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 Viruses

  virus is a microscopic organism that can replicate only inside the cells of a host organism. Most viruses are so tiny they are only observable with at least a conventional optical microscope. Viruses infect all types of organisms, including animals and plants, as well as bacteria and archaea. Approximately 5000 different viruses have been described in detail at the current time, although it is known that there are millions of distinct types.[1]  Viruses are found in virtually every ecosystem on Earth, and these minute life forms are thought to be the most abundant type of biological entity.[2]  The study of viruses is known as virology, a specialty within the field of  microbiology.

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The common concept of viruses focuses on their role as pathogen. Actually, there are vast numbers of viral entities that are beneficial to individual species as well as providing ecosystem services. For example, a class of viruses known as bacteriophages can kill a spectrum of harmful bacteria, providing protection to humans as well as other biota.
Viruses are key in the carbon cycle; their role in ocean biochemistry includes microbiological metabolic—including decomposition—processes. It is this decomposition that stimulates massive carbon dioxide respiration of marine flora. That respiration annihilates effectively about three gigatons of carbon each year from the atmosphere. Significantly, viruses are being developed as tools for constructive modern medicine as well as the critical field of nanotechnology.
Unlike prions and viroids, viruses consist of two or three parts: a helical molecule, protein coat and sometimes a viral wrapper. All viruses have genes constructed from either deoxyribonucleic acid (DNA) or ribonucleic acid (RNA)—long helical molecules that carry genetic information. All viruses have a protein coat that protects these genes, and some are wrapped in a viral envelope of fat that surrounds them when they are outside a cell. (Viroids do not have a protein coat and prions contain neither RNA nor DNA).
Viruses vary from simple helical and icosahedral shapes to more complex structures. Most viruses are approximately one hundred times smaller than an average bacterium. The origins of viruses in the evolutionary history of life are unclear. Some may have evolved from plasmids—fragments of DNA that can migrate between cells—while others may have evolved from bacteria. In evolution, viruses are an important means of horizontal gene transfer, which increases genetic diversity.

Lifeform or not?

Viruses have no ability to metabolize on their own, but depend upon a host organism for replication and manufacture of chemicals needed for such replication. Rybicki has characterized viruses as a form "at the edge of life."[3]  Viruses are found in modern taxonomy, which considers viruses as a totally separate form of life from cellular organisms—some would say that they are merely complex molecules with a protein coating and not a lifeform at all. Since viruses are capable of self-replication, they are clearly some type of lifeform, and likely involved with the early evolutionary development of such other simple lifeforms as bacteria and protists.
Viruses differ, however, from the simpler autonomous replication of chemical crystals. This is due to the fact that a virus can inherit a genetic mutation and is also subject to similar natural selection processes of cellular organisms. A virus cannot be labelled simply, therefore, as inanimate or lifeless. Here, we consider it a lifeform, but we adhere to current taxonomy and do not credit it with a parallel domain to other recognized cellular lifeforms.

Evolution

Although there is no detailed catalogue of the evolutionary relationships of viruses and hosts, certain general characterizations can be made. In such viral groups as poxviruses, papillomaviruses, and tobamoviruses, molecular taxonomy aligns generally with the genetic relationships of their hosts.[4] This suggests that the affiliations of those viral groups predate their present derivatives, and, in fact, that these three viral groups and their hosts likely co-evolved. There are clear examples of an otherwise genetically close group like the tobamoviruses including a genetically outlying host; in particular, the tobamoviruses generally utilize plants of the Solanaceae family, but an orchid and a cactus virus can also be found in the group.
Recombination of genome parts of viruses poses a more vexing puzzle, since the events are virtually random pieces of an evolutionary chain. Retroviruses and luteoviruses are examples of viral groups in which large numbers of recombinations have occurred to produce new organisms. Sometimes these produced genome splices occur naturally, using fragments that are either viral or cellular in nature. In some cases the product is more of a rearrangement of genomic parts—referred to as pseudo-recombination. The Western Equine Encephalovirus is a known example of this last category.
It is likely that viruses began host relationships with archaea and bacteria about two billion years ago; it has been suggested, however, that the proliferation of terrestrial vascular plants was the watershed event in evolution that enabled the explosion of numbers of viral organisms and pathways.[5]

Taxonomy

There are two complementary systems for viral taxonomy: the ICTV and Baltimore approaches. In the case of the ICTV taxonomy, there are five distinct orders: Caudovirales, Herpesvirales, Mononegavirales, Nidovirales, and Picornavirales. Within that hierarchy reside 82 families, 307 genera, 2083 species.[6]
David Baltimore devised an earlier system based on the method of viral messenger RNA synthesis.[7] The Baltimore scheme is founded on the mechanism of messenger RNA production.  Although viruses must replicate mRNAs from their genomes to produce proteins and reproduce, distinctly different mechanisms are employed within each viral family. Viral genomes may be single (ss) or double-stranded (ds), may be RNA or DNA based, and may optionally employ reverse transcriptase (RT); furthermore single-strand RNA virus helices may be either sense (+) or antisense (−). These nuances divide viruses into seven Baltimore groups.
This Baltimore classification scheme is centered around the concept of messenger RNA replication, since viruses generate messenger RNA from their genomic coding to produce proteins and from that point replicate themselves. The resulting Baltimore groups are:
•    I: dsDNA type (examples: Adenovirus, Herpesvirus, Poxvirus)
•    II: ssDNA type (+)sense DNA (example: Parvovirus)
•    III: dsRNA type (example: Reovirus)
•    IV: (+)ssRNA type (+)sense RNA (examples: Picornavirus, Togavirus)
•    V: (−)ssRNA type (−)sense RNA (examples: Orthomyxovirus, Rhabdovirus)
•    VI: ssRNA-RT type (+)sense RNA with DNA intermediate to life-cycle (example: Retrovirus)
•    VII: dsDNA-RT type (example: Hepadnavirus)

Morphology

The majority of viruses characteristically measure between 10 and 300 nonometers (nm), although certain filoviruses extend to a length of up to 1400 nm, with a diameter of approximately 80 nm.
A complete virus, known as a virion, consists of nucleic acid encased within an exterior protective coating of proteins termed a capsid—constructed from identical protein subunits called capsomers.
Very few viruses cannot be observed with a basic light microscope, but scanning and transmission electron microscopes can be employed to observe the virion. To increase the contrast between viruses and the background, electron-dense staining is invoked; this technique involves solutions of heavy metal salts (e.g., tungsten) that can scatter impinging electrons from regions covered with the stain. When virions are coated with positive stain, fine detail is obscured, and negative stains (of the background only) are applied to complement the positive staining observations. There are four major distinct structural forms:

• Helix:  This group is characterized by single type of capsomer stacked around a core axis to form a helical structure, which may have a central cavity within the helix. This geometry results in rod-shaped or filamentous structures, which may be quite long, flexible, and filamentous or abbreviated and rigid. Most often the core genetic macromolecule is single-stranded RNA bound inside the protein helix by polar interactions between the negatively charged nucleic acid and effective positive charge at the protein surface. Tobacco mosaic virus is a prominent example of a helical virus.
• Envelope:  In some cases a cell membrane of the host is utilized for encasement of the virus; this may be either the external cell membrane or the nuclear membrane. These membranes become the outer lipid bilayer known as a viral envelope. The membrane is studded with proteins coded by the viral genome and host genome; the lipid membrane and any carbohydrates present derive exclusively from the host. Influenza and HIV viruses use this strategy.
• Icosahedral:  These are the main shapes occurring in viruses infecting animal hosts. They have icosahedral or near-spherical geometries with icosahedral symmetry. A regular icosahedron is nature's optimum method of producing a closed shell from identical subunits. Twelve is the minimum number of identical capsomers required for this formation, each capsomer being comprised of five identical subunits. A number of viruses (e.g., rotavirus) have more than 12 capsomers and appear spherical, but reflect the underlying symmetry. Capsomers at the apices are surrounded by five other capsomers and are called pentons. Capsomers on the triangular faces are surrounded by six other capsomers, and are termed hexons. 
• Complex structures:  More complex viral structures may have a capsid that is neither purely helical, nor purely icosahedral, and that may possess such ancillary structures as protein tails or a complex outer wall. Some bacteriophages, including Enterobacteria phage T4, possess a complex structure of an icosahedral head bound to a helical tail that may have a hexagon-shaped base plate with protruding protein tail fibers. Such a tail performs as a molecular syringe, first attaching to the bacterial host, and then injecting the viral RNA or DNA into the host cell.

Replication

The virus, totally dependent upon its host for reproduction, manifests six essential stages in its life cycle:

• Attachment is the intermolecular binding between viral capsid proteins and receptors on the outer membrane of the host cell. The specificity of binding determines the host species and cell types that are receptive to viral infection. For example, HIV infects only human T cells, because the surface protein interacts with CD4 and chemokine receptors on the surface of the T cell itself. This mechanism is thought to have evolved to discriminate in favor of those viruses that only infect cells in which they are capable of replication. Attachment to the outer host cell membrane may induce the viral-envelope protein to undergo changes that result in the fusion of virus and host cell membranes.
• Viral entry is the next step, wherein a virus penetrates the host cell wall. In the case of plant cells, the cell outer membrane is composed of cellulose, such that cell wall trauma must be usually precedent; however, certain plant viruses (for example, tobacco mosaic virus) can pass from cell to cell through plasmodesmata, or pore structures. Also, bacteria have significantly strong cell walls. Some viruses have evolved mechanisms that inject their DNA or RNA into a bacterium, with the viral capsid remaining outside.
• Uncoating is the step in which viral enzymes degrade the virus capsid; sometimes host enzymes also play a role in this dissolution, that then exposes the viral genome to the interior of the host cell's chemical factory.
• Replication is the actual synthesis of (i) the virus messenger RNA (except for the case of positive sense RNA); (ii) synthesis of virus proteins; and (iii) assembly of replicated genomic material and subsequent protein binding.
• Post-translational modification of viral proteins sometimes transpires. For example, in the case of HIV, such a step (often termed maturation) happens once the virus has escaped out of the host cell.
• Lysis is the final step, in which the host cell dies through the act of its membrane being burst by the viral escape. In some cases the new virus genome becomes dormant in the host, only to come to life at a later time, when the activated virus subsequently lyses.

Pathology

There are numerous mechanisms by which viruses induce disease in an organism, chiefly depending on the viral taxon. At the cellular level these mechanisms often include cell lysis, the breaking open and subsequent death of the cell. In multicellular organisms, if sufficient numbers of cells die, the whole organism may suffer gross metabolic disruption or even mortality. Although viruses may cause disruption of normal homeostasis, resulting in disease, in some cases viruses may simply reside inside an organism without significant apparent harm. An example, termed latency, is the ability of the herpes simplex virus, which includes cold sores, to remain in a dormant state within the human body.
Pathways of viral attack include respiratory intake, ingestion, body fluid contact, and dermal contact. Each virus may have a different set of attack pathway characteristics, but prevention is difficult due to the microscopic size and ex vivo durability of viruses. The extremely small subcellular scale makes trapping of viruses by masks or filters virtually impossible.

Infections in humans

Human diseases caused by viruses include chickenpox, HIV, influenza, Marburg, Ebola, Hanta, avian flu, cold sores, and the common cold. The relative strength of viruses to induce disease is denoted by virulence.
Some viruses can induce chronic infection, such that a virus replicates over the entire remaining life of the host, in spite of the host's defense mechanisms. This syndrome is common in hepatitis B and C viral infections. Those with chronic infections are deemed to be carriers—they are reservoirs of infectious virus as long as they live. For regional populations with a high carrier percentage, the disease is termed endemic.
Viral transmission may be vertical (from mother to child) or horizontal (from individual to individual), with horizontal being the most common mechanism of viral propagation. Horizontal infection can occur via exchange of blood, exchange of body fluid by sexual activity, oral exchange of saliva, from contaminated food or water, respiration of viruses contained in aerosols, or through animal or insect vectors such as mosquitoes. Each virus has a preferred method of transmission. The velocity of spread of viral disease correlates with a number of factors, human population density and sanitation being two of the most significant. There is evidence that many highly lethal viruses lie in biotic reservoirs in remote areas, and epidemics are sometimes triggered when humans encroach on natural areas that may have been isolated for long time frames; this theory has been advanced for Ebola and HIV, which are thought to have resided in isolated African habitats for millennia.

Plant viruses

There are a large number viruses that may manifest only as such superficial effects as fruit blemishing; however, crop yield reductions may result or even catastrophic loss of an entire plant population in a local area. Furthermore, control of these viruses may not be economically viable. In many cases viruses affecting vegetation may spread horizontally via third-party organisms, termed vectors, which may be insects, fungi, nematodes, or protozoans. Control of plant viruses usually consists of killing or removal of vectors that transmit the virus or removal of weed populations among crops that are secondary hosts. Plant viruses are ineffective in infecting animals, since their replication is only functional in living plant cells.
Vegetative species exhibit elaborate defense mechanisms to ward off viral attack. One of the most effective defense mechanisms is the presence of resistance (R) genes. Each R gene confers resistance to a particular virus by triggering localized areas of cell death in proximity to the infected cell, which is often visible to the naked eye as large splotches. This phenomenon prevents the viral infection from spreading. An alternative defense is via RNA interference.

Bacteriophages

A bacteriophage is a virus that attacks a bacterium host, and is one of the most abundant organisms on our planet; they are found in soil, ocean water, aerosols, and within animal intestinal tracts. For example, as many as 900 million viruses may occur in one milliliter of seawater, situated in surface microbial matting; RNA synthesis.[8] The associated infection rate of marine bacteria may approach seventy percent.
The bacteriophage may inject its genome into the bacterial cell though its tail structure after planting itself with long tail fibers atop the host cell wall. Each bacteriophage is minuscule in relation to its host bacterium cell. Since many bacteria have become resistant to a spectrum of drugs, bacteriophages are viewed now as possible agents against certain drug-resistant bacterial pathogens.
Double-stranded, DNA-tailed bacteriophages comprise approximately 95 percent of the bacteriophages currently known. The major defense tactic bacteria employ is the production of enzymes that kill foreign DNA. These restriction endonucleases cut up the viral DNA that is injected into the host cell.

Marine ecology and carbon cycling

Bacteriophages, in particular, have a central function in marine ecology and carbon cycling. These organisms are extremely widespread in the world's oceans, sometimes occurring in concentrations as high as 900 million bacteriophages per milliliter. Secondly, they have a very rapid attack and replication cycle, being capable of attaching and injecting genomic material into a host bacterium in a matter of minutes, and achieving genetic replication of new viruses in about 20 minutes. They are capable, therefore, of very rapid rates of multiplication in the marine environment.
Next, it is important to note that bacteriophages are highly correlated with concentrations of sewage. This is due to the presence of such bacteria as E. coli present in untreated sewage. In many world regions, large volumes of untreated sewage are discharged to the oceans. Without the ability of bacteriophages to systematically decompose the resulting high bacteria levels, not only would the bacterial concentrations be very high, but opportunity for enhanced carbon dioxide respiration at the atmosphere/ocean interface would be reduced. The outcome respiration rate for ocean absorption of atmospheric carbon is approximately three gigatons per annum,[9]  which is a significant percentage of the fossil fuel combustion input to the atmosphere. Thus, further understanding of these viral processes may be key to grasping the world's carbon balance, and perhaps even making intelligent management decisions to avoid global greenhouse gas buildup.

References

1. M. Breitbart and F. Rohwer. 2005. Here a virus, there a virus, everywhere the same virus?, Trends Microbiol., vol. 1, issue 6, pp 278-284
2. R. A. Edwards and F. Rohwer. 2005. Viral metagenomics. Nat. Rev. Microbiol., vol 3, issue 6, pp 504–510
3. E. P. Rybicki. 1990. The classification of organisms at the edge of life, or problems with virus systematics. S Aft J Sci 86:182–186 Advances in Virus Research. 394 pages
4. Adrian J. Gibbs, Charles H. Calisher and Fernando Garcia-Arenal. 1995. Molecular basis of virus evolution. 603 pages
5. Karl Maramorosch, Frederick A. Murphy and Aaron J. Shatkin. 2003. Advances in Virus Research. 394 pages
6. International Committee on Taxonomy of Viruses. 2008. Virus Taxonomy 2008. [Retrieved on May 11, 2010]
7. David Baltimore. 1974. The strategy of RNA viruses. Harvey Lectures. vol 70, pp 57-74
8. K. E. Wommack and R. R. Colwell. 2000. Virioplankton: viruses in aquatic osystems Microbiol. Mol. Biol. Rev. vol. 64, issue 1, pp 69–114
9. C. A. Suttle. 2007. Marine viruses--major players in the global ecosystem. Nature Reviews. Microbiology. 5 (10):801–12

 

Plants

Photo credit: Malcolm NQ, Fish-bone fern (cultivated), CC BY-NC- SA

Introduction

A plant is any one of the vast number of organisms within the biological kingdom Plantae; in general, these species are considered of limited motility and generally manufacture their own food. They include a host of familiar organisms including trees, forbs, shrubs, grasses, vines, ferns, and mosses. Conventionally the term plant implies a taxon with characteristics of multicellularity, cell structure with walls containing cellulose, and organisms capable of photosynthesis. Modern classification schemes are driven by somewhat rigid categorizations inherent in DNA and common ancestry.[1]

Taxonomy and terminology

Throughout most of the history of science from Aristotle to Linnaeus and into the 20th century, species were divided into two kingdoms: animals and plants. Driven by DNA characterizations and other modern analysis, fungi and bacteria have now been removed to separate kingdoms; in particular, fungi have cell walls that contain chitin rather than cellulose. Lichens, which are a symbiotic association of a fungal and photosynthetic organism, are generally not considered plants in the purest sense of taxonomy, although earlier classification schemes viewed them as plants. Viruses are also not considered to be plants, since they do not have a cell of their own, but inhabit a host cell of another organism; moreover, in many classifications they are not considered a living organism at all. Myxomycetes, or slime molds, are also not considered plants, but rather are heterotrophs that can ingest bacteria, fungal spores, and other items.
The scientific study of plants, known as botany, has identified about 350,000 extant taxa of plants, defined as seed plants, bryophytes, ferns and fern allies.  As of 2008, approximately 400,000 plant species have been described,[2] of which roughly ninety percent are flowering plants.
Vascular plants have lignified tissue and specialized structures termed xylem and phloem, which transport water, minerals, and nutrients upward from the roots and return sugars and other photosynthetic products. Vascular plants include ferns, club mosses, flowering plants, conifers and other gymnosperms. A scientific name for this vascular group is Tracheophyta.[3]

The major divisions of Plantae are:

• Anthocerotophyta (hornworts: nonvascular plants with one chloroplast per thallus cell)
• Bryophyta (mosses: nonvascular plants with wiry stems that reproduce by spores)
• Cycadophyta (cycads: nonflowering vascular plants with large pinnately compound leaves)
• Ginkgophyta (gymnosperm with one extant tree species, Ginkgo biloba)
• Gnetophyta (woody plants having some angiosperm and some gymnosperm features)
• Lycopodiophyta (vascular fern allies without seeds or flowers, having single microphyll leaf veins)
• Magnoliophyta (flowering plants that have vascular systems and are seed producing)
• Marchantiophyta (liverworts: nonvascular plants with one-celled rhizoids)
• Pinophyta (gymnosperm conifers that have vascular systems and cones, but no flowers)
• Pteridophyta (ferns: vascular plants lacking flowers and seeds, reproducing by spores)

Several groups of algae are under debate as to whether they should be included in Plantae; however, we will follow a definition of plants that excludes algae. Green plants, often termed Viridiplantae, derive the majority of their energy from sunlight via photosynthesis and are a subset of Plantae.
Structure in this group is fairly diverse, but almost all species retain a few basic characters that help to identify them as ciliates. The first character is the presence of cilia on at least one developmental stage of the organism. Modifications from the full body covered norm include a single ring of cilia, grouped ciliary organelles called cirri, and restriction of cilia to feeding tentacles. Most species also bear toxicysts that are most likely used to capture and stun prey. These toxicysts can be found around the mouth, along the length of tentacles or anywhere else on the surface of the cell body.

Morphology

Plant morphology involves the study of organism structures, including reproductive structures, and also addresses the pattern of development of these structures as the plant matures.[4] For vascular plants the principal structures involved are roots, stems, and leaves; for flowering plants the development of floral structures and seeds is of great importance in plant identification.  When structures in different species are thought to result from common, inherited genetic pathways, those structures are termed homologous. For example, cacti spines share the same fundamental structure and development as leaves of other vascular plants, thus cactus spines are homologous to leaves. Plant morphology observes both the vegetative structures of plants and reproductive structures.  The vegetative structures of vascular plants includes the study of the shoot system, composed of stems and leaves, as well as the subsurface or root system. The reproductive structures are more varied, and are usually specific to a particular group of plants, such as flowers and seeds for flowering plants, sori for ferns, and capsules for mosses. Analysis of plant reproductive structures has led to the discovery of the alternation of generations present in most plants (as well as algae). This area of plant morphology overlaps with the study of biodiversity and plant systematics.
Plant structure manifests at a range of geometric scales. For the genetic level, intricate microbiology analysis of DNA and RNA structure is required. At the cellular level, optical microscopy must be used.  At the macroscopic scale, the visually observable architecture of a plant's structure is under scrutiny. Plant morphology also addresses the pattern of development: the process by which structures originate and mature as a plant grows.  While animals produce all the body parts they will ever have from early in their life, plants periodically produce new tissues and structures throughout their life cycles. A living plant continues to have embryonic tissues even in advanced stages of development.[5]  The way in which new structures mature as they are produced may be affected by the point in time when the plant begins to develop, as well as by the habitat.

Metabolism and growth

Plant growth is governed by environmental and ecological factors. Chief environmental factors include meteorological parameters such as temperature, precipitation, wind velocity, and available sunlight, and edaphic factors such as soil nutrients, soil moisture, soil granularity and compaction, as well as topographic factors. Ecological factors include competition for water, nutrient, and light resources from other members of the plant community, as well as herbivory and trampling factors. In addition, the presence of plant diseases plays a role in the successful growth and propagation of plant species. In the last millennium, the role of humans has become a major factor in habitat destruction and fragmentation, and there is evidence of the imprint of humans on selective cultivation of species.
The majority of biomass created by a plant is typically derived from the atmosphere. Through a process known as photosynthesis, most plants use the energy in sunlight to convert carbon dioxide from the atmosphere, plus water, into simple sugars, which are used as building blocks and form the main structural components. Chlorophyll, a molecule that lends a green appearance, is typically present in plant leaves as well as and often in other plant parts to absorb sunlight to power the photosynthetic process. Parasitic plants, conversely, derive nutrient resources from a host. Carnivorous plants actually capture small animal prey to gain many essential nutrients. Plants typically depend on soil for architectural support and water uptake, but also obtain nutrients such as nitrogen and phosphorus from soil. Epiphytic and lithophytic plants often depend on rainwater or other sources for nutrients. Some specialized vascular plants, such as mangroves, can grow with their roots in anoxic conditions.

Ecology

Plants constitute most of the primary production of the Earth's ecosystems; that is, they produce the bulk of the biomass from light, carbon dioxide, and basic nutrients.[6] The cornerstone of this primary productivity is photosynthesis, which has radically altered the composition of early Earth's atmosphere, resulting in air that is 21% oxygen. Animals rely on oxygen as well as food sources for herbivores; plants also provide shelter and nesting locations for many species.
Land plants are key components of the water cycle and several other biogeochemical cycles. Some plants have coevolved with nitrogen- fixing bacteria,[7] making plants an important part of the nitrogen cycle. Plant roots play an essential role in soil development and prevention of soil erosion.
The majority of plants have fungi associated with their root systems in a kind of mutualistic symbiosis known as mycorrhiza; an important function of this type of symbiosis is the enhancement of phosphorus uptake.[8] The fungi help the plants gain water and mineral nutrients from the soil, while the plant gives the fungi carbohydrates manufactured in photosynthesis. Some plants serve as homes for endophytic fungi that protect the plant from herbivores by producing toxins.[9] In fact, most plants contain a variety of endophytic micro-organisms, each of which produces a unique set of chemicals that can be useful to the host plant.
Various forms of parasitism are also fairly common among plants, from the semi-parasitic mistletoe that merely extracts nutrients from its host, but also has photosynthetic capability, to the fully parasitic toothwort that acquire all their nutrients through conduits to the roots of other plants.

Plant associations

In a given ecosystem there is typically a well-defined plant association, which commonly is characterized by a canopy layer, an intermediate (or shrub) layer, and an understory or forest floor layer. In the case of grasslands, tundras, and certain other treeless habitats, the upper one or two layers may be absent, although in those cases there are often material differences in the grassland plant height layering.  A given plant association will, of course, be dependent on certain soil types, meteorology, and mixture of fauna; moreover, the plant association may manifest marked seasonal differences in temperate and boreal settings, although this appearance will simply conceal certain plants that are dormant or leafless in a given season.[10] Characterization of a plant association is helpful to botanists as a guide to plant identification and other ecological research; furthermore, understanding of a plant association is critical to studies of plant succession, where environmental changes in a given landscape lead to a series of plant communities, before a stable equilibrium is attained.[11]

Interactions with humans

Most of the human diet is plant derived; in addition, a large fraction of raw materials for shelter, clothing and other life necessities of Homo sapiens is obtained from plant products. Furthermore, countless medicinal extracts have been produced from plants. Tree rings are a method of dating in archaeology and serve as a record of past climates. Basic biological research has often been done with plants, such as use of pollen core records to study the distant past or the pea plants used to derive Mendel's laws of genetics. The field of ethnobotany studies plant use by indigenous cultures, which helps to conserve endangered species as well as discover new medicinal herbs. Gardening is the top leisure activity in many world regions.
Plants have served as a source of interest to humans for millennia beyond their use as food. Gardening for ornamental purposes and use of cut flowers for decoration have been noted at least as early as the Bronze Age by Egyptian, Cretan, and Celtic cultures, for example. Early scientists such as the Greeks spent considerable effort engaging in describing and characterizing morphology of various species. Plants have been an important element of human art, with elements of plant architecture appearing as ornamentation for ceramics and other decoration in Neolithic and Bronze ages in China, Crete, Southern Africa, British Isles, Egypt, and in the Mayan civilizations. As an example, glyphs found in Middle Minoan pottery as early as 1850 BC contain designs of olive sprig, saffron, wheat, and silphium.[12]  In the history of art, plants played an important role as subjects in classical still-life paintings, and may have reached a crescendo with obsessions by 18th- and 19th-century European printmakers in creating myriads of botanical prints.
Specific to gardening, plants have been used throughout history not only as adornment for indoor and outdoor spaces of human habitation, but also to modify microclimates for more comfortable habitation. For example, treelines and shrub borders have been used, particularly in the last millennium in Europe to provide windscreens for livestock and separation of pastures to secure livestock ownership. Landscaping has also been used for centuries as a method of microclimate amelioration for human habitation, including wind protection, thermal buffering, and atmospheric humidity modification.

References

1. Carl R. Woese, Otto Kandler and Mark L. Wheelis: Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proceedings of the National Academy of Sciences of the United States of America, 87(12):4576-9.
2. Botanic Gardens Conservation International. Plant Species Numbers
3. Abercrombie, Hickman & Johnson. 1966. A Dictionary of Biology. Penguin Books
4. Harold C. Bold, C. J. Alexopoulos, and T. Delevoryas. 1987.Morphology of Plants and Fungi, 5th ed., Harper-Collins, New York ISBN 0-06-040838-1
5. Andrew J. Lack and David E. Evans. 2005. Bios instant notes plant biology. Taylor & Francis. 351 pages
6. Martin A. Abraham. 2006. Sustainability science and engineering: defining principles. 518 pages
7. Dietrich Werner and William Edward Newton. 2005. Nitrogen fixation in agriculture, forestry, ecology and the environment. Springer. 347 pages
8. Teja Tscharntke and Bradford A. Hawkins. 2002. Multitrophic level interactions. Cambridge University Press. 274 pages
9. Arun Arya and Analía Edith Perelló. 2010. Management of Fungal Plant Pathogens. CABI.388 pages
10. A.G.Tansley. 2003. An Introduction To Plant Ecology. 228 pages
11. J.H. Connell and R.O. Slatyer. 1977. Mechanisms of succession in natural communities and their role in community stability and organization. American Naturalist 111: 1119-44
12. C.Michael Hogan. 2007. Knossos fieldnotes. The Modern Antiquarian. ed. Julian Cope

This article was adapted from the Encyclopedia of Earth.
Available under CC BY-SA-2.5
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