochemical and structural characteristics with plants. The similarities are so great that it is generally agreed that plants were derived from green algae, and specifically from organisms that had many of the features of the multicellular, freshwater alga Coleochaete . The cellulose cell walls that are such an important feature of the adaptation of plants on land originated among the green algae, as did the ability to form starch granules within the chloroplasts rather than free in the cytoplasm, and as did certain unique features of cell division that are common to all plants. The ancestors of plants invaded the land at least 430 million years ago, already multicellular and thus protected from the environmental extremes that they were to encounter there. The earliest plants were evidently mycorrhizal, the adaptive features of their symbiosis with fungi assisting them in growing on and eventually molding the features of the raw soils of those ancient times.

With their rigid cellulose cell walls, the bodies of plants are put together as if from a series of bricks. The sorts of cellular movements characteristic of animal embryology are impossible among such organisms, as is the ability to move from place to place in search of more suitable habitats or mates. Consequently, plants have evolved features that suit them to a sessile existence. Their life processes are bathed by a continuous stream of water that moves steadily from their root hairs into their roots, up through specialized conducting cells called xylem through the stems and into their leaves, and then mostly dissipates through the leaves through specialized openings called stomata, which also admit the carbon dioxide that plants require for photosynthesis. A waxy cuticle, similar to the outer covering of many arthropods, evolved among the earliest plants and helps to protect them from drying out.

Rooted in one place, many kinds of plants must tolerate a wide variety of environmental extremes. The consequent selection pressures led to the evolution of plant species that can withstand temperatures ranging from that of liquid nitrogen (-195.8°c) to 90°C and that could grow between temperatures lower than 0°C and higher than 60°C. Some plants are able to grow in solutions as concentrated as saturated salt and to withstand desiccation to the air-dry state.

An additional characteristic of plants not found in animals is the ability to grow endlessly from areas of cell division, or meristems, that occur at the tips of the roots and shoots. New plants can be propagated from such meristems, and, depending on their growth form, may grow through the soil into areas of favorable nutrient status. Each plant can be both embryonic and senescent simultaneously, and the entire history of a plant's development can often be traced in a single organ.

Understanding Plant Characteristics Is Important to Agricultural Development

In nature, the ability of plants to reproduce is of fundamental importance. When plants are grown as crops, it is often their seeds, fruits, or vegetative reproductive structures, such as tubers or fleshy roots, that people desire. The characteristics of crops have been modified by selection and hybridization for at least 11,000 years and are now being modified more precisely by the techniques of genetic engineering. Cultural practices are also important in promoting crop yield. In all types of agriculture, opportunities exist to improve yield in different areas of the world.

The optimal yield of particular strains of plants is usually tested by growing them in nonlimiting conditions—ones in which they do not encounter stress from drought, lack of nutrients, pests, or for any other reason. Such conditions are approximated when crops achieve their highest recorded yields. Record yields may be some three to seven times as high as average yields obtained under more usual conditions in the same year. In the United States, for example corn (maize) had a record yield of 19,300 kilograms per hectare in 1975, but yielded only 4,600 kg/ha on average.

Average agricultural productivity, therefore, falls far short of the genetic potential present in today's crops. Major environmental pressures must affect plants in ways that prevent the expression of their full genetic potential. Thus, improvements in productivity need not rest solely on increases in genetic potential. For this reason, both the identification of the environmental forces and the manipulation of crops to express their genetic potential more fully are important research areas in plant biology.

What are some of the environmental pressures that decrease productivity in plants? Diseases and insects are important contributors: These pests depress U.S. crop yields by an estimated 5.1 and 3.0 percent, respectively, below their genetic potential. In addition, weeds, which compete with the crops, depress yields another 3.5 percent overall, despite the widespread and relatively efficient application of control measures. An additional large depression in yields must be attributed to the only other factor that can be unfavorable, the physicochemical environment. An unfavorable physicochemical environment is found in soils and climates that are ill suited for plants. Adverse physicochemical environments—such as an insufficient supply of water or nutrients—caused yields to be far below their genetic potential. Sometimes the environments in which crops are grown are inherently unfavorable, and sometimes farmers choose not to improve these conditions or cannot afford to do so. At any rate, physiochemical limiting factors are the most important negative influence on U.S. agriculture. In many other parts of the world, crop losses caused by diseases, insects, and weeds are considerably more severe than in the United States, but physiochemical factors usually predominate everywhere in limiting agricultural yields.

The major physicochemical resources for plants are water, soil type, nutrients, carbon dioxide, oxygen, and solar radiation. Of these, water is generally the most limiting. Permanently dry and shallow (drought-prone) soils make up about 45 percent of the total U.S. land area. About 40 percent of insurance payments for crop losses are made to drought-stricken farmers. Cold and wet environments are also important limiting factors, followed by salinity, hail, and wind. To cope with water deficits, farmers have for thousands of years irrigated their fields, which has contributed significantly to higher yields. However, water has become increasingly scarce, and many alternative uses compete with agriculture for it. In addition, water of poor quality causes progressive soil degradation and a consequent loss of overall productivity. Irrigation, therefore, affords only an incomplete solution to the water limitations encountered by plants.

Plant nutrients will probably be less limiting than water in the immediate future because they are more abundant or can be produced in sufficient quantities at an acceptable cost. Supplies of nitrogen, phosphorus, and potassium are likely to be sufficient to support U.S. agriculture for the next 30 to 40 years. However, energy must be used in the manufacture of ammonia (the major source of nitrogen), and this is the largest energy input to the nonirrigated farm. Thus, the cost of energy will be a major constraint on the availability of nitrogen. Similarly, the cost of pesticides will increase with energy costs. Thus, the use of water, certain nutrients, and pesticides will be increasingly restricted, either because resources are limited or for economic reasons. These limitations may be overcome, in part, by the use of plants with lower requirements for these resources, a key aspect of the potential of genetic engineering in combination with other methods for crop improvement.

The Mechanisms by Which Plants Cope with Adverse Environments Have Only Begun to Be Understood in Molecular Detail

Unfavorable environmental conditions depress the rate of photosynthesis, and we are starting to understand the mechanisms by which this process occurs. Such knowledge will be highly applicable for the improvement of crop performance. The expansion of cell walls during plant growth is also affected by unfavorable environmental conditions. These walls contain cellulose as reinforcing microfibrils embedded in a carbohydrate and protein matrix that can flow in a plastic manner. The large pressures inside the cell, which are generated by osmotic forces, can cause plastic deformation of the wall and cell enlargement. The orientation of the cellulose microfibrils determines the direction of growth. Plant cell enlargement is extremely sensitive to certain environmental conditions and is retarded by low temperatures and drought. Such adverse conditions, for example, can cause seeds to fail to germinate or flowers to fail to open. The changes in molecular architecture of the cell wall that take place under such circumstances are largely unknown, as are the roles of water transport and plant hormones. Understanding these factors more completely bears directly on our ability to improve agricultural yield and quality.

The mechanisms of inorganic ion accumulation by plants also constitute a critical area for investigation. Plants differ genetically in their ability to accumulate nutrients—specially nitrogen, phosphorus, and iron—from a given kind of soil, but the molecular bases of these differences are poorly understood. By manipulating these features, performance would be improved.

Plants vary in their ability to withstand freezing temperatures; for example, some plants have developed a way to keep water unfrozen in cells at temperatures as low as -40°C. This ability permits some kinds of trees and shrubs to survive the extreme freezing temperatures that occur seasonally at high latitudes and high altitudes, but we do not understand its structural and molecular underpinnings at all. The reproductive structures of plants are characteristically more susceptible to low temperatures than their stems and leaves, but, again, we do not understand the mechanisms involved.

Many tropical and subtropical plants die when temperatures drop below 12°C, but some, such as cotton, can become acclimated to such chilling conditions. Acclimation is accompanied by a change in the phospholipid composition of the outer membranes of the cells and probably includes similar changes in the energy-transducing membranes of the mitochondria. Energy metabolism seems to play an essential role in the breakdown of cellular functions in cold-sensitive plants. Many of the storage problems of fruits and vegetables can be traced to the breakdown of membranes and the derangement of energy metabolism that occur at these temperatures. The biochemical basis for chilling resistance and acclimation needs to be established much more firmly to form a basis for improving the ability of subtropical plants to resist cool temperatures.

A better understanding of water transport in plants can likewise improve crop performance. The transport of water through the vascular system occurs under great tension (negative hydrostatic pressures), and the continuity of the water pathways is sometimes broken—an abrupt event that seems to be caused by cavitation of water under tension. An embolism that forms in the vascular tissue blocks further transport in that section of the system. Modern methods of electronic analysis indicate that such events occur frequently and are influenced by vascular architecture. Knowledge of how to keep the vascular pathways intact and filled with water is an important need.

Accurate studies of plant biology demand access to controlled environments. Growth chambers and similar facilities permit the efficient evaluation of factors affecting growth of plants throughout their entire life cycles. In addition, tissue culture and seedling culture systems provide convenient ways to study problems of plant growth. Such systems provide opportunities to explore how limiting water affects the growth of roots and shoots and allows the use of biophysical methods, growth regulators, genetic mutants, and molecular genetics to explore some of the reasons for altered development. Tissue culture systems likewise permit experimentation under controlled conditions. They have the additional advantages that metabolites can be supplied in the culture medium and that selection pressures can be created to identify desired genotypes at the cellular level.

Taken together, these research areas illustrate some of the ways a better understanding of plant growth could improve agricultural productivity. In principle, most of the features we have discussed should have a genetic basis. Thus, selection for more efficient water use and nutrient acquisition, as well as for the ability to avoid toxic ions, should help produce plants able to withstand unfavorable environments. The genetic and molecular mechanisms of plant resistance to disease and insect attack are also becoming known. Pest organisms are not only responsible for crop loss in the field, but also for a large amount of loss during storage. In these areas, as in many others, an improved understanding of the ways plants grow and develop will enhance our ability to produce better crops.

• Photosynthesis

A Better Understanding of Photosynthesis Is Crucial for our Future

Plants, like all organisms, depend on the products of photosynthesis for their growth ( Figure 11-1 ). The accumulation of plant biomass is a measure of the plant's total photosynthesis less the respiratory losses that have occurred during its growth. Crop productivity is linked to the seasonal photosynthetic performance of the crop canopies. For this reason, knowledge of the relation between productivity and photosynthesis has largely provided the incentive for the broadly based research effort into this elementary plant process.

Figure 11-1

Diagrammatic illustration of carbon processing in green plants. [B. B. Buchanan, University of California, Berkeley]

Advances in Photosynthesis Research Utilize the Full Range of Modern Biological Approaches from Biophysics to Molecular Biology

Tremendous strides have been made in gathering information about the catalytic components of photosynthesis at the level of atomic structure. Wide-ranging discoveries have created the opportunity to understand photosynthetic mechanisms at a molecular level. The most significant of these breakthroughs has been the recent crystallization of the photosynthetic reaction center of the purple bacterium Rhodopseudomonas viridis and the determination of its three-dimensional structure by x-ray diffraction analysis (see Figure 3-2 ). The wealth of existing knowledge concerning the mechanistic features of these complexes, which lends significance to this structural information, calls for corresponding structural work on other catalytic components of photosynthesis. The new structural information contributed immediately to our understanding of the molecular functioning of photosynthetic bacterial reaction centers. The three-dimensional structure along with the biochemical and biophysical information about the various catalytic and redox-active sites (sites of electron transfer) have focused attention on specific regions of the amino acid sequence, which seem to have special significance in light absorption and in charge-transfer processes. In this prokaryotic photosynthetic organism, designed alterations in the genes coding for polypeptides that make up the reaction center are possible and becoming routine. This sort of molecular engineering, coupled with the sophisticated capabilities of molecular spectroscopy and biochemistry, is certain to contribute much to our understanding of photosynthesis.

The crystallization of the Rhodopseudomonas reaction center has significance beyond the information obtained from its x-ray structure since it represents a fundamental discovery pertaining to the crystallization of integral membrane proteins. An intensive effort is under way to crystallize other major polypeptide complexes of bacterial and plant photosynthetic membranes.

The development and refinement of numerous other physical techniques are contributing to the revolution in structural information about the catalytic components of photosynthesis. In particular, dynamic information about structural transformations occurring during catalysis, which cannot be obtained from the static picture provided by x-ray analysis, is now becoming available through the use of powerful physical methods. The development of high-resolution nuclear magnetic resonance (NMR) techniques and their application to biology have been particularly successful. For instance, spin-echo NMR techniques allow the selective detection of a small subset of highly mobile, charged amino acid side chains that extend from the protein into the surrounding aqueous environment. The focus of this technique can be narrowed further to those amino acid residues that respond during catalysis; in other words, attention can be focused on the catalytic site as has been done for the chloroplast's coupling-factor enzyme. Even greater detail about the identity and rearrangements of catalytic site groups can come from other NMR techniques, such as double resonance and two-dimensional methods.

NMR is but one example of the army of physical techniques being used to analyze the structural basis of photosynthetic reaction mechanisms. Neutron scattering, electron scattering and electron microscopy, linear and circular dichroism, resonance Raman spectroscopy, Fourier transform infrared spectroscopy, extended x-ray absorption fine structure, and electron paramagnetic resonance spectroscopy are all contributing to the accumulating wealth of information about the molecular structure of the photosynthetic apparatus.

The amino acid sequence of photosynthetic membrane polypeptides has recently been determined from the nucleotide sequence of the corresponding genes. This advance, in turn, has permitted estimation of the two-dimensional folding patterns of these proteins by hydropathy analysis. This information has been taken into account in the most recent models of electron transfer through the complex.

Much Has Been Learned About Regulatory Mechanisms in Photosynthesis, but Much Remains to Be Done

With our current knowledge about the component processes of photosynthesis, it has become possible to investigate specific questions about their interdependence. The most important mechanism in the regulation of chloroplast processes is light activation, a central feature that coordinates the light-driven reactions with the so-called dark reactions of photosynthesis. Light is absorbed by chlorophyll and is converted to regulatory signals that modulate the activity of selected enzymes. Such regulation is essential because enzymes that degrade carbohydrates coexist in chloroplasts with enzymes of carbohydrate synthesis. Some biosynthetic enzymes are activated by light, whereas degradative enzymes are deactivated by light. In this way, the concurrent functioning of pathways that operate in opposing directions (futile cycling) is minimized and the efficiency of temporally disparate metabolic processes is maximized.

A number of soluble enzymes of photosynthetic carbon dioxide assimilation and other biosynthetic pathways show a similar activation response to light. Light regulates specific enzymes through a number of complementary mechanisms that have been identified during the past few years. These include changes in the concentration of certain ions, the concentration of regulatory metabolites, and the oxidation state of thiol groups (-SH) on key regulatory enzymes. Important in such thiol changes is the ferredoxin-thioredoxin system, a system in which thioredoxins—small regulatory proteins—are reduced in the light by the photosynthetic apparatus. The reduced thioredoxins, in turn, reduce and thereby activate selected target enzymes. In this way, the cell can adjust flux through the metabolic pathways associated with oxygenic photosynthesis in accordance with energy and metabolite status.

The catalytic activity of ribulose bisphosphate carboxylase/oxygenase (rubisco) is also modulated by light. Rubisco, which is the most abundant enzyme in the biosphere, performs the carboxylation reaction, the basis for photosynthetic carbohydrate production. Studies on the mechanism of rubisco activation have taken an unexpected turn with the recent discovery of the involvement of a polypeptide dubbed ''activase." In certain plants, a newly identified inhibitor, 2'-Carboxyarabinitol-1-phosphate, turns off the enzyme at night. The mechanisms controlling the formation of this inhibitor and the mode of regulation by the activase are currently under active investigation.

During the past years, much progress has been made in understanding the regulation of sucrose production in plants. Sucrose is the mobile form of energy that most plants form for transport to photosynthetic sinks; for example, to storage organs such as tubers and seeds that are the source of most of the world's food. During photosynthesis, chloroplasts convert carbon dioxide, water, and phosphate to triose phosphates, which migrate to the cytosol and combine to form sucrose. Photosynthesis requires inorganic phosphate, which is released during sucrose synthesis; therefore, photosynthesis and sucrose synthesis must be closely coordinated. There is evidence that this coordination is provided in part by phosphate. Recently, a second compound specifically serving this function has been identified. Fructose-2,6-bisphosphate coordinates the metabolism of sucrose and starch and, in so doing, links metabolic processes of the chloroplast with those of the cytosol. Recent results suggest that fructose-2,6-bisphosphate may also coordinate cytosolic and amyloplast (a starch containing plastid) metabolism in sink tissues.

Our Current Knowledge of the Biochemistry and Physiology of Photosynthesis Has Made It Possible to Study the Process in Whole Plants or Intact Tissues

Studies on photosynthesis have important applications to the improvement of agricultural productivity. Low temperatures; drought; photoinhibition; the accumulations of herbicides, pesticides, or fertilizers; and pollution are examples of frequently encountered conditions that compromise the efficiency of production in crops. Impaired photosynthesis is a major contributor to these losses, and we need to understand the mechanisms by which it takes place, something we are now in a position to do.

One area poised for major advances is the application of recently developed and adapted physical techniques to investigate component processes of photosynthesis in situ. Techniques such as kinetic absorption spectroscopy, delayed light imaging ( Figure 11-2 ), NMR spectroscopy, flash fluorescence, and photoacoustic spectroscopy are now applied to diagnostic studies of how particular environmental conditions may influence intersystem electron transfer, adenosine triphosphate formation and consumption, enzyme activation, light regulation, photosynthetic reaction center activity, and the transfer of light energy. The usefulness of these techniques depends on an underlying experimental basis for interpreting the often complex results obtained from in situ measurements. This fact points to the need for expanding this information base.

Figure 11-2

Delayed light imaging in herbicide-treated bean leaves. Leaves normally emit a tiny portion of the photosynthetically active radiation that they absorb. Defects in certain chloroplast processes increase the amount of light that is emitted. This feature (more...)

The development of "model" plant systems will unquestionably contribute to the solution of problems in photosynthesis related to agriculture. A notable recent advance has been the development of vigorous photoautotrophic cultured cell lines. Because of the difficulty of growing plants to maturity under heterotrophic conditions, the screening and selection of photosynthetic mutants is generally limited to positive selection methods. The advent of these photoautotrophic cell lines and the promise they hold for expanding the use of mutants in photosynthesis research emphasizes the need for substantial effort aimed at developing reliable plant regeneration procedures. It is becoming increasingly evident that cyanobacteria represent a highly useful model system for chloroplasts. The progress that has been made in developing a genetic transformation system for cyanobacteria highlights their potential for the investigation of photosynthetic processes and events generally. Among plants, Arabidopsis and Petunia are genetically tractable, and they lend themselves particularly well to being modified through genetic engineering. They offer many approaches to long-standing agricultural problems with new research strategies having potential far beyond what could be imagined just a few years ago.

Another area with potential for advances concerns the central enzyme of the carbon reduction cycle, rubisco. Competition by molecular oxygen for the carboxylation substrate at the catalytic site of this enzyme considerably lowers the efficiency of photosynthesis. Since the discovery of natural interspecific variation in the severity of the competition between carbon dioxide and oxygen, the possibility of substantially reducing the enzyme's oxygenase activity, perhaps to negligible levels, has been recognized. Accumulating information about the catalytic site and its reaction mechanism, coupled with the ability to make designed alterations in the gene, is a promising approach toward elucidating the molecular factors that control the discrimination between CO 2 and O 2 . The evolution of rubisco in an ancestral anaerobic atmosphere rich in CO 2 produced an enzyme with a flaw that now burdens plants living in CO 2 -poor, oxygenic atmospheres. Molecular genetics, guided by an in-depth understanding of the molecular basis for the competition between O 2 and CO 2 , may enable scientists to design a more efficient enzyme. Genetic transformation of the plant gene coding for the catalytic subunit of rubisco appears now to have gone beyond cloning in bacteria. Transfer of the chloroplast gene into the nucleus and addition of a chloroplast-targeting sequence to the protein is a major step toward producing plants with an "engineered" rubisco gene, which will yield a more efficient enzyme.

Photosynthesis depends on processes occurring elsewhere in the plant. In particular, the developing portions of the plant and specialized storage organs, which are considered "sinks" for photosynthate, exert a poorly understood control on processes that occur in the chloroplasts. Basic information is lacking about the mechanisms that control the development of photosynthate sinks and that determine the priorities of individual sinks for available photosynthate. Little is known about how the various chemical forms of photosynthate cross cellular and organellar boundaries in either source or sink tissue. In many cases, it is not even known whether specific transporters are involved. In contrast, excellent progress has been made in discovering the mechanistic basis for carbohydrate transport across bacterial membranes. Much of this recent success has been fueled by the application of elegant new techniques of immunology and molecular biology. The approaches and mechanistic principles established by this pioneering work in bacterial carbohydrate transport will have a great impact on research in photosynthate transport and partitioning.

The diverse disciplines of photosynthesis research are beginning to converge in a meaningful and synergistic fashion. As a consequence, the prospects for applying what has been learned about photosynthesis to problems relevant to agriculture and the prospects for seminal discoveries about photosynthesis have never been better.

• Nitrogen Fixation

Nitrogen, Which Is Abundant in the Atmosphere, Is Essential for All Organisms

Even though nitrogen constitutes some 80 percent of our atmosphere, it is relatively difficult for organisms to obtain. Since it is an essential constituent of proteins, nucleic acids, many enzymic cofactors, and other essential metabolites, nitrogen is required by all organisms, which obtain it primarily as a result of the nitrogen-fixing abilities of a very few kinds of bacteria. These bacteria convert nitrogen from its gaseous form (N 2 ) into ammonia (NH 3 ), which can be used by other organisms. Because it is so scarce in an appropriate form, nitrogen deficiency is a common limiting factor in the growth of plants, animals, and microorganisms. Biological nitrogen fixation in bacteria, in which nitrogen is converted to ammonia catalytically by the enzyme nitrogenase, has been studied intensively as a biological process of considerable fundamental interest and of potentially substantial energy savings through the use of less nitrogen fertilizer.

Research on nitrogen fixation is carried out at levels of biological organization ranging from ecology to molecular biology. The biochemistry and molecular genetics of nitrogen fixation have been greatly advanced by studies on a model organism, Klebsiella pneumoniae , whose relationship to the common colon bacterium Escherichia coli allows the application of many sophisticated techniques that have been developed for use with its extensively studied relative. Other bacteria have also been important as experimental material for investigations on how nitrogen fixation functions in various ecological niches and takes place in connection with a number of different biochemical strategies. Among the achievements of the past few years have been the identification of all the genes required for nitrogen fixation ( nif) in Klebsiella and the demonstration of function for several of them. Among these genes are the three coding for the enzyme nitrogenase and several whose products are important for combining nitrogenase with its molybdenum-iron cofactor and for the delivery of electrons to the enzyme. The energetics of nitrogen fixation is an important concern if this process is to find new agricultural uses. It is being explored in several systems, including complex symbiotic associations such as those that involve the nodule-forming bacterium Rhizobium , which lives on the roots of the plant family Fabaceae, the legumes.

Several major advances have been made in understanding how nitrogen fixation is regulated. These findings tie in with new understanding of the overall regulation of nitrogen metabolism. Specifically, cells with adequate nitrogen reserves do not fix nitrogen because nif genes are not transcribed. Their activation requires the general nitrogen regulatory system Ntr to induce the expression of a nitrogen-fixation-specific activation system (Nif). After activation, the gene product of nifA then induces transcription of all the other nif genes. It has been found that the Nif regulatory system is evolutionarily related to the Ntr regulatory system, which also controls genes responsible for ammonium assimilation and amino acid catabolism. Furthermore, both nif and ntr genes have specialized promoters whose nucleotide sequences differ from the promoter sequences of most prokaryotic genes. This information is significant with regard to our concepts concerning the regulation of transcription in bacteria and the regulation of numerous physiological systems.

Another major achievement has been the demonstration that gene expression of the nitrogenase loci ( nifHDK ) in the filamentous cyanobacterium Anabaena involves the rearrangement of the DNA itself. In vegetative photosynthetic cells, the nifHD and nifK genes are separated in the genome. When cells differentiate to become nitrogen-fixing heterocysts, the DNA is rearranged to align nifHDK as a continuous operon, as in Klebsiella. Our ability to understand the cyanobacterial system has been revolutionized recently by the development of techniques for genetic conjugation in these bacteria, which have made possible experimentation on genes and their expression. Unicellular cyanobacteria that show temporal separation between oxygen-producing photosynthesis and oxygen-sensitive nitrogen fixation are ideal models for the possible compatibility of nitrogen fixation and photosynthesis in plants in the absence of symbiosis.

The most extensively studied association between plants and nitrogen-fixing microorganisms is that of Rhizobium and its legume hosts, which include such important crop plants as alfalfa, soybean, peanut, vetch, cowpea, beans, peas, and clover, as well as a number of important tropical timber trees, the winged bean, and the "miracle tree," Leucaena , now being used to vegetate large areas in the Asian and Pacific tropics and as a ready source of fuel. The family Fabaceae consists of some 18,000 species of plants; because of their ability to grow in relatively infertile soils, they are often locally prominent in vegetation. Colonies of Rhizobium form nodules on the roots of legumes and live within them, where both the presence of the bacteria and the structure and biochemistry of the nodules play key roles in the process of nitrogen fixation. This association is the most important single contributor to the supply of nitrogen on earth that is available for biological reactions.

Substantial advances have been made in understanding the genetics of the Rhizobium- legume nitrogen-fixing system during the past decade. The nif genes of Rhizobium meliloti were identified by their DNA homology to the cloned nifHDK of Klebsiella . Subsequently, their functionality was proven by a site-directed gene replacement technique, which has since become indispensable for the genetic manipulation of Rhizobium, Agrobacterium , and other bacteria associated with plants. Other genes important for host recognition, formation of nodules, and efficiency of nitrogen fixation have been identified, cloned, and analyzed. In most species studied so far, these genes lie on large native plasmids. An exception appears to be the genes for symbiosis and nitrogen fixation in the Bradyrhizobium (slow-growing Rhizobium ) strains, which nodulate soybean, peanut, cowpea, and other legumes.

A new view of what happens in the rhizosphere as soil microbes such as Rhizobium encounter their legume hosts has emerged from studies of nodulation gene expression. The nod genes of Rhizobium are required for recognition and invasion of the plant hosts and for nodule formation on their roots. As such, they appear to be the earliest-acting genes in the legume -Rhizobium association. These genes are not transcribed by Rhizobium cells grown in pure culture; their expression is activated in the presence of host plants, indicating that a signal is sent from the host to the bacteria.

Legumes themselves play an important role in the symbiotic fixation of nitrogen by Rhizobium bacteria. Certain proteins, which are produced only in nodules and not in uninfected roots, seem to be essential for nodule function. One of these is leghemoglobin, an oxygen-binding protein that helps to protect the oxygen-sensitive enzyme nitrogenase. Soybean leghemoglobin genes have been cloned, and their synthesis is controlled at the transcriptional level by an unknown signal from the bacterium. The primary amino acid sequence of plant leghemoglobin strikingly resembles that of animal myoglobin. Whether this similarity reflects common descent is not known, but nitrogen-fixation is an ancient process, still carried out under the anaerobic condition in which life first evolved. Other nodule proteins, called nodulins, appear at specific times during infection; their synthesis is also regulated at the transcriptional level. Further investigations of the loci encoding nodulins may help us to understand how nodules form and function and why legumes are appropriate hosts for Rhizobium , whereas other plants are not.

Many Questions Concerning the Physiology, Biochemistry, and Molecular Biology of Nitrogen Fixation and Symbiosis Are Still to Be Answered

The active site of nitrogenase and the mode of catalysis need to be elucidated. Why is nitrogen fixation coupled to hydrogen evolution? What is the basis for the oxygen sensitivity of the enzyme? What is the structure of the iron-molybdenum cofactor and what is its relationship to the active site? Understanding the mechanism by which nitrogenase reduces nitrogen may enable us to synthesize catalysts that will perform this process more efficiently. The symbiotic relationship between plants and nitrogen-fixing organisms also raises questions. What determines the host range of symbionts, and why do not all plants form symbioses? What signals pass between bacteria and plants, and how do these signals regulate gene expression in each of them? What metabolic exchanges occur between the symbiotic bacteria and the plant? Why do nitrogen-fixing microorganisms export their fixed nitrogen? What are the energetic costs of symbiotic nitrogen fixation at the cellular, organismal, and ecological levels? More research is also required on the symbiosis between plants and nitrogen-fixing organisms other than Rhizobia . Another genus of bacteria, an actinomycete of the genus Frankia , commonly forms root nodules within which nitrogen fixation occurs with certain plants other than legumes, such as Ceanothus, Myrica, and Alnus . We need to understand these interactions better and to determine how they resemble and differ from the better-known one between Rhizobium and legumes. Our understanding of the biology of free-living nitrogen-fixing bacteria, some of which are photosynthetic and some not, also contains gaps. How do they solve the problems of protection against oxygen and generation of energy? Can such organisms provide solutions to the limitations in agronomically important nitrogen fixation? Work on nitrogen fixation not only advances our knowledge of a complex process that has great economic impact, but also answers basic questions of biology, such as classical questions concerning the nature of symbiosis. More detailed studies of plant-bacterial associations may point the way to an improved understanding of the functions of plant cells and theft components, just as the study of bacterial and animal interactions has revealed fundamental aspects of both bacterial and animal cells.

MESSENGER MOLECULES IN BACTERIAL-PLANT INTERACTIONS

Soil bacteria interact with plants in a variety of ways. Some establish beneficial symbiotic relationships with specific hosts, whereas others invade the plants and cause pathological tumors to form. The successful infection of the plant requires the host to be recognized and genes in both the plant and the microorganism to be activated. Recent discoveries demonstrate that plants release low-molecular-weight organic compounds that activate microbial genes whose products are needed to infect plants.

Bacteria of the genus Rhizobium invade the roots of leguminous plants, where they cause root nodules to form. Within these nodules, rhizobia bacteria fix atmospheric nitrogen, which is then used by the plant as an important nutrient. Exudates from alfalfa roots activate a set of genes in Rhizobium meliloti , whose expression stimulates the earliest detectable host responses, consisting of root-hair curling and cortical cell divisions. Plant scientists have identified compounds in the exudate of alfalfa roots that induce nodulation genes in R. meliloti . These signaling molecules, of which luteolin is the most active, are flavonoids—secondary metabolic products found in virtually all plants. The important flower-coloring pigments known as anthocyanins, which are responsible for most of the reds and blues seen in flowers and leaves, constitute one group of flavonoids. Other flavonoids may have roles in food-choice preference by insects, as blocks to ultraviolet radiation, or possibly in protecting plants from pathogens.

The crown-gall bacterium Agrobacterium tumefaciens infects plants through wounds and causes the formation of tumors. Tumorous growth is based on the integration of a specific segment of bacterial DNA into the genome of the plant. For transformation to occur, a set of virulence genes has to be activated in the bacterium. Scientists found that virulence genes are activated by phenolic compounds that are present only in the exudate of wounded, metabolically active cells. Thus, injury to the plant tissue not only provides a portal of entry for the bacterium, but also is necessary for the production of the signaling molecules that activate the infection process.

• Plant Growth And Development

Plants Have an Open System of Growth in Which the Role of a Very Few Kinds of Plant Hormones Is of Critical Importance

Many developmental processes in plants are regulated by a relatively small number of substances called plant hormones. In addition, environmental cues, such as the duration of the daily light and dark period or the ambient temperature, help synchronize the life cycle of plants with the changing seasons. In at least some instances, environmental effects on plant development are mediated by hormonal factors. An understanding of these regulatory mechanisms is needed if one is to optimize the growth of crop plants.

Plant Hormones

Plant hormones have complex and often overlapping functions.

The five known groups of plant hormones are auxins, gibberellins, cytokinins, abscisic acid, and ethylene. These substances often fulfill similar functions. For example, auxins, gibberellins, and cytokinins all induce cell division in different tissues. In addition, auxins and gibberellins both regulate cell elongation, although they probably do so by different mechanisms. Each plant hormone shows a wide spectrum of activities and affects different processes. Ethylene, for example, induces fruit to ripen, flowers to fade, stems of semiaquatic plants to elongate rapidly (for example, in rice growing in deep water), and bromeliads to flower (such as pineapple). The specificity of action of plant hormones is determined by the chemical structure of the compound and by the nature of the target tissue. In some instances, the increased synthesis of a plant hormone initiates a new developmental process. In other cases, the responsiveness of the plant to a given concentration of hormone changes under different conditions of growth.

In recent years, progress has been made in understanding the biosynthesis of plant hormones, most notably that of gibberellins and ethylene. The pathway of gibberellin biosynthesis has been elucidated with a variety of techniques. Enzymological work and the application of radiotracer technology led to the identification of gibberellin intermediates. The availability of so-called growth retardants—compounds that inhibit specific enzymes of gibberellin biosynthesis—has been of great help in isolating gibberellin precursors. Equally important was the use of well-characterized dwarf mutants, which are impaired at different steps of gibberellin biosynthesis. A combination of genetic and biochemical work has brought order into the confusingly large army of different gibberellins; more than 70 kinds are known in plants and in the fungus Gibberella fujikuroi . Probably only one of these, however, actively controls shoot elongation in most plants. Other gibberellins are either hormone precursors or inactive metabolites.

Ethylene, the simplest unsaturated hydrocarbon, hardly conforms to our chemical concepts of a hormone; yet it regulates, at extremely low concentrations, a number of key developmental plant processes. Some of these such as fruit ripening are of considerable agronomic importance. Much effort has been invested in elucidating the pathway of ethylene biosynthesis in the hope that control of this process will lead, for example, to extended storage life for perishable agricultural products. Although the enzyme whose activity determines the level of ethylene biosynthesis in most plants is present at vanishingly low levels, even in ripening fruit, it has now been purified, and monoclonal antibodies against it are available.

The genes responsible for auxin (indoleacetic acid) and cytokinin biosynthesis have been isolated from the plant pathogenic bacteria Agrobacterium tumefaciens and Pseudomonas savastanoi . The cytokinin gene encodes an enzyme that is similar to an enzyme that has been isolated from plants. The bacterial genes for indoleacetic acid synthesis encode two enzymes, a tryptophan monooxygenase and indoleacetamide hydrolase. Auxin biosynthesis in plants is mediated by different enzymes.

Abscisic acid plays an important role in the water relations of plants. When the water supply becomes limiting, a rapid increase in abscisic acid is, at least in part, responsible for the closure of the stomata in the leaves and other green parts of the plant and, as a consequence, for the reduction in the rate of transpiration. The pathway of abscisic acid biosynthesis has not yet been elucidated.

In contrast to the progress made in the elucidation of plant hormone biosynthesis, relatively few advances have occurred in our understanding of the mode of action of these substances. A few exceptions can be mentioned, however. In cereal grains, starch and other reserves are mobilized during germination. This process is initiated by the secretion of gibberellin into the aleurone layer of the seed. There, the hormone induces the synthesis of hydrolytic enzymes, most notably that of α-amylase. From the aleurone cells, hydrolases are secreted into the endosperm, where they break down stored food reserves, for example, starch. The induction of α-amylase by gibberellin is based on enhanced transcription of genes encoding this enzyme.

In the case of the aleurone system, the mechanism of hormone action could be approached successfully because the biochemical response was well defined.

Most other hormonally regulated processes in plants are more complex and, therefore, less tractable. Generally, we know too little about the biochemical reactions underlying particular developmental phenomena, such as growth. It has been known for many years that auxin promotes cell elongation by increasing the plasticity of the cell wall. As a result, water enters the cell, and the hydrostatic pressure extends the wall. A number of polysaccharide and proteinaceous components of the cell wall have been characterized, but their interconnections are only partly understood, and a detailed picture of cell wall architecture is missing. For this reason, it is not clear which bonds have to be broken for the cell wall to loosen and whether this is achieved enzymatically or through the action of protons that are secreted into the cell wall. Molecular biology has permitted scientists to bypass the existing gap of biochemical knowledge and to isolate genes that are activated within minutes as a result of auxin treatment. Study of such hormonally regulated genes may be rewarding, and their hormone-responsive regulatory elements can be identified.

Almost nothing is known about the site of action of plant hormones. Binding proteins have been described for all plant hormones, but no receptor function has been established for any of them. In no instance has it been possible to connect hormone binding and a hormonally regulated biochemical response. Not even in the aleurone system has it been possible to initiate, in vitro, the transcription of hormonally regulated genes.

The Chain of Events from the Initial Interaction of Plant Hormones with Their Receptors to the Manifestation of the Response Must Be Established

Agriculture has benefited greatly from the use of plant hormones and synthetic growth regulators. The first selective herbicides, for example, were synthetic auxins. Growth retardants, which inhibit gibberellin biosynthesis, have been used extensively to stunt the growth of wheat and, thereby, to reduce losses caused by lodging (collapse of the wheat stem from excessive height). Practical applications for plant growth regulators have often been found empirically. The targeted use of plant hormones and synthetic plant growth regulators requires detailed knowledge of their mode of action. In most instances, the response is well characterized at the physiological level. What is urgently needed is the identification of plant hormone receptors and the elucidation of the primary biochemical reactions that underlie the physiological response. Just as mutants blocked in hormone production have helped to establish the pathway of hormone biosynthesis, so can mutants blocked in their response to plant hormones help us to identify hormone receptors and components of the hormonal transduction chain. Isolation of genes whose transcription is regulated by plant hormones will also advance our knowledge of the mechanism of hormone action, especially when the gene products are identified.

Plant enzymes mediating gibberellin and ethylene biosynthesis have been described in recent years. The prospects are good that genes encoding key enzymes in these pathways will be isolated and characterized in the near future. Similar progress has yet to be made in the elucidation of abscisic acid and auxin biosynthesis.

Environment

Environmental factors play a key role in plant development.

Since plants are sessile organisms, they must adjust their life cycles to the annual changes in the environment. The timing of such events as seed germination, flowering, the onset of dormancy, and the breaking of dormancy has to be coordinated with the seasons of the year. Plants achieve this coordination by measuring the duration of day and night length and the time over which they are exposed to low temperatures.

When a seedling emerges from the soil and is exposed to light, the growth pattern and the metabolic activities of the plant change completely. The rate of stem elongation is reduced, the leaves unfold, and the photosynthetic apparatus differentiates. These changes are all controlled by phytochrome, the best characterized regulatory photoreceptor. Phytochrome is a protein that occurs in two forms, a red- and a far-red-light absorbing one. Red light of 660 nanometers activates phytochrome by switching it to the far-red-absorbing form. Far-red light (730 nm) converts phytochrome back to its original form and cancels the effect of the initial red illumination.

In many plants, the time of flowering is determined photoperiodically, by the relative length of the daily period of light and dark. This ensures seed production at the proper time of the summer or fall. Photoperiodic induction also prepares perennial plants for the advent of winter. As the nights get longer, buds become dormant, leaves abscise, and the plant acquires cold hardiness. In one instance, the enhanced growth of spinach under long days, the biochemical basis for photoperiodic induction has been elucidated. The greatly increased rate of growth reflects the enhanced activities of two enzymes in the pathway of gibberellin biosynthesis. These photoperiodic processes are under phytochrome control.

Much has been learned in recent years about the phytochrome molecule in terms of its spectral, physicochemical, and immunochemical properties. The gene encoding phytochrome has been cloned and sequenced, and it has been shown that phytochrome controls the expression of its own gene through a feedback mechanism. Phytochrome also regulates the expression of other genes.

In addition to phytochrome, plants contain at least one other pigment that regulates developmental processes, the blue-light photoreceptor. This pigment mediates phototropism and resembles a pigment with analogous functions in fungi. It has not yet been isolated, and the chemical structure of its chromophore has not been determined.

The cold temperatures of winter are often used as an environmental cue for the initiation of developmental processes that take place in Spring or early summer. Dormancy in many plant species is broken after exposure to a critical number of cold days; flowering of some plants will occur only if they have experienced a cold period of a certain duration (vernalization). Even though these responses are well characterized at the physiological level, nearly nothing is known about the mechanism of cold perception and the biochemical reactions that underlie the breaking of dormancy or vernalization.

Much Research Is Yet to Be Done on the Effect of Environmental Factors on Plant Development

The perception of nonphotosynthetic light, of cold temperature, and of gravity permits plants to orient themselves in time and space. Much progress has been made recently in research on phytochrome, a pigment of central importance in light perception. Despite this progress, little is known about the transduction of the red-light stimulus perceived by this pigment. What chain of biochemical reactions is set into motion by the activation of the photoreceptor? Because of the central role of phytochrome in the control of many plant processes, research on its mode of action is of prime importance.

Tropic responses to light and gravity probably have a number of reactions in common. How does a plant determine the direction of light and gravity, and how does it orient its growth toward or away from these stimuli? A wealth of knowledge dates back to Darwin on tropic phenomena in plants. However, new approaches are needed if one is to understand, in molecular terms, the mechanisms that govern such responses. Current work with photo- or geotropic mutants of Arabidopsis thaliana , a plant with an exceptionally short life cycle, may lead to identification of the blue-light photoreceptor pigment, of gravity sensors, and of biochemical reactions that underlie the tropic response.

The problem of how plants measure temperature, how they determine the duration of the cold period, and how they translate this information into developmental responses requires renewed research efforts. These questions are among the most difficult ones in plant biology because basic concepts, on which testable hypotheses can be built, axe largely lacking. Precisely because of this gap in our knowledge, work in this area may be particularly rewarding.

Plant Reproduction

Many aspects of plant reproduction are now amenable to detailed analysis.

Most crop plants are grown for their seeds and fruits. Understanding the biology of plant reproduction, including flowering, fertilization, and the development of fruits and seeds, is therefore of great economic importance. The production of hybrid plants from inbred parents is an important aspect of reproductive plant biology. Such hybrids often produce substantially higher yields than do the inbred parental lines. Growth of hybrid plants is possible only when self-fertilization is excluded. Reproductive self-incompatibility and cytoplasmic male sterilty are the best known mechanisms to prevent inbreeding in plants. Both are processes of great inherent scientific interest that remain poorly understood at the molecular level despite recent advances.

Genetic Self-Incompatibility Precludes Self-Fertilization in Bisexual Plants

Genetic self-incompatibility, which is widespread among plant species in nature, has been known to plant geneticists for a century. Several mechanisms for self-incompatibility exist; in gametophytic incompatibility, a sperm with a particular haploid S genotype ( S is the incompatibility locus) is unable to fertilize an egg having the same allele. Another mechanism, sporophytic incompatibility, is determined by the diploid genotype of a parent plant. The tissues of this plant, including those of its style (part of the flower holding the stigma), will contain two alleles at the S locus, and pollen containing either of these will fail to germinate on the stigma of that plant. How does identity at genetic loci lead to the rejection of a germinating pollen grain? This question can now be approached with new tools, thanks to the identification of the genes responsible for self-incompatibility reactions in tobacco and in mustard.

Cytoplasmic Male Sterility, Which Causes Bisexual Plants to Serve as Female Parents Only, Is Mainly Controlled by Mitochondrial Genes

Cytoplasmic male sterility (CMS) is the basis for the production of hybrids with increased vigor in such important crop plants as corn and sorghum. More than 140 plant species have genes for CMS. Such plants do not produce viable pollen, a trait that is inherited in a non-Mendelian fashion (uniparental inheritance). Substantial evidence now indicates that the CMS trait is encoded by mitochondrial genes in maize, petunia, and sorghum. CMS is probably associated with mitochondrial genes in other plant species as well, although chloroplast genes and viruses cannot be discounted as the cause of CMS in some instances. The CMS trait can be suppressed by nuclear genes known as restorer genes. In the presence of restorer genes, male-sterile cytoplasms are restored to pollen fertility.

In maize, the mitochondrial gene responsible for the cms -T type of sterility has been isolated. This gene codes for a polypeptide of molecular mass 13,000 daltons (13 kD), which is located in the inner mitochondrial membrane. The origin of this gene is unusual; it has arisen by a series of recombinational events that have placed its coding sequence behind a mitochondrial promoter. Moreover, this gene is unique in that the gene and its product are not found in other maize cytoplasms or, for that matter, in other plant species. Although the function of the 13-kD protein is unknown, its location in the inner mitochondrial membrane suggests that it may impair electron transport or ATP formation. The investigations of cms -T have also shed some light on the function of at least one of the nuclear restorer genes. In this case, a restorer gene has been shown to alter the transcription of the gene encoding the 13-kD polypeptide.

THE MOLECULAR ANALYSIS OF GENETIC SELF-INCOMPATIBILITY

Genetic self-incompatibility is known in some species of most families of flowering plants and doubtless evolved in the earliest members of the group or their ancestors more than 135 million years ago. In such systems, pollentube growth is blocked by incompatibility mechanisms either in the stigma or in the style. In the mustards, cabbages, and their relatives, the genus Brassica , the pollen tubes fail to emerge from the pollen grains or are inhibited at the surface of the stigma if the allele at the S , or incompatibility, locus, is the same as one of the two alleles at this locus in the stigma. Researchers have found that inhibition occurs in self-incompatible species of Brassica within minutes of the initial contact between the pollen or pollen tube and the papillar cells that line the outer surface of the stigma. Incompatible pollen grains usually fail to germinate or, more rarely, germinate to produce pollen tubes that coil at the surface of the papillar cells and fail to penetrate the surface layer of stigma cells.

The stigma of Brassica produces S -allele-specific glycoproteins, which, on the basis of several criteria, are believed to be the products of the S locus. Nucleic acid sequences derived from the self-incompatibility genes were isolated from a complementary DNA library constructed from stigma messenger RNA. These sequences have been used to study the regulation of the expression of the self-incompatibility genes during flower development. The self-incompatibility sequences are expressed in stigma and anther tissue only during a specific period of the developmental process. The technique of in situ hybridization made it possible to determine that these genes are expressed exclusively in the surface papillar cells, the site of first contact with the pollen ( Figure 11-3 ). The nature of allelic variability at the S locus is being analyzed by comparing the nucleic acid sequences derived from different S genotypes. In this manner, relatively conserved regions of the S -allele-specific glycoproteins, as well as highly variable regions, which may determine allelic specificity, have been identified.

Self-incompatibility has already been used extensively in the production of new hybrid strains of kohl, oilseed rape, and other commercially important species of Brassica . The manipulation of genetic self-incompatibility is both agriculturally important and of fundamental biological importance; clearly these systems played a significant role in the evolution of the flowering plants, the dominant photosynthetic organisms on land.

Figure 11-3

Expression of the self-incompatibility genes in the papillar cells of the stigma of Brassica flowers as shown by in situ hybridization. [June Nasrallah, Cornell University]

Seed-Storage Proteins Are Important in Human Nutrition, but Often Lack Essential Amino Acids

The seeds of certain plants play an important role in human nutrition because of their high content of storage reserves. Some seeds are particularly important because they provide protein as well as calories. However, some of these proteins lack essential amino acids, and people whose diet is based largely on such seeds may experience net amino acid deficiencies. Biochemical studies carried out during the 1960s and 1970s showed that seed-storage proteins are specific to certain stages of embryonic development or to particular embryonic organs and that they are contained within protein storage vacuoles.

The cloning and analysis of the genes for seed-storage proteins revealed that they are encoded by multigene families and that the messenger RNAs for some carry universal signals for sequestering the protein into membrane-bound organelles. Studies of gene expression of storage proteins in transgenic plants have shown that the promoter for embryo-specific gene expression functions across species boundaries and that genes for seed-storage proteins from French bean or soybean are also expressed at the proper developmental time in tobacco seeds. Transcriptional and possibly translational controls for the expression of seed-storage protein genes are influenced both by hormones, such as abscisic acid, and by intrinsic, as yet unidentified developmental signals.

Research On Plant Reproduction Offers Great Potential in Both Applied and Basic Biology

The switch from vegetative to reproductive growth at the shoot apex is the earliest step in flower formation. Physiological experiments have provided strong evidence that photoperiodic induction of flowering is perceived in the leaves and transmitted to the apex by a flowering hormone, often termed florigen. One large gap in our knowledge on the regulation of flowering concerns the nature of this floral stimulus. In many instances, it would be useful to control the time of flowering of crop and horticultural plants. Isolation and chemical identification of the floral stimulus would be a major step toward attaining this goal.

Research on self-incompatibility in plants is of fundamental as well as applied importance. A major question concerns the biochemical mechanism that operates in the incompatibility reaction. What is the function of the glycoprotein associated with pollen recognition in the stigma or style, and how does it interact with its counterpart in the pollen? Although it is most unlikely that self-incompatibility genes will resemble those of immunoglobin families of animals, it will be intriguing to compare the ways in which the animal and plant kingdoms have generated systems for recognizing self, kin, and foreign cells, permitting common mechanisms to be used in diverse species. Genetic engineering methods could be used to introduce barriers to fertilization in cases in which the production of hybrid progeny may increase yields, and they could also be used to help to remove such barriers when self-pollination would prove advantageous.

Much remains to be learned about CMS. It is not clear how a mitochondrial gene product is involved in pollen development. Several types of CMS and restorer genes have functions that need to be explained. Research on CMS is also relevant to our understanding of susceptibility to certain fungal diseases. A strain of southern corn leaf blight fungus, which destroyed a large part of the corn crop of the United States in 1970, affects only plants that carry the cms -T gene. The basis for the connection between susceptibility and the CMS trait is not yet fully known.

Finally, it is evident that plant mitochondria differ from those of other organisms. Plant mitochondrial genomes are much larger than those of animals; they are also organized differently and encode additional gene products. Research on mitochondrial functions that are unique to plants offers opportunities for advances in organelle biology.

Continued investigations on seed-storage proteins will help us to understand how external and internal developmental signals regulate gene expression in plants. In addition, such work opens new approaches toward improving the nutritional quality of seeds. It is now possible to correct the amino acid deficiency of seed-storage proteins by altering the gene sequences that encode them. With available transformation systems, such modified protein genes can be replaced into the original plant to complement protein composition there. Since the same controlling sequences for storage-protein gene expression seem to function in distantly related plant species, modified storage-protein genes might also be expressed in the seeds of unrelated species. The consequences of this relation could have considerable economic importance.

• Plant-Pathogen Interactions

Interactions Between Plants and Pathogens Are Biologically Intricate and of Fundamental Scientific and Commercial Interest

Plant pathogens cause serious losses to our major crop plants and have had a substantial impact on society. Even though myriad microbes interact with plants, very few have attained the capacity to cause disease. Susceptibility to invasion by pathogens is the exception rather than the rule in the plant world. This is merely an expression of the highly complex relationship that must be established between host and pathogen in a compatible (susceptible) interaction. Much of the modem research in this area attempts to explain the nature of the signals exchanged between host and potential pathogen and of the genes that control such interactions. Research on these systems has led to exciting new avenues of fundamental inquiry and highly promising results for practical applications.

Crown Gall Is an Disease of Plants That Shares Some of the Properties of Cancer in Animals

Crown gall, a disease of some plants, is caused by a bacterium, Agrobacterium tumefaciens , which invades its host through a wound and genetically transforms plant cells into tumorous ones. Bacteria-free tissue from a crown-gall tumor can be cultivated on a synthetic medium and maintained indefinitely in a rapidly proliferating condition. When grafted onto healthy plants, cultured crown-gall tissue produces tumors indistinguishable from those incited by the bacterium. Unlike their untransformed, normal counterparts, tumorous plant cells grown on a synthetic culture medium require no exogenous sources of the growth substances cytokinin and indoleacetic acid. Crown-gall tumor cells have therefore acquired the capacity to produce these growth regulators as a result of their transformation.

Tumorigenicity of the crown-gall bacterium is conferred by genes present on a large plasmid called Ti ( Figure 11-4 ). A fragment of the Ti plasmid, called transfer DNA (T-DNA) is transferred from the pathogen and integrated into a chromosome of the host plant. Genes on the integrated piece of bacterial DNA code for enzymes responsible for the production of the cytokinin isopentenyl adenosine and the auxin indoleacetic acid. Since these genes are expressed only in the plant cell and not in the donor bacterium, their regulatory sequences are designed to function in the eukaryotic environment of the plant cell. Both cytokinins and auxins are natural plant constituents, and their overproduction in the transformed plant cells leads to undifferentiated rapid proliferation characteristic of tumorous growth. T-DNA also contains a gene coding for the synthesis of a novel opine amino acid, such as octopine or nopaline, substances that can serve as nitrogen sources for the bacterium. Their production is also used by scientists to determine whether transformation has occurred. Another region of the Ti plasmid, the vir region, contains six genes necessary for the events leading to the integration of the T-DNA into the plant genome. Genes in the vir region are activated by messenger molecules that are released by the plant.

Figure 11-4

Transformation of plants with the T-DNA of Agrobacterium tumefaciens used as vector. [Tsune Kosuge, University of California, Davis]

In some characteristics, crown gall strikingly resembles a disease on olive and oleander plants caused by the bacterium Pseudomonas savastanoi . This bacterium induces tumorous growth by secreting high concentrations of indoleacetic acid and cytokinin into the tissues surrounding the point of infection. The enzymes necessary for the production of these growth regulators in P. savastanoi are functionally identical to those encoded by A. tumefaciens T-DNA, although the genes in P. savastanoi are located on separate plasmids and expressed in the bacterium. No transformation of the plant genome occurs. The nucleotide sequences in the coding regions of the genes for cytokinin and indoleacetic acid synthesis show a high degree of homology with those of the corresponding genes from T-DNA. However, the promoter regions, which control the expression of these genes, are entirely different in A. tumefaciens and P. savastanoi . This difference in structure was expected since the Pseudomonas genes are designed for expression in a bacterial (prokaryotic) cell, whereas the T-DNA genes must function in a plant (eukaryotic) cell. The similarities in the structural genes indicate that the growth-hormone genes in the two tumorigenic systems have a common origin.

The Ti Plasmid Provides an Vehicle For Gene Transfer in Plants

Once it was known that A. tumefaciens actually transforms its plant hosts, scientists recognized the potential usefulness of the Ti plasmid as a means of introducing foreign genes into plants. In a number of laboratories, they designed so-called disarmed versions of the Ti plasmid. The genes associated with growth-hormone production were removed from the T-DNA, thereby preventing tumor formation in transformed plants. An antibiotic resistance gene was introduced as a selectable marker in an existing T-DNA gene for opine synthesis, and gene-cloning sites were constructed within the disarmed T-DNA. The genes of the vir region necessary for the integration process must be retained on the Ti plasmid or placed into a second helper plasmid. Once the desired gene is spliced into the T-DNA of the vector plasmid, the recombinant plasmid is reintroduced into A. tumefaciens . The bacterial cells are incubated with plant protoplasts or with leaf disks to allow transformation to occur. The protoplasts or leaf disks are then freed of the bacterium and placed upon a medium favoring plant regeneration. This transformation procedure has become so standardized that it is now routine in the hands of trained scientists.

The Ti vector system has been used to introduce DNA sequences that cause disease and insect resistance into plants. For example, genes responsible for the production of an insect toxin have been transferred from Bacillus thuringiensis into plants. These plants became resistant to certain insects as a result of this transformation. Disease resistance to some viruses has been introduced by genetically engineering tobacco and tomato plants to produce the coat protein of tobacco or alfalfa mosaic virus. These plants show resistance to virulent strains of these viruses. An alternative method to introduce virus resistance into plants makes use of small RNA molecules known to act as ''parasites" of some plant viruses. These entities, called satellite RNA, replicate only in plant tissues that are infected with a specific virus, frequently reducing the extent of replication of the virus and ameliorating the symptoms that the virus alone would induce. The satellite RNA becomes embed in the coat protein of the virus and thus may be co-transmitted from plant to plant with the virus. The protective effect of the satellite RNA continues even in the subsequently infected plants. Recently DNA copies of cucumber mosaic and tobacco ringspot virus satellite RNA have been introduced into tobacco plants. Plants transformed with either one of the satellite RNAs and then inoculated with the respective virus showed greatly reduced symptoms in comparison with similarly inoculated, untransformed plants.

Virulence Factors of Certain Plant Pathogens Are Natural Herbicides

Many pathogens produce secondary metabolites that are toxic to plants. These chemicals are side-products of amino acid, carbohydrate, nucleotide, and lipid metabolism. One such chemical is tabtoxinine-ß-lactam, which is produced by a bacterium, Pseudomonas syringae pv. tabaci . If secreted into the cells of its host, tobacco, tabtoxinine-ß-lactam specifically inhibits the plant's glutamine synthetase, an enzyme essential for the production of precursors for protein and nucleic acid synthesis. The pathogen escapes the inhibitory action of its own toxin by several mechanisms, among them being the production of a glutamine synthetase that is less sensitive to the toxin. This phenomenon, called self-protection, is common among pathogens that produce toxins as a part of their repertoire of pathogenic determinants.

Because toxins produced by plant pathogens kill or injure plant cells, they may be viewed as natural herbicides. The activity of such toxins in selective instances provides a conceptual basis for the use of chemicals for weed control. Indeed, there is an herbicide that imparts its weed-killing effects by inhibiting the glutamine synthetase of plants. An alternative to the use of synthetic chemicals for the control of weeds is seen in fungi that are selectively pathogenic for weedy plants. Since the basis for this host selectivity is the production of a host-selective toxin, this phenomenon is being explored as a way to control weeds.

Recognition and Defense Molecules Function in Pathogen-Plant Interactions

Specific molecules function in the maintenance of many kinds of order in biological systems. Enzymes recognize substrates, cells recognize other cells and pollen compatibility, and incompatibility determines fertility in plants. Recognition molecules also mediate the interactions between pathogens and their plant hosts. An example for this is the specific messenger function of small polysaccharide fragments of fungal cell walls, called elicitors, which induce plants to produce chemicals called phytoalexins, which in turn might confer disease resistance to plants because they are toxic to the microorganisms that induce phytoalexin production. A specific molecular configuration is recognized by the plant because any rearrangement in elicitor structure either abolishes or greatly reduces its activity.

GENETICALLY ENGINEERED RESISTANCE AGAINST PLANT VIRUSES

The traditional method of protecting crop plants against specific virus diseases has been to search for resistant strains of the crop or its close relatives in the wild and then to introduce the genes responsible for this resistance into cultivated strains with desirable agronomic properties. Typically, the production of disease-resistant plants with favorable agronomic traits requires 6 to 10 years, a relatively long period. Furthermore, suitable resistance genes for many important diseases have not been identified in many cases. Therefore, many crop plants are vulnerable to viral attack, a situation that has negative economic consequences.

Over the past 20 years, plant pathologists have also used the method of cross-protection to generate resistance against viral diseases in crops. This method is based on an observation, made more than 60 years ago, that tobacco plants could be protected against virulent strains of tobacco mosaic virus (TMV) if they were first inoculated with a mild strain of the virus. This approach has its risks since mild viral strains can give rise to virulent ones, which may devastate rather than protect the plant. Also, virus strains with mild effects can develop synergistic interactions with other viruses. Nonetheless, the method has been useful in enhancing crop resistance in some instances.

The phenomenon of cross-protection provided the conceptual basis for genetically engineered resistance against two different types of plant viruses, TMV and alfalfa mosaic virus (AIMV). The Agrobacterium transformation system was used to introduce the genes that encode the ooat protein of TMV and AIMV into tomato and tobacco plants. Coat protein is normally wrapped around the viral nucleic acid to form the virus particle. Plants regenerated from the transformed cells (transgenic plants) produced TMV and AIMV coat protein, but appeared to be normal in all other respects. When progeny of the transgenic plants were inoculated with virulent strains of TMV or AIMV, the plants either escaped infection or developed a less severe form of the disease than did the nontransformed plants ( Figure 11-5 ). The molecular mechanism responsible for engineered cross-protection has not yet been elucidated. Recent results indicate that fewer infection sites are established in transgenic plants, probably because of some block at an early stage of the infection process. If infection does occur, the rates of viral replication and spread through the plant are reduced. Studies in progress aim at explaining the mechanism of protection, increasing the level of protection, and extending protection to other viruses and other plant species. It is expected that genetically engineered cross-protection will relatively soon become a generally applicable method to introduce viral resistance into plants.

Figure 11-5

Genetically engineered cross-protection against tobacco mosaic virus (TMV). (Left) Control tobacco plant (VF36) inocculated with a severe strain of TMV (PV 230). (Right) Transgenic tobacco plant that expresses the TMV coat protein gene (VF36 +CP) also (more...)

The biochemical basis for disease resistance and susceptibility is particularly well investigated in the case of root rot in peas. When attacked by the pathogenic fungus Nectria haematococca, peas produce a phytoalexin called pisatin. Some strains of the fungus are sensitive and others tolerant to pisatin. The sensitive strains cause mild disease in peas, from which the plants recover, whereas pisatin-tolerant strains are highly virulent and kill the plants. Tolerant strains respond to pisatin by producing an enzyme, pisatin demethylase, which degrades pisatin to a nontoxic product. Thus, the fungus has developed a way to circumvent a defense mechanism of the plant. Pisatin demethylase is a cytochrome P 450 monooxygenase, the same type of enzyme that functions in mammalian livers as a detoxifying agent. The gene encoding pisatin demethylase has been isolated from N. haematococca . Study of the cloned gene will help us to understand how the fungus recognizes phytoalexins and how it has evolved the capacity to live in their presence.

In solanaceous plants, such as tomato and potato, small cell-wall fragments called oligogalacturonides are released when plant tissue is injured by chewing insects or mechanical rupture. Such oligogalacturonides, or perhaps some other signal molecules, are transported throughout the plant and systemically induce the production of a powerful proteinase inhibitor that interferes with the digestion of proteins. In the initial act of feeding, chewing insects seem to activate a defense system that renders the plant less digestable and may discourage further feeding. The systemic production of proteinase inhibitors in response to injury also occurs in nonsolanaceous plants; it might represent a general plant defense against insect predation.

In some pathogen-plant interactions, a plant's susceptibility or resistance to a particular pathogen is determined by a single gene in the host and another in the pathogen. This gene-for-gene relationship implies a high degree of specificity and recognition between plant and pathogen. Resistance may arise from a specific interaction between gene products of the pathogen and the host plant. Susceptibility would result from a lack of such an interaction. These hypotheses are being tested by isolating genes from bacteria that confer race specificity for their hosts. The products of the genes are being identified, and the structures responsible for specificity will be determined.

With Today's Technology, Fundamental Problems of Plant-Pathogen Interactions Can Be Investigated at the Molecular Level

The intimate relationship that has evolved between plant and pathogen is now the focus of attention by plant scientists. These studies have been greatly enhanced by new techniques in cell culture, chemical analysis, and molecular biology. It should be possible now to obtain answers regarding the responses of plants to challenge by abiotic factors, pathogens, or pests. What is the nature of disease or insect resistance in plants? How are resistant responses induced? What controls the expression of these resistance genes? Why are these genes not expressed in certain host-parasite combinations? Central to much of this research is our current ability to study mechanisms of communication between organisms and between cells. Transmembrane signaling, second messenger activity, and long-distance communication will be areas of active research during the next decade.

Other research areas with exceptional opportunity include the nature of pathogen genes that are essential for causing disease. Is specificity determined by the nature of the plant products that induce the expression of pathogenicity genes or is it determined by regulatory functions that modify the response of pathogens to these products? The recent success in conferring resistance to plants by introducing vital coat-protein genes suggests that, as we understand the mechanisms of cross protection, we will also be able to exploit this phenomenon to control virus disease.

The excitement generated by our ability to transform plants by means of the Agrobacterium T-DNA should be tempered by our ignorance as to how this plant pathogen is able to transfer DNA or how this DNA is integrated in the plant chromosome. The search for other pathogens that can serve as sources of vectors to introduce useful genes in our major cereal crops will, in the near future, greatly expand our ability to improve plants by genetic engineering.

Rapidly expanding computer technology has increased our knowledge of how plant pathogens are disseminated. Cooperation among mathematicians, computer experts, and plant pathologists will continue to lead to better prediction of epidemics and, thus, to more rational application of control procedures. There is now renewed interest in the ability of bacteria to colonize leaf surfaces, for example. What triggers the change from epiphytic to parasitic habit in certain bacteria? The recent interest in the possible use of epiphytic, non-ice nucleating bacteria (which do not act as ice-nucleation centers) to prevent frost damage to plants is an example of how answers to some fundamental questions in plant-pathogen interactions can help stimulate the plant biotechnology industry.

• Genetic Improvement of Plants

Plant-Breeding Programs Can Now Be Enhanced By Molecular Biology

During this century, plant breeding has led to substantial increases in crop yield through the production of hybrids with increased vigor, the modification of plant chemical composition or morphology, and the genetic transfer of disease resistance, among others. The methods of molecular biology can now be applied to complement those of conventional genetics, especially where barriers of sexual incompatibilty or of sterility preclude the introduction of desirable traits through breeding. Genetic engineering has also made it possible to introduce into plants genes from other organisms, regardless of their genetic relationship. In addition, plants such as Arabidopsis thaliana are being used as models for the study of plant molecular genetics, which will provide basic insights into plant biology.

Tissue Culture

Plant improvement through tissue culture is feasible, but remains technically difficult.

Plant cell and tissue culture is an important tool for improving plant characteristics. Calli originally derived from plant tissue can be subcultured indefinitely on suitable synthetic media and induced to regenerate roots or shoots by altering the proportion of auxin to cytokinin in the culture medium. The resulting plants can be grown to maturity. Alternatively, plant cell walls can be digested and calli regenerated from single protoplasts. The fusion of protoplasts permits the recombination of genetic material, even from unrelated kinds of organisms. Some plants can also be regenerated by the induction of embryos in cells derived from tissue that is not normally embryonic. Despite these advances, however, we know virtually nothing about the principles that allow the regeneration of some kinds of plants from protoplasts and that seem to preclude such regeneration (at least by the available techniques) in many others, such as most commercially grown cereals.

ARABIDOPSIS—A TOOL FOR PLANT MOLECULAR GENETICS

The use of Arabidopsis thaliana , an annual, weedy member of the mustard family (Brassicaceae), for studies in plant genetics was suggested more than 80 years ago by the German botanist Eduard Strasburger. Among the advantages are the small size, short generation time, and copious seed production of this common plant ( Figure 11-6 ). Several plants can be grown per square centimeter, one plant yields thousands of seeds, and its life cycle may be completed within less than 6 weeks. For screening purposes, as many as 10,000 seeds can be germinated in one Petri dish.

Recent studies have revealed additional advantages that make Arabidopsis a prime object for studies in plant molecular genetics. Arabidopsis has the smallest genome known in plants, with about 70,000 kilobase pairs per haploid chromosome set—a genome about 1/80 of the size of the wheat genome. The relative simplicity of the Arabidopsis genome facilitates the cloning of particular genes, which can be used either as probes for isolating corresponding genes from other species or in transformation experiments.

New impetus for intensified research with Arabidopsis arose from the realization that desired mutations can be obtained with relative ease. In this process, the seeds are treated with a mutagen and germinated, and the resulting plants are allowed to self-fertilize. The progeny of these plants, called the M 2 generation, are used for screening for mutants. Many mutations with a loss in some metabolic function have been found at a frequency of one in 2,000 M 2 plants. Specific metabolic pathways, such as that involved in photorespiration, to be traced. Other mutants that have been isolated include some that are altered in the fatty acid complement of their membranes, others in which starch synthesis is blocked, and still others in which hormone biosynthesis is blocked or hormone sensitivity altered. Such mutants are valuable tools for the study of plant physiology and development.

Recently, Arabidopsis was used in the isolation of herbicide-resistance mutants. About one out of 100,000 M 2 seeds sown on an agar medium containing a sulfonylurea herbicide proved to be resistant to this compound. Sulfonylurea herbicides inhibit acetolactate synthase, an enzyme in the biosynthetic pathway of branched amino acids. The mutated gene for acetolactate synthase was cloned from Arabidopsis and was used to transform tobacco cells. The regenerated tobacco plants showed stable herbicide resistance. Experiments of this kind underscore the practical and theoretical importance of the Arabidopsis system and its potential for future contributions.

Figure 11-6

Arabidopsis thaliana. [Chris Somerville, Michigan State University]

A serious problem that limits the utilization of plant tissue cultures for various purposes, including the preservation of desirable strains, is the high frequency of genetic changes in such cultures, a phenomenon called somaclonal variation. Such changes include alterations of chromosome number, chromosomal breakage, genomic rearrangements, and point mutations. Some of these changes may be advantageous, conferring such features as disease resistance, increased sugar yields (sugar cane), tuber uniformity (potatoes), and high levels of fruit solids (tomatoes). In some widely used cultivars of agronomically important plants, in which infertility has precluded the introduction of new traits by breeding, genetic diversity provided by somaclonal variation can be exploited for the selection of desired phenotypes.

We Need To Learn More About the Principles That Underlie Plant Regeneration

How do nutritional and hormonal factors influence the developmental fate of plant cells? What biochemical pathways have to be activated for root and shoot differentiation to occur? How are these pathways regulated? Cultured cells should be particularly well suited for such investigations because their growth conditions can be controlled rigorously. Somaclonal variation raises some basic questions concerning genomic organization and stability in plants. What factors lead to the observed destabilization of the plant genome, and, conversely, what factors maintain stability? What precise changes occur in the genome as a result of culmring? Answers to these questions will have direct consequences for the application of tissue culture technology to plant improvement and for our basic understanding of the mechanisms of plant growth and development.

Plant Cell Transformation

Plant cell transformation in agrobacterium has become an important research tool in plant molecular biology.

Such fundamental questions as the way gene expression is regulated in plants have been investigated through the use of Agrobacterium-induced transformation. Nuclear genes under phytochrome control—for example, the gene encoding the small subunit of the chloroplast enzyme rubisco—have been transferred from one species into another in such a way that the regulation of gene expression by light can be studied against a background of precisely defined gene constructions. In particular, it has been possible to identify the promoter and enhancer sequences that regulate the expression of these genes. These achievements constitute the first steps in clarifying the mechanisms by which environmental signals are transduced in plants.

The T-DNA of Agrobacterium has also been used successfully to transfer herbicide resistance into plants. The mode of action of three commonly used herbicides has recently been elucidated. Glyphosphate and sulfonylureas inhibit specific enzymes in the biosynthetic pathways of aromatic and branched-chain amino acids, respectively. Triazines block the binding of plastoquinone to an electron transport protein of the photosynthetic apparatus. Mutant plants that are insensitive to sulfonylureas and triazines have now been characterized at the molecular level. In each instance, herbicide resistance was associated with a single nucleotide change in the genes encoding the two target proteins. Resistance to sulfonylureas and triazines has been conferred on susceptible plants by transformation, through the use of the respective genes from herbicide-resistant plants. Plants with increased resistance to glyphosphate have also been obtained through genetic engineering. Creating herbicide-resistant plants is especially worthwhile in the case of medium- to low-acreage crops, which do not warrant the development of selective herbicides. The methods of weed control that become possible in such systems decrease production costs and increase yields.

The use of the Agrobacterium transformation system is limited by the host range of the bacterium. Although most dicotyledonous plants are susceptible to crown-gall disease, most monocotyledonous plants, including cereals, are not. Therefore, only a few monocotyledonous species have been transformed with Agrobacterium until now. However, striking success has been achieved by transforming plant cells directly with DNA. With polyethylene glycol used to perturb the plasma membrane of protoplasts, an antibiotic resistance gene has been introduced into tobacco cells. Plants regenerated from such transformed cells and their sexual offspring express the antibiotic-resistance trait in a stable manner. This same technique was also successful in transforming the cells of a monocotyledonous plant, the ryegrass ( Lolium perenne ).

A technique called electroporation offers another method to transform plants that do not become infected by Agrobacterium . Electrical pulses are used to temporarily perforate the cell membrane of protoplasts, permitting DNA to enter the cell. With electroporation, protoplasts of maize have recently been transformed with an antibiotic resistance gene. All that stands in the way of stably transforming many species is our inability to regenerate whole plants from protoplasts or calli. To get around the problem of regeneration from protoplasts or calli, it is possible to shoot DNA-coated microprojectiles directly into intact plant cells. Potential targets include meristems and pollen, which can be cultured in vitro or used in sexual crosses, respectively.

The Techniques of Genetic Engineering Hold Enormous Promise For Agriculture

Potential improvements in crop plants through genetic engineering include increased yield, lowered production costs, improved nutritional qualities, adaptations to unfavorable growing conditions, and new biosynthetic capacities. The feasibility of obtaining a number of traits of these kinds by genetic engineering has already been demonstrated in laboratory trials. Other applications of gene transfer technology, such as the utilization of the plant's biosynthetic machinery for the production of foreign compounds with high commercial value, have not yet been realized. "Custom" crop plants capable of synthesizing specific proteins, valuable oils, or secondary metabolites for medical use could be the bases of new agricultural industries.

To attain these goals, research in the plant sciences must proceed at all levels. Discoveries in plant physiology and biochemistry must keep pace with the rapidly progressing field of plant molecular biology. The metabolic functions of plants must be explored further. Enzymes involved in the synthesis of plant products must be characterized and regulatory mechanisms in plant metabolism elucidated. The mode of action of plant hormones requires intensive study as do the reactions that mediate compatibility and incompatibility between pollen and stigma, symbionts and roots, and pathogens and plants. A thorough knowledge of the processes that could be altered for the improvement of plants provides the basis for the application of recombinant DNA and transformation technologies.

• Cite this Page National Research Council (US) Committee on Research Opportunities in Biology. Opportunities in Biology. Washington (DC): National Academies Press (US); 1989. 11, Plant Biology and Agriculture.
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How to Write Scientific Names of Plant and Animal Species in Journal Manuscripts (Part 1)

The format for writing scientific names of animals and plants is standardized and internationally accepted. “Scientific nomenclature” refers to various names according to a specific field of study. This article is the first in a series on scientific nomenclature within specific kingdoms.

Usually, animals & plants are identified by common and scientific names.

Common name: These are used locally and may vary by region or country. Scientific name: These are unique names used by the scientific community to accurately and universally identify species.

International Codes of Nomenclature

Taxonomists have established several “codes” for scientific nomenclature. These codes are universal and are periodically updated by consensus. The protocol for naming species was invented in the 1700s by Swedish botanist Carl Linnaeus. Linnaeus created the system of “binomial nomenclature,” which uses only two designations – genus and specific epithet as the species name.

In the mid-1800s, scientists agreed on an expanded system of nomenclature. The following codes are used today:

• International Code of Nomenclature for algae, fungi, and plants.
• International Code of Zoological Nomenclature.
• International Code of Nomenclature of Bacteria recently changed to International Code of Nomenclature of Prokaryotes.
• International Code of Nomenclature for Cultivated Plants.
• International Code of Phytosociological Nomenclature.
• International Committee on Taxonomy of Viruses–publishes several reports including How to Write a Virus Name.

Common names of species can vary by geographic region but a universal protocol helps avoid ambiguity and ensures consistency.

Known as the “ taxonomic hierarchy ,” the system consists of several groups of species based on genetic and phylogenic characteristics. The highest level is the “kingdom.” The first kingdom comprised only two types of living organisms—animals and plants. We have seven classifications within the kingdom domain—Bacteria, Archaea, Protozoa, Chromista, Plantae, Fungi, and Animalia.

Note that the designations are in Latin . This could be challenging for some who are not familiar with that language; however, the terms are globally consistent. There is no need to interpret them or translate them into another language.

Using this system, the gray wolf, for example, would be identified as follows:

• Domain: Eukarya.
• Kingdom: Animalia.
• Phylum: Chordata.
• Class: Mammalia.
• Order: Carnivora.
• Suborder: Caniformia.
• Family: Canidae.
• Genus: Canis.
• Species: lupus.

Binomial Name

The binomial name consists of a genus name and specific epithet.  The scientific names of species are italicized . The genus name is always capitalized and is written first; the specific epithet follows the genus name and is not capitalized. There is no exception to this.

From above example, note that the classifications go from general (Animalia) to specific ( C. lupus ). A species, by definition, is the combination of both the genus and specific epithet , not just the epithet. For example, we can use the term gray wolf but we cannot use just Canis or lupus to describe this animal. Canis lupus is a species.

Writing Scientific Names of Animals

When writing, we use both the scientific name and the “common” name on the first mention. We then choose which to use throughout and make it consistent.

• Gray wolf ( Canis lupus ) is native to North America and Eurasia.

In subsequent references, we can use either the common or scientific name. If we use the scientific name, we need only to use the first letter of the genus followed by a period and the specific epithet. For example:

• In North America, the gray wolf was nearly hunted to extinction.
• In North America, C. lupus was nearly hunted to extinction.

It is also common to refer to several species under one genus when you want to point out some similar characteristics within a genus. For example:

• All species of Canis are known to be moderate to large and have large skulls.

You could also write this same information another way as follows:

• Canis spp. are known to be moderate to large and have large skulls.

In this case, “spp.” is an abbreviation for “several species” (“sp” is the designation for one species) in the genus. Either of the above is acceptable. If you are focusing on a few species in particular, you would refer to the species name of each one.

You might also see a scientific name followed by an initial or abbreviation. This would denote the person who discovered or named the species. For example, in Amaranthus retroflexus L., the L (not italicized) refers to the original name given by Linnaeus.

There are a few exceptions to some of these rules. First, the entire genus name must be spelled out if it begins a sentence, even if a subsequent reference:

• Canis lupus was nearly hunted to extinction in North America.

Second, when more than one species has the same genus initial but come from different genera, the genera names are spelled out to avoid confusion:

• Both the gray wolf ( Canis lupus ) and the beaver ( Castor canadensis ) are native to North America.

In this case, it is best to use the common name after the first mention, but either format is correct.

Related: Do you have questions on manuscript drafting? Get personalized answers on the FREE Q&A Forum!

Titles and Headers

In titles, it is appropriate to write the entire scientific name of animals in uppercase letters. For example:

• A Study of the History of CANIS LUPUS in North America

In an italicized header, the species name can be written in non-italic style. For example:

• Canis lupus is nearly extinct in North America

Writing Scientific Names of Plants

Plant names also follow binomial nomenclature (similar to animal names).

• Royal grevillea (Grevillea victoriae) is found in New South Wales and Victoria.

In the plant kingdom , classification after species is subspecies (subsp.) and variety (var.). For example, there are three subspecies of Grevillea victoriae.

•   Grevillea victoriae  subsp.  victoriae
• Grevillea victoriae  subsp.  nivalis  
• Grevillea victoriae  subsp.  brindabella

When the species of a plant is unknown, a plant can be referred as Grevillea sp.

Moreover, when we collectively want to refer few or all species, we use Grevillea spp.

Similar to animal names, it is common to see a specific epithet that refers to a geographic area or the person who discovered it. For example, Grevillea victoriae F.Muell. Although these are proper nouns, they are still written in lowercase font. Be mindful that some word processors might attempt to capitalize these references.

This is something to check when proofreading your text.

Cultivar names are dictated by International Code of Nomenclature for Cultivated Plants

When writing, the cultivar name is added after genus or specific epithet and is put in single quotes without italicization. For example,  

•   Grevillea  ‘Robyn Gordon’       
•  Grevillea rosmarinifolia  ‘Rosy Posy’

Consistency

One of the basic rules of scientific writing is consistency. Regardless of your choice of scientific or common name, you must maintain consistency. Always check the author guidelines when preparing manuscripts. Formats for citations and references, headings, and section placement can be different. Be assured that the format for writing scientific names is internationally consistent regardless of the intended journal. The rules presented above will help.

In the next article in this series, we will discuss tips on how to write scientific names of bacterial species in a journal manuscript.

You see that the common name of the species you are studying has several variations depending on the geographic area. Which do you use and why? What other challenges do you face when using scientific nomenclature? Please share your thoughts with us in the comments section below.

Trying to identify species of plants is difficult when it changes from one reference to another. Is there a classification resource available to laymen with the most recently agreed upon name?

Hi Sandra, Thank you for your question. Some databases give you updated information on plant taxonomy. Integrated Taxonomic Information System (ITIS) https://www.itis.gov/ is one such database. It gives you the flexibility to search taxonomic data of a particular plant based on its common name, scientific name, or taxonomic serial number. This database is not limited to plants and can be used to access taxonomic information about other organisms as well. Meanwhile, please visit https://www.enago.com/academy/ and consider subscribing to our newsletter. Need instant answers for burning queries on academic writing and publishing? Install our mobile app today! https://www.enago.com/academy/mobile-app/

when we write only the genus name should it be italicized? for example we wan t to write leishmania parasites is that necessary to write the genus name italicized?,

Hi Mohammad,

The rules for the scientific nomenclature vary with the organism. In case of botanical nomenclature, generally both the genus and the species names have to be italicized. For protozoans, the genus name when used in singular form should always be in italics. e.g., Leishmania donovani . However, when used in the plural form, you need not italicize the genus name. e.g., Leishmania are responsible for causing the disease leishmaniasis.

Explained in a simple and easy to understand way. It was helpful.

when writing the manuscript, does the family name of the plant have be italicized?

Which one is inside the parenthesis in the title, common name or scientific name?

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162 Best Animal Research Topics To Nail Your Paper In 2023

The world is filled with living things. There are some animals that we know about, some that we will discover, and there are many that we might never know about. All our knowledge about animals is mostly dependant on researchers. Well, we are rooting for you to be the next great researcher. Be it zoology, veterinary, or live wild stock, your study needs a research topic. If you’re looking for the best animal research topics to nail this year, we’re here with your help.

Table of Contents

Best Animal Research Topics

We have 162 Animal Research Topics that will help you get the best grades this year.

Physiology of Animals Research Topics

• Description of the knowledge required to work in animal physiology
• Study of animal species with different specialties in the sciences of nature and life
• Life sciences and socioeconomic impacts
• Neurulation appendages birds
• Exercises on gastrulation and neurulation
• Gastrulation amphibians birds
• Fertilization segmentation in the sea species
• Gametogenesis: A Detailed Introduction
• Study of Delimitation: bird appendages
• Particularities of the developmental biology of certain species
• Technical-commercial animal physiology
• Terrestrial and marine ecosystems
• Animal biology and forensic science: Is there a connection?
• Animal Biology Biotechnology and molecules of interest regarding food and industry
• The interest in biology in the diagnosis of animal and plant diseases
• Toxicology and environmental health concerns in animal physiology
• Animal and plant production
• Fundamentals of animal physiology research and analysis
• Behavior and evolution Genetics of behavior in animals
• Adaptation and evolution of behavior
• Comparative studies of general ecology, zoology, and animal physiology
• Study of animals about the conditions prevailing in their immediate environment
• Endocrine and neuroendocrine systems in animals
• Studying the nervous systems in birds
• Genitals and reproductive physiology of birds
• Understanding of the anatomical and functional particularities of invertebrates
• Biology and physiology of invertebrates
• Reconstruction of phylogenetic trees
• Morpho-anatomical arguments and the importance of fossils
• Argued classification of animals
• Study of the evolution of living organisms by making updates on recent advances in Animalia
• Phylogeny and animal evolution
• Principles of echolocation in the bats
• Possible evolution of the increase in complexity of the primitive nervous system
• The nervous system of the insect
• Circulation in animal physiology
• Animals without a differentiated circulatory system
• Water and mineral balance in animals
• Thermoregulation in animals
• Musculoskeletal system in animals
• Study of animal blood
• Biological rhythms of animals
• Skin and teguments of mammals
• Animal nutrition and metabolism
• Hormones and endocrine system of animals
• Emerging organic pollutants
• Mechanisms of toxicity in animals
• Animal physiology in animals from temperate regions
• Genetic correlations between animal species
• Animal communities, forest ecology, and forest birds
• Wildlife-habitat modeling

Looking for research topics in general? Read 402  General Research Paper Topics

Animal Research Topics For Student

• Impact of the agricultural raw materials crisis on the marketing of livestock feed
• Analysis of the competitiveness of poultry produced in the USA
• Animal cruelty in USA and European countries
• Seroprevalence of neosporosis in cattle herds
• The peri-urban dairy sector
• Effect of the liberalization of the veterinary profession on the vaccination coverage of livestock
• Why do people kill animals? The psyche behind animal cruelty
• Evaluation of the growth performance of three sheep breeds
• Study on the protection of terrestrial ecosystems
• Ecology of African dung beetles
• Effects of road infrastructure on wildlife in developing countries
• Analysis of the consequences of climate change related to pastoral livestock
• Strategies for management in the animal feed sector
• The feeding behavior of mosquitoes
• Bee learning and memory
• Immediate response to the animal cruelty
• Study of mass migration of land birds over the ocean
• A study of crocodile evolution
• The cockroach escape system
• The resistance of cockroaches against radiation: Myth or fact?
• Temperature regulation in the honey bee swarm
• Irresponsible dog breeding can often lead to an excess of stray dogs and animal cruelty
• Reliable communication signals in birds

Also see:  How to Write an 8 Page Research Paper ?

Animal Research Topics For University

• Color patterns of moths and moths
• Mimicry in the sexual signals of fireflies
• Ecophysiology of the garter snake
• Memory, dreams regarding cat neurology
• Spatiotemporal variation in the composition of animal communities
• Detection of prey in the sand scorpion
• Internal rhythms in bird migration
• Genealogy: Giant Panda
• Animal dissection: Severe type of animal cruelty and a huge blow to animal rights
• Cuckoo coevolution and patterns
• Use of plant extracts from Amazonian plants for the design of integrated pest management
• Research on flying field bug
• The usefulness of mosquitoes in biological control serves to isolate viruses
• Habitat use by the Mediterranean Ant
• Genetic structure of the  African golden wolf  based on its habitat
• Birds body odor on their interaction with mosquitoes and parasites
• The role of ecology in the evolution of coloration in owls
• The invasion of the red swamp crayfish
• Molecular taxonomy and biogeography of caprellids
• Bats of Mexico and United States
• What can animal rights NGOs do in case of animal cruelty during animal testing initiatives?

Or you can try 297 High School Research Paper Topics to Top The Class

Controversial Animal Research Topics

• Is it okay to adopt an animal for experimentation?
• The authorization procedures on animals for scientific experiments
• The objective of total elimination of animal testing
• Are there concrete examples of successful scientific advances resulting from animal experimentation?
• Animal rights for exotic animals: Protection of forests and wildlife
• How can animal rights help the endangered animals
• Animal experimentations are a type of animal cruelty: A detailed analysis
• Animal testing: encouraging the use of alternative methods
• Use of animals for the evaluation of chemical substances
• Holding seminars on the protection of animals
• Measures to take against animal cruelty
• Scientific research on marine life
• Scientific experiments on animals for medical research
• Experimentation on great apes
• Toxicological tests and other safety studies on chemical substances
• Why isn’t research done directly on humans rather than animals?
• Are animals necessary to approve new drugs and new medical technologies?
• Are the results of animal experiments transferable to humans?
• Humans are not animals, which is why animal research is not effective
• What medical advances have been made possible by animal testing?
• Animals never leave laboratories alive
• Scientific interest does not motivate the use of animal research
• Animal research is torture 
• How can a layperson work against the animal testing?

Every crime is a controversy too, right? Here are some juicy  Criminal Justice Research Paper Topics  as well.

Animal Research Topics: Animal Rights

• Growing awareness of the animal suffering generated by these experiments
• What are the alternatives to animal testing?
• Who takes care of animal welfare?
• Major global organizations working for animal rights
• Animal rights in developing countries
• International animal rights standards to work against animal cruelty
• Animal cruelty in developing countries
• What can a layperson do when seeing animal cruelty
• Role of society in the prevention of animal cruelty
• Animal welfare and animal rights: measures taken against animal cruelty in developing countries
• Animal cruelty in the name of science
• How can we raise a better, empathetic and warm-hearted children to put a stop to animal cruelty
• Ethical animal testing methods with safety
• Are efforts being made to reduce the number of animals used?
• The welfare of donkeys and their socioeconomic roles in the subcontinent
• Animal cruelty and superstitious conceptions of dogs, cats, and donkeys in subcontinent
• Efforts made by international organizations against the tragedy of animal cruelty
• International organizations working for animal welfare
• Animal abuse: What are the immediate measures to take when we see animal cruelty
• Efforts to stop animal abuse in South Asian Countries
• Animal abuse in the name of biomedical research

Talking about social causes, let’s have a look at social work topics too: 206  Social Work Research Topics

Interesting Animal Research Topics

• The urbanization process and its effect on the dispersal of birds:
• Patterns of diversification in Neotropical amphibians
• Interactions between non-native parrot species
• Impact of landscape anthropization dynamics and wild birds’ health
• Habitat-driven diversification in small mammals
• Seasonal fluctuations and life cycles of amphipods
• Animal cruelty in African countries
• Evolution of the environmental niche of amphibians
• Biological studies on Louisiana crawfish
• Biological studies on Pink bollworm
• Biological studies on snails
• Biological studies on Bush Crickets
• Biological studies on Mountain Gorillas
• Biological studies on piranha
• Consequences of mosquito feeding
• Birds as bioindicators of environmental health
• Biological studies on victoria crowned pigeon
• Biological studies on black rhinoceros
• Biological studies on European spider
• Biological studies on dumbo octopus
• Biological studies on markhor
• Study of genetic and demographic variation in amphibian populations
• Ecology and population dynamics of the blackberry turtle
• Small-scale population differentiation in ecological and evolutionary mechanisms
• Challenges in vulture conservation

Also interesting: 232  Chemistry Research Topics  To Make Your Neurochemicals Dance

Submarine Animals Research Topics

• The physiology behind the luminous fish
• A study of Fish population dynamics
• Study of insects on the surface of the water
• Structure and function of schools of fish
• Physiological ecology of whales and dolphins
• Form and function in fish locomotion
• Why do whales and dolphins jump?
• Impact of Noise on Early Development and Hearing in Zebrafish
• Animal cruelty against marine life on the hand of fishermen

Read More:  Accounting Research Topics

Animal Biology Research Topics

• Systematic and zoogeographical study of the ocellated lizards
• Morphological study of neuro histogenesis in the diencephalon of the chick embryo
• Anatomical study of three species of Nudibranch
• The adaptive strategy of two species of lagomorphs
• The Black vulture: population, general biology, and interactions with other birds
• Ocellated lizards: their phylogeny and taxonomy
• Studies on the behavior of ocellated lizards in captivity
• Comparative studies of the egg-laying and egg-hatching methods of ocellated lizards
• Studies on the ecology and behavior of ocellated lizards
• The taxonomic and phylogenetic implications of ocellated lizards
• Research on the egg-laying and egg-hatching methods of ocellated lizards
• Studies on the ecology and behavior of ocellated lizards in their natural environment
• Comparative studies of the egg-laying and egg-hatching methods of ocellated lizards in different countries
• Studies on the ecology and behavior of ocellated lizards in their natural environment in the light of evolutionary and ecological insights

Animal research topics are not hard to find for you anymore. As you have already read a load of them. You can use any of them and ace your research paper, and you don’t even need to ask permission. If you are looking for a research paper writing service , be it animal research, medical research, or any sort of research, you can contact us 24/7.

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Plant and Animal Habitats (Science Grade 2 Lesson Plan/Activity)

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• By Simpkins, Grace ; Irving, Michael
• Personal Author: Simpkins, Grace ; Irving, Michael Simpkins, Grace ; Irving, Michael Less -
• NOAA Program & Office: OAR (Oceanic and Atmospheric Research) ; Sea Grant OAR (Oceanic and Atmospheric Research) ; Sea Grant Less -
• Sea Grant Program: WHOI (Woods Hole Sea Grant)
• Description: In this 2nd grade unit, the students will explore the habitats of plants and animals. A habitat is a place where an animal or plant lives that meets its need to survive. Students will learn that animals must have oxygen, food/water, and shelter. Students will learn that plants need carbon dioxide, sun, water, and food (minerals). Students will also observe adaptations that allow animals and plants to avoid predators. Finally, the students will learn how plants and animals rely on each other to survive and reproduce. Included are the digital for the lesson plan, observation sheet, Venn Diagram, Human habitat worksheet, Marine Animals I have seen worksheet, Plant observation worksheet, and Master unit vocabulary list. More ▼ -->
• Keywords: [+] Lesson plan
• Sea Grant Document Number: WHOI-E-20-003
• Document Type: Instructional Material
• Funding: Grant no. NA18OAR4170104
• Rights Information: Public Domain
• Compliance: Library
• Main Document Checksum: [+] urn:sha256:825d86c67187d6af6527dc86fb25d608c83d53c0d8f535e3375de8e41f0bad3c
• Download URL: https://repository.library.noaa.gov/view/noaa/39080/noaa_39080_DS1.pdf

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New light shed on circadian rhythms

New study links positively charged amino acid blocks with changes to our internal clocks.

Circadian clocks, which drive circadian rhythms, are entwined with many essential systems in living things including plants, fungi, insects, and even humans. Because of this, disruptions to our circadian clocks are linked to higher disease rates in humans, including certain cancers and autoimmune diseases. Rensselaer Polytechnic Institute's Jennifer Hurley, Ph.D., Richard Baruch M.D. Career Development Chair and Associate Department Head of Biological Sciences, has dedicated her career to understanding the mechanisms that allow our circadian clocks to keep time.

"As proteins are the building blocks of life, it's important to gain a fundamental understanding of how these proteins work together," said Hurley. "Knowing how proteins interact can teach us how an organism will behave, and can also give us the opportunity to alter that behavior."

In research recently published, Hurley and team discovered that the disordered clock protein, FRQ, in a fungus called Neurospora crassa , interacted with a protein called FRH in an unexpected way. They found regions or "blocks" on FRQ that were positively charged. These blocks allowed FRQ and FRH to interact across many different regions.

"While proteins are often thought of as having a well-ordered shape, there is a whole class of proteins that are more flexible, like wet spaghetti noodles" said Hurley. "This flexibility can be important in proteins interactions. In the case of FRQ, we think that its 'noodliness' allows the blocks of positive charge to bond to FRH, perhaps like a bear hug."

"We expected a simple, straightforward interaction between FRQ and FRH," said Hurley. "And we found the interaction was much more complex than we expected."

Hurley and team found that this so-called bear hug causes the molecular circadian clock to flip from being an hourglass, which needs to be reset every day by light, to a persistent oscillator, which allows for a continuous rhythm without needing to be reset by light. This persistent circadian oscillator is the fundamental way in which the circadian clock keeps time, regulating anything from our behaviors to how an animal in the Arctic knows when to hunt, even when there is no light available in the winter months.

Each new insight into the mechanisms of our circadian clocks brings us closer to being able to make alterations for great practical benefit. If we could manipulate the circadian clock, it could help in the production of biofuels, in combating jet lag, and in ensuring the health of shift workers and others with irregular schedules.

Health care offers vast opportunities to apply our knowledge of circadian rhythms. "Our field refers to this as 'chronotherapy,'" said Hurley. "If you get injured at one time of day, you heal much faster than at another. Therefore, we can schedule surgeries at the right time of day. We can even time chemotherapy treatments to when healthy cells are not dividing but cancer cells are, lessoning side effects and increasing treatment efficacy."

"With this research, Professor Hurley and her team have, once again, advanced our understanding of how circadian rhythms work on a molecular level," said Curt Breneman, Ph.D., dean of Rensselaer's School of Science. "This kind of in-depth understanding of the mechanisms of circadian processes opens the door to better mitigation of their effects in higher organisms and humans."

Hurley was joined in research by Meaghan S. Jankowski, Divya G. Shastry, Jacqueline F. Pelham, Joshua Thomas, and Pankaj Karande of Rensselaer; and Daniel Griffith, Garrett M. Ginell, and Alex S. Holehouse of Washington University School of Medicine.

• Molecular Biology
• Cell Biology
• Biotechnology
• New Species
• Animal Learning and Intelligence
• Circadian rhythm
• Microorganism
• Vaccination

Story Source:

Materials provided by Rensselaer Polytechnic Institute . Original written by Katie Malatino. Note: Content may be edited for style and length.

Journal Reference :

• Meaghan S. Jankowski, Daniel Griffith, Divya G. Shastry, Jacqueline F. Pelham, Garrett M. Ginell, Joshua Thomas, Pankaj Karande, Alex S. Holehouse, Jennifer M. Hurley. Disordered clock protein interactions and charge blocks turn an hourglass into a persistent circadian oscillator . Nature Communications , 2024; 15 (1) DOI: 10.1038/s41467-024-47761-z

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How to Write Scientific Names of Plants and Animals

Scientific names, or taxonomic names, are the unique nomenclature used in biology to refer to specific species. The purpose of these names is to standardize species names across regions, languages, and cultures to avoid confusion and ambiguity.

Updated on September 15, 2022

While these Latin names may seem intimidating (they even confuse journal editors), they become easy to use once you understand where they come from and how to use the formatting, notations, and abbreviations associated with them.

What is scientific/binomial nomenclature?

In the 1750s, Carl Linnaeus developed the system of binomial nomenclature (a two-part naming system) that we use today to name and classify living things. Species names consist of two parts: the first part is the generic name (genus name), while the second is the specific epithet (species name).

Species with the same generic name are closely related species grouped into the same genus. The specific epithet by itself is meaningless, almost like an adjective without a noun. Unrelated species can have the same specific epithet, such as Melilotus albus (white sweetclover) and Procnias albus (white bellbird). Albus means white.

Some animals have species names where the specific epithet repeats the genus name, such as Gorilla (Western gorilla). This is called a tautonym. While often used in animal names, tautonyms aren’t allowed in plant, fungi and algae names according to the International Code of Nomenclature for Algae, Fungi, and Plants  guidelines .

Some examples of common and scientific animal names:

Some examples of common and scientific plant names:

Rules for writing scientific names of plants and animals

Scientific names are made up of Latin, or latinized, words. The scientific name often describes some aspect of the organism. For example, the blue jay’s scientific name is Cyanocitta cristata, which means chattering, crested blue bird.

Sometimes, species are named after a person (e.g., a black-eyed satyr butterfly, Euptchia attenboroughi, was named after David Attenborough), or the place where it occurs (e.g., the Arabian gazelle is called Gazella arabica).

How to format scientific names

Scientific names are in Latin, so, similar to other words from foreign languages, they’re always written in italics. The generic name is always capitalized, while the species epithet is never capitalized.

If the species name appears in a sentence where the text is already italicized, such as in a heading or figure legend, the species name can be unitalicized to distinguish it from the rest of the text. If written by hand, the name should be underlined.

How to abbreviate scientific names

If a species name is repeated multiple times in a written piece, such as a research paper, it can be abbreviated after the first time the name is written out in full. For example, the mosquito Anopheles stephensi can subsequently be abbreviated as A. stephensi. In the same written piece, you can also refer to another species from the same genus in the same way, such as A. funestus. In some journals, this must be done in both the abstract and main text of the paper.

If there are two genus names in the text that start with the same letter, the genus name can be abbreviated using its first two letters.

For example, if you also mention Aedes vexans mosquitoes in your text, you can abbreviate the two species as An. stephensi and Ae. vexans.

However, as with all abbreviations, these abbreviations should be used sparingly and only if there is no possibility for confusion. Only use an abbreviation if you use the term multiple times in your text. The general guideline is three or more times, but this will depend on the length of your text, so use your own judgement.

Always keep your reader in mind. If there are genera with similar names, rather write them out in full. If you only have one species name in your text that you use repeatedly, abbreviating it is not a problem, but if you mention 10 different species, abbreviations could confuse and frustrate your reader.

When referring to an unknown species in a genus, you can write the generic name followed by the abbreviation “sp.” The plural form is “spp.” The abbreviation “sp. novo” indicates a species that hasn’t been described yet.

For example: “During their bat survey in Guinea, they caught a Myotis sp. in one of their traps. Its distinctive coloring set it apart from other Myotis spp. and they knew it had to be a new species. The discovery of Myotis sp. novo highlights the importance of these surveys.”

How to add the taxonomic authority of a scientific name

Sometimes, the taxonomic authority is added to the scientific name. The taxonomic authority is the surname of the person who first described the species.

In plant names, the taxonomic authority is abbreviated (e.g., Panicum virgatum L., where the L is the abbreviation for Linnaeus). In animals, the surname is written out in full followed by the date when it was first described (e.g., Balaena mysticetus Linnaeus, 1758). A name following in brackets means that the name has been amended subsequent to first descriptions (e.g., Pulchrapolia gracilis (Dyke and Cooper).

How to indicate subgenus, subspecies, form, and variety

Other information that can be added include subgenus, subspecies, forms, and varieties. Subgenus is a classification level below genus, but above species level. If a subgenus is included in the scientific name, it’s placed in parentheses between the generic and specific name, with the first letter capitalized, for example Nereis (Hediste) diversicolor.

A subspecies is a further division of a species into groups of individuals that are distinguishable, but not different enough to be classified as a separate species. In animal names, the subspecies name is written after the species name, in lowercase italics. For example, the Bengal tiger is Panthera tigris and the Sumatran tiger is Panthera tigris sondaica. The Bengal tiger is found in India, while the Sumatran tiger is only found on the island of Sumatra and is much smaller than the Bengal tiger. Despite the differences in their distribution and appearance, they can interbreed, making them subspecies and not different species.

In plant names, the abbreviation subsp. is added between the species and subspecies name. For example, Cornus sericea subsp. sericea.

A variety is a population of individuals with distinct, inheritable differences and are indicated with the abbreviation var., for example Gleditsia triacanthos var. inermis refers to the thornless variety of the thorny honeylocust. Form refers to occasional variations in individuals, such as variation in flower color. For example, Cornus florida f. rubra refers to individuals of the flowering dogwood with pink flowers instead of the usual white.

How to write the name of a hybrid

Hybrids are indicated with an “x”. Hybrids that have been named are written with the x between the genus and species name. For example, Solanum x procurrens is the hybrid between S. nigrum and S. physalifolium. If a hybrid hasn’t been named, or if you want to specify the parentage, the same hybrid can be written as S. nigrum x S. physalifolium.

How to write the name of a cultivar

Cultivar names are written inside quotations, capitalized, and not italicized. If the cultivar was bred from a single species, the cultivar name follows the specific epithet; for example Zea mays “Wisconsin 153.” If the cultivar was bred by hybridizing several species, the cultivar name replaces the specific epithet, for example, Rosa “Iceberg” is a cultivar derived from crosses between Rosa chinensis, Rosa multiflora, Rosa gigantea, and several other Rosa spp.

Can two species have the same scientific name?

When two genera from the same kingdom have the same name, this is called a homonym. This is similar to homonyms in grammar, which refers to words with the same spelling but different meanings. While homonyms aren’t allowed in scientific nomenclature, errors sometimes slip through as shown in this  online list of homonyms . For example, Colobus is a genus of beetles and a genus of primates.

When two genus names from different kingdoms have the same name, this is called a hemihomonym. For example, Ficus is a genus of plants and a genus of snails.

Hemihomonyms are allowed since the scientific names of different kingdoms are governed by different regulatory bodies. The  International Code of Nomenclature  (ICN) governs the naming of algae, fungi, and plants, while the  International Commission on Zoological Nomenclature  (ICZN) regulates the naming of animals. A  recent publication highlighted the problem with and extent of this phenomenon and compiled an online list of hemihomonyms .

It can happen that two species from generic hemihomonyms also have the same specific epithet, resulting in identical scientific names. In the previous example of the hemihomonym, Ficus, there’s both a  sea snail  and a fig named Ficus variegata. Another example is Orestias elegans, which is the scientific name of both an  orchid  and a  fish .

Resources for finding scientific nomenclature

The  Integrated Taxonomic Information System  (ITIS) and  The Catalogue of Life  are online data bases where you can find the scientific name of any life form by searching either the common name or the scientific name. They provide the full taxonomic classification, from kingdom to species level, the taxonomic authority, and references to the publications where these species were described.

The  IUCN Redlist  is another trusted source and provides a list of animal, plant, and fungi species with their taxonomic information and conservation status details, including population numbers, distribution, and current threats.

However, species names can change when new taxonomic information becomes available. Keeping track of the taxonomic changes of all organisms is a huge task. While the above-mentioned lists are a good starting point to finding a species name, do some further research to be sure you have the latest accepted scientific name.

A scientific name in a database might have been correct at the time it was last updated, but it could be outdated. For example, the name of the sweet thorn tree was changed to Vachellia karroo as described by  Banfi and Galasso in 2008 . However, in the ITIS database, Acacia karroo is still listed as the correct name, while the IUCN Redlist and The Catalogue of Life have the correct accepted name, with Acacia karroo listed as the synonym.

Region- or taxon-specific resources such as recent, regional field guides or online databases are often better resources. For example, a good reference for bird species would be the  Birdlife International website . The  World Register of Marine Species  (or WORMS) is a database of marine organisms. However, the gold standard would be the most recent taxonomic publications on the species.

If you really want to be sure you’ve got your taxonomy right…

AJE offers editing by experts who know these subjects inside and out. While they polish your English to a level fit for publication, they’ll also fix up your scientific and technical terminology. Check out  AJE Editing services here .

The AJE Team

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