Microbes are the oldest life-forms and the foundation for all of life.

They are prokaryotic in nature, though extremely small; they have the most important impact on our world. In the modern world, the microbes are found everywhere and fulfill numerous roles. Most are harmful, but many are also beneficial in the environment. From the air we breathe to the soil we rely on for farming to the water we drink, everything humans need to survive is intimately coupled with the activities of microbes. In the oceans, algae, protozoa and bacteria are the most numerous and important members of the plankton communities that are the basis of all marine food chains. The microbes can reproduce a generation through binary fission within 1-3 hrs. Reproduction is limited due to nutrient exhaustion, metabolic waste poisoning, or being consumed by other organisms. They also face competition from other microorganisms. Some microbes can survive under harsh conditions and where there is no food like the Bacillus anthracis. Microbes perform innumerable functions on earth; On land, bacteria dominate in soils and are the most important decomposers, being responsible for the recycling of almost all organic materials and without them eukaryotes would not exist. The microbes help recycle chemicals and clean up the environment. They play a defining role in the chemical cycle as they are nitrogen producers and decomposers. Bioremediation; here organisms are used to remove pollutants from soil, air, or water. In sewage systems: they decompose sludge that can later be used as fertilizer. Bacteria produce compounds that help certain Achaea consume methane, a greenhouse gas Liquid wastes that are put into a trickling filter system are mixed with microbes that absorb its organic material that is later released into a body of water. They have also been used to carry out chemical transformations of inorganic materials in order to make those products less mobile or bioavailable in the environment. Fertilizers make oil eating bacteria that can help clean up oil spills. Microbes aid in mining operations. Bacteria are used in microbial enriched oil recovery and to extract precious materials from ore. They can be used to manufacture biofuel and other energy products. Bacteria are used to digest corn and sugarcane in the manufacture of ethanol, and researchers are exploring their use in transforming chemical energy into electrical energy in microbial full cells. Hundreds of species of microbes live in and on the surface of the human body. They supply vitamins to the body and help it digest food.

Microorganisms are the chief causes of transmittable diseases and affect the evolution of their hosts as weaker organisms succumb to disease while stronger individuals survive to pass on their genes. Bacteria are used to digest grasses and other fodder to make silage, a feed material that can be stored for use during winter months when pastures are not available. Also, legume seeds, such as beans and peas, are often coated with nitrogen-fixing bacteria prior to planting to ensure the plants develop the proper nitrogen-fixing community. Finally, the bacterial compound monensin is used to increase digestion efficiency in dairy cattle. Microbes are used in food manufacture in many different capacities, including fermentation processes and flavor enhancement. Microbes are also significant in terms of food spoilage and food safety. There have been enormous food recalls due to microbial contamination. Heat stable enzymes isolated from thermophilic bacteria, like Taq, lipase, esterases and others, have proven extremely useful in biotechnology. These roles are all important but it is four billion years ago that microorganisms changed the earth forever. Life evolved from large organic molecules about four billion years ago. At that time the earth was still hot, with a poisonous atmosphere. At some point, the boundary was crossed from nonlife to life when RNA and DNA molecules began to self replicate and then used proteins and lipids to encase and protect themselves in the first cells. These simple cells had no nuclei or other organelles. They were primitive but alive, being capable of growth, movement and reproduction and they shaped the earth's atmosphere and future evolution over a period of one to three billion years. These first microbes were heterotrophs, consuming loose organic molecules and nutrients, plus each other. During shortage of available nutrients, the first cyanobacteria used the pigment chlorophyll to capture sun energy and make sugars from water and carbon dioxide. This brought about the first autotrophs, the ancestors of modern blue green algae, to radically alter the earth's atmosphere by producing oxygen, as a byproduct of photosynthesis. During the next three billion years, microorganisms continued to evolve. They developed the ability to manufacture a huge number of chemicals, becoming sophisticated biochemical factories. They also developed organelles to make themselves more efficient. These cells evolved

nuclei where the chromosomes are stored and where the control functions of the cells occur. Ribosomes developed and other cell organelles, important for microorganisms but also important later when cells joined together to form multicellular organisms. Without the biochemical abilities of individual cells which evolved by microorganisms, multicellular life would not be possible. Our structures and abilities all come from the information stored at the cellular level and the chemicals that they can make, from the digestive juices that allow us to process our food to the pigments that colour our eyes, hair and skin, to the oxygen carrying capacity of our blood: all was made possible by our microorganism ancestors. The second major evolutionary advance made by microorganisms was the explosion of life forms in the Cambrian Period. Until that point, evolution could only proceed slowly at the rate of mutations. With the sexual revolution and subsequent genetic recombination, new forms evolved quickly and life really took off. By the Cambrian Period there was enough oxygen in the ocean and the atmosphere for numerous new aerobic life forms to evolve. All the major phyla of animals appear in this period, as if life was experimenting on a grand scale with all the potential shapes, forms and types. Some succeeded while others became extinct, but in all that period and up to the present, microorganisms continued to survive, compete, thrive and adapt. Some took on parasitic lifestyles, taking advantage of larger multicellular hosts to protect themselves. Parasites and disease-causing microorganisms are important in driving natural selection, taking out weak individuals and thus promoting the evolution of fitter species. Many higher organisms also took advantage of microorganisms and formed symbiotic relationships with them. Without microorganisms, termites could not digest wood and cows could not digest grass. We too are dependent on our gut flora to help digest our food. Virtually every plant and animal has symbiotic bacteria that they are dependent upon for their survival. Existing somewhere in every part of the biosphere, microorganisms serve many purposes. While, from the point of view of some other organisms, these might not all be positive, each and every one is important to the survival of life on Earth. One of the primary roles played by microorganisms is decay. Without the elimination of dead biological material there is no way for the various cycles of life to continue. Microscopic bacteria, fungi and animals consume dead plant and animal material. In so doing they release the

carbon and nutrients that are tied up in the structures of these dead organisms releasing them back to the soil and the atmosphere. In the oceans, microscopic plants and animals, phytoplankton and zooplankton, gather nutrients in the waters and make up the base of the oceanic food chain. Consumed by the smallest and the largest of ocean life these microbes are the key to life on the planet. Phytoplankton, microscopic plants, absorb nutrients and carbon dioxide dissolved in the oceans water. Through photosynthesis they combine the carbon dioxide with water to make sugars. This process is the same as that used by trees and grasses and all other plants. Zooplankton, microscopic animals, consume phytoplankton as well as bits of dead life whether floating in the oceanic currents or fallen to the sea beds. As the next step in the food chain of the oceans, zooplankton are also essential to life. While most zooplankton is invisible to the naked eye, and therefore qualifies as being considered microorganisms, some macroscopic free floating shrimp, jellyfish and other animals are considered zooplankton as well. An additional form of plankton, bacterioplankton, acts in a manner similar to both phytoplankton and zooplankton. Because of their cellular structure, bacterioplankton can't be considered the same as either of those. However, some bacteroplankton have chloroplasts and can perform photosynthesis, like phytoplankton. Others can't do that and serve in the same ecological niche as zooplankton. Zooplankton consume phytoplankton and bacteroplankton, as well as one another. Also living on these microorganisms are the small filter feeders such as clams and coral. But, even the largest animals on the planet survive on plankton. Large baleen whales are filter feeders. Using structures in their mouth to bring in enormous quantities of ocean water, these giant animals separate the plankton from the water for sustenance. Even the largest fish in the oceans, whale sharks, oceanic sunfish and giant manta rays, survive by filtering plankton from the seas. Symbiotic microorganisms are essential to many, if not all, forms of macroscopic life. Coral cannot survive without the symbiotic algae that they harbor and protect within their small bodies. Termites could not digest the cellulose that they consume from wood without bacteria that live within their guts. Even humans rely on symbiotic microbes to help digest their food. Even those processes that we might consider to be negative serve a useful purpose to the ecosystem as a whole. Microorganisms are often responsible for disease and can cause death. To the creatures that are sick this can be a terrible thing. But, when looked at from the perspective of

the ecosystem this can result in an overall benefit. Disease is more likely to eliminate those organisms that are weak. In so doing they make room for the stronger to survive and become healthier. Often a sad fact, in the long run this can make for a stronger environment. The interactions of microorganisms on our planet are diverse and essential. Without this, all life on Earth would cease to exist.

Their influence can be felt in the structure of food webs, bioenergy production, waste management and treatment, food production, and symbiotic nitrogen fixation for plants, to name a few examples. As human populations climb, reliance on microorganisms to perform these functions and others for maintaining human and ecological health also grows.

The Radiolarians have silica made internal structure, surrounded by a test, mainly marine. When they die, their hard parts become sediment

16.5) Prokaryotes obtain nourishment in a variety of ways mode of nutrition: how they obtain energy and carbon 1. Source of energy-Phototrophs; from sunlight. Chemotrophs; from organic or inorganic molecules 2. Source of carbon-Autotrophs-making organic compounds through inorganic sources. Heterotrophs obtain carbon from organic compounds. Mode of Nutrition 1. Photoautotrophs-cyanobacteria 2. Photoheterotrophs-purple nonsulfur bacteria, found in anaerobic aquatic sediments

3. Chemoautotrophs-sulfur bacteria in deep sea vents, soil bacteria 4. Chemoheterotrophs-most diverse group of prokaryotes -Biofilms-surface-coating colonies. They use signaling molecules to recruit nearby cells. Cells produce proteins that allow them to attach to the substrate and each other. Biofilms have channels that exit wastes and lead in nutrients. -Harmful: dental plaque, ear infections, and urinary tract infection -. 16.6) 16.7) Bacteria include a diverse assemblage of prokaryotes -bacterial phylogeny is based on molecular systematics and occasionally on phenotypic traits The relationships between the domains Archaea, Eukarya, Bacteria are due to the study of DNA/RNA. 1. Bacteria: one kind of RNA polymerase, small and simple. Introns are rare. Sensitive to antibiotics. Peptidoglycan is present in cell wall. Histones associated with DNA are absent. 2. Both Archaea and Eukarya: have several kinds of complex RNA polymerase. Insensitive to antibiotics. Peptidoglycan is absent. Unique to Eukarya: Introns are present. Histones are present. -Over the long course of their reproduction, prokaryotes have acquired genes from other species. -Archaea shares more similar traits with Eukarya than with Bacteria. 16.3) Prokaryotes come in a variety of shapes 1. cocci-spherical prokaryotic cells, bacilli-rod-shaped, vibrios-like commas, spirilla-helical, short and rigid, spirochetes-longer, flexible. Some are curved or spiral. Staphyle (cluster), Strepto (chains). 16.4) Various structural features contribute to the success of prokaryotes -Most are unicellular and function on their own, live in diverse habitats. External Structures 1. Cell wall: protection, maintain shape, prevents from bursting in a hypotonic environment. 2. Gram-positive bacteria-simple walls, thick layer of peptidoglycan. 3. Gram-negative- complex walls, less peptidoglycan, lipids surround membrane. They are more harmful due to toxic lipids, a membrane that prohibits antibiotics entry and combats bodys defenses. 4. Capsule-sticky layer of polysaccharides or protein. It helps attach to substrate, other

individuals. It shields attacks from immune system. 5. Pili-hairlike appendages; stick to other prokaryotes, surfaces, or substrate. Sex pili link prokaryotes during conjugation. Motility -flagella-a naked protein structure(lacks microtubules) that help the cell move. They scattered over cell or on one or both ends of the cell. They are attached to cell surface by rotating rings that give the flagellum a propeller-like rotary movement. . There are nine groups, 5 which are subgroups. 1. Proteobacteria-gram-negative bacteria with 5 subgroups -The alpha proteobacteria Rhizobium species fix atmospheric N2. -Gamma-sulfur bacteria oxidizes H2S -Delta-myxobacteria 2. Chlamydias-live inside eukaryotic host cells. They cause STDs, blindness. 3. Spirochetes-spiral through environment w/ rotating filaments, pathogens cause syphilis, Lyme disease 4. Gram-positive bacteria-have subgroups of: -Actinomycetes-decomposers, Streptomyces-source of many antibiotics 5. Cyanobacteria-prokaryotes with plant-like oxygen generating photosynthesis -They provide food for freshwater and marine ecosystems. 16.8) Some bacteria cause disease -How: 1. Exotoxin-proteins secreted by bacterial cells; poison -Clostridium tetani-causes muscle spasms and lockjaw that prevents mouth from opening -S. aureus produces exotoxins that: sheds skin, causes shock syndrome, vomiting, diarrhea -E. coli O157: H7 causes bloody diarrhea and death 2. Endotoxins-components of the outer membrane of gram-negative bacteria is released when the cell dies or is digested by a defensive cell. All have general symptoms of-fever aches, drop in blood pressure -Neisseria meningitidis-kills healthy person within days or hours -Salmonella-food poisoning and typhoid fever *Lyme disease- caused by Borrelia burgdorferi, a spirochete. It starts as a bulls eye rash, treated

by antibiotics within a month. If not treated, it can lead to arthritis, heart disease, nervous disorders. 16.9) -Ciproflaxin-antibiotic kills the bacteria but not the toxin 2. Yersinia pestis-causes plague, moves from rodents fleas humans. If it progresses, it causes egg-sized swellings, black blotches of bacteria under skin, deadly toxins move to bloodstream -Pneumonic plague-infects lungs, disintegrating lung tissue coughs out becoming airborne 3. Clostridium botulinum-the harmful part is the exotoxin it produces, Botulinum. Its the deadliest poison on Earth, causes paralysis in muscles required for breathing. 16.10) 2. Prokaryotes can extract metals and gold from ore. 16.11) Protists are an extremely diverse assortment of eukaryotes -Protists-diverse collection of mostly unicellular eukaryotes -Algae-autotrophic, protozoans-heterotrophic; eat bacteria and protists. -Most are aquatic or are endosymbionts, live within host organisms. -Symbiosis-close relationship between 2 or more species 16.12) Secondary endosymbiosis is the key to much of protist diversity Hypothesis for the origin of eukaryotic cells 1. Primary endosymbiosis-eukaryotic cells evolved when prokaryotes began to live in larger prokaryotes. 2. Heterotrophic eukaryotes with mitochondria evolved first 3. Autotrophic eukaryotes-heterotrophic engulfed an autotrophic cyanobacterium. Photosynthesis was a steady source of food for the heterotrophic host. Cyanobacteria could replicate with their own DNA and could be passed on to future generations. Cyanobacteria evolved into chloroplasts. -These eukaryotes evolved into green and red algae. 4. Secondary symbiosis: heterotrophs engulfed algae that replicated themselves. -Euglenozoans-were autotrophs but could be heterotrophic under limited sunlight. Red algae-includes dinoflagellates, stramenopiles -Apicomplexans-parasitic, organelle that is vital to a protists survival 16.13) A tentative phylogeny of eukaryotes includes multiple clades of protists -Protists are extremely diverse so theyre hard to categorize. They are the first eukaryotes,

ancestral to all other eukaryotes. Categories: Alveolates, Stramenopiles, Green Algae, Amoebozoans 16.14) Diplomonads and parabasalids contain modified mitochondria 1. Diplomonads-heterotrophs that me be the most ancient surviving lineage of eukaryotes. They have no DNA or electron transport chains, most are anaerobic. -Giardia intestinalis-causes severe diarrhea 2. Parasite-derives nutrition from living hosts while harming them 3. Parabasalids-heterotrophs that generate energy anaerobically -T. vaginalis-resistant to antibiotics, produces new infections. It feeds on white blood cells and bacteria lining vagina. They infect the males urethra but show no symptoms; easy to transfer to other women 16.15) Euglenozoans have flagella with a unique internal structure 1. Euglenozoans-protists with a crystalline rod of unknown function in flagella. -Trypanosoma-causes sleeping sickness by inhibiting red blood cells 16.16) Alveolates have sacs beneath plasma membrane -Characterized by alveoli, sacs that help stabilize cell surface or regulate water and ion content -Dinoflagellates-common components of microscopic autotrophs that provide food for coral reef communities. Population booms expose red toxins can kill many fish. -Ciliates-use cilia to move and feed, are free-moving, have two types of nuclei: single macronucleus for everyday activities and multiple micronuclei for sex reproduction -Example of apicomplexans is a Plasmodium: causes malaria. 16.17) Stramenopiles have hairy and smooth flagella -Stramenopiles are characterized by flagella; the clade includes heterotrophs and autotrophs 1. Water molds-fungus-like stramenopiles, act as decomposers 2. Diatoms-unicellular with a glassy cell wall that has silica. They provide food (organic molecules) for fresh/saltwater environments. -They store energy in oil droplets which keep it buoyant so its near sunlight. 3. Brown algae-large, complex, autotrophic, multicellular; most are marine. Ex: seaweeds, kelp 16.18) Amoebozoans have lobe-shaped pseudopodia -Pseudopodia-temporary extensions of cell 1. plasmodial slime mold-plasmodium are brightly pigmented, lie in moist, decaying matter

2. Plasmodium-unicellular, multinucleate mass of cytoplasm undivided by plasma membranes. -The cytoplasm streams in different directions to distribute nutrients and oxygen. -In unfavorable conditions-it stops growing, starts producing spores (reproductive structures) -Favorable conditions-open spores to release cells and form a zygote 3. Cellular slime mold-solitary amoeba cells also lie in decaying matter. If food is scarce, they group together and wander. Some dry up to form a stalk for asexual reproductive structures. 16.19) Foraminiferans and radiolarians have threadlike pseudopodia -They feed using pseudopodia; they are only distantly related to amoebozoans. 1. forams-live in fresh/saltwater, have porous shells (tests) where pseudopodia extend through 2. . 16.20) Red algae and green algae are the closest relatives of land plants 1. Red algae live in tropic, coastal waters. Those with hard, chalky deposits are important in reef building -Carrageenan, nori, and agar come from red alga. 2. Green algae-split into chlorophytes and charophytes (closest living relatives of land plants). -Chalmydomonas-unicellular alga common in freshwater, uses two flagella. -Volvox-consists of colonial biflagellated algae 3. alternation of generations-multicellular diploid form (sporophyte) alternates with a multicellular haploid form (gametophytes). It occurs in many multicellular algae and all plants. 16.21) Multicellularity evolved several times in eukaryotes -Multicellular organisms are linked to unicellular protists colonies 1. Ancestral colonies: cells divide and stick to each other 2. Cells become specialized and interdependent, more efficient at performing limited tasks. 3. Additional specialization leads to the boundary between gametes and somatic cells. . Major advances have been made in the understanding of disease and the use of microorganisms in the industrial production of drugs, food products and wastewater treatment. However, our understanding of many complicated microbial environments (the gut and teeth), soil fertility, and biogeochemical cycles of the elements is lagging behind due to

their enormous complexity. Inadequate technology and limited resources have stymied many lines of investigation. Today, most environmental microorganisms have yet to be isolated and identified, let alone rigorously studied. Ignorance of the microbial world and of the specific roles microorganisms play in the biogeochemical cycles that sustain our planet is a massive waste of the enormous potential for microorganisms to benefit humankind. Through fossil fuel burning, pollution, and resource exploitation, humans have impacted the very ecosystems that provide the essential elements for our continued existence. Researchers currently lack an understanding of the normal, baseline state of many microbial systems, and they know even less about how microorganisms will be affected by drastic environmental changes, whether microbes will amplify or dampen these effects in their habitats and what those effects signify for human beings. For example, it is not known how climate change will impact carbon cycling by microorganisms, an important factor in predicting the future concentrations of carbon dioxide in the atmosphere. Also, clearing forested land for farming increases the emission of nitrous oxide (a significant greenhouse gas) from soil and diminishes the soils ability to absorb methane (another important greenhouse gas), but it is not known why this happens or whether it can be prevented. Microbial systems are robust but can be pushed to the limit, and science needs to find ways microbial consortia may eventually fail in their roles in maintaining ecosystem integrity. These scientific challenges must be met with a resolve befitting the real urgency of the environmental problems we face. ESTIMATES OF THE NUMBER OF MICROORGANISMS ON THE PLANET On a global scale, one estimate places the total number of microbial cells at 10 30 and the number of viral particles at 10 31 (Whitman, 1998), but these large

numbers are associated with uncertainty, particularly with respect to inaccessible environments like deep sediments, which are little explored and poorly characterized as to their microbial inhabitants. Moreover, estimates of the total number of microbes on the planet are less instructive than estimates of total microbial biomass or biomass turnover, which are not available. In individual microbial systems, it can be useful to derive estimates of the number of participating microbial cells, since fluctuations in cell density can be an indication of perturbation. However, for many health applications and most environmental systems, baseline shifts can go undetected because information about cell Commercial applications for microbes and microbial products include: Bioremediation and bioaugmentation. Microbes have been put to use degrading organic chemicals through direct metabolism (in which the microbe uses the material for food or energy) and through co-metabolism (through which the microbe apparently gains nothing). . Applications include both in situtreatment (at the site of contamination) and treatment of waste streams in manufacturing settings. Wastewater treatment. This exploits the natural capability of microorganisms to degrade and recycle the essential elements on Earth. Millions of tons of organic and inorganic waste are treated annually, and more and more of the energy contained in this waste is recovered as biogas (methane). Important advances have also been made in recycling of sulfur and heavy metals. Others .Microbes are used in the manufacture of biodegradable plastics, green chemistry applications, and bacterial ice nucleation proteins are used in Despite the extensive amount of work done to characterize microbes and their communities, many unknowns remain at the genetic level. Today, as much as a third of the genetic content of even the most thoroughly studied organisms remains to be

annotated, so although the sequences of many genes (in many organisms) are known, the functions and significance of these genes remain unresolved. Judging from what is already known of the functional diversity of the microbial world, the potential locked up in poorly understood genes is considerable. These unknown genes could reveal useful processes for industry, bring to light processes that science has not yet conceived of, fill gaps in our understanding of metabolic pathways, be responsible for disease processes not yet understood, and unearth previously unknown functions of microorganisms in the environment. Since the functions of many of the genes in well-known microbial species are not known, many of the current predictions about microbial metabolism may be incomplete, and serious limits are placed on the ability to carry out genomic and metagenomic studies. Every new gene that is characterized has multiplicative value in sciences ability to identify similar, related genes in other organisms. Functional studies of genes in the past 20 years show that, although general categories of function can often be assigned, specific functions of genes are often not predictable from their sequences, so care must be taken in extrapolating the functions of unknown genes from the gene sequences of known proteins. been a successful approach in the past, but it remains impossible in most cases to isolate and express entire pathways, due to a lack of suitable expression hosts. It may be important to develop more and better hosts for expression of uncultivated microbial genes in the future. Targeting uncultivated microorganisms and their animal hosts in the search for bioactive compounds is often rewarding, since symbionts and hosts often develop chemical defenses to prevent other microbes from establishing spurious infections. It is important to note that useful compounds that may eventually come from uncultivated microorganisms are not limited to antibiotics; microorganisms produce an incredibly diverse array of bioactive compounds. The availability of appropriate screening methods to test the activities of these substances currently limits the ability to find and use them. Novel enzymes, which may eventually be identified and from DNA extracted from uncultivated microorganisms in the environment, also present a great poten-

tial resource for commercial use. The symbionts of termite guts, for example, are thought to be species-specific, and each symbiotic community produces a vast number of biocatalysts for wood degradationa process that is critical for any number of industrial processes, including ethanol manufacturing. Considering that there are over 2,600 different species of termites, the commercial resource these communities represent is impressive. A number of enzymes from other uncultivated microorganisms are already on the market, including enzymes that can tolerate detergents and heat. An understanding of microbial ecology/diversity should enable more effective devel-opment of both probiotics and prebiotics. (Prebiotics are defined as nondigestible food ingredients that may beneficially affect the host by selectively stimulating the growth and/or the activity of a limited number of bacteria in the colon.) Ecological species concepts Most ecological theory depends on a concept of species: population ecology counts individuals within species whereas community ecology and macroecology count the number of species. Species are most commonly defined through the biological species concept promoted by Mayr 4 . This is a genetic definition that envisages a species as a group of interbreeding individuals that is isolated from other such groups by barriers to recombination. If genetic exchange within a species is sufficiently extensive, and that between species is sufficiently low, species will be relatively homogeneous in themselves and ecologically distinct from other species. Unfortunately, prokaryotes

(and some eukaryotes) are asexual, thereby violating these assumptions, and do not form species in this genetic way. An alternative, the ecological species concept, defines a species as a set of individuals that can be considered to be identical in all relevant ecological properties. Cohan 5 has argued that bacteria have ecological species (ecotypes). He postulates that bacteria occupy discrete niches and that periodic selection will purge genetic variation within each niche without preventing divergence between the inhabitants of different niches. So, genetically and ecologically distinct species will arise, provided there is little or no recombination, and ecological theories that assume such species should apply to bacteria. This also predicts that molecular diversity should relate directly to ecological diversity. Cohans ecotypes depend on discrete niches but speciation is more difficult to envisage when the relevant environmental variables are continuous. Bacterial speciation in these situations could be explored using the theory of adaptive dynamics

6,7 , but this might not lead to simple mapping between molecular markers and an ecological niche. More crucially, speciation, and ecological species definitions, must consider bacterial gene-transfer processes, which are erratic and transfer only a small part of the genome. They provide a potential mechanism for maintaining biological species in Mayrs sense 8 , because an incoming gene can replace the homologous copy in the genome, maintaining the genetic cohesion of the species. In addition, these processes can also result in the horizontal transfer of genes with no counterpart in the recipient that can be maintained on a plasmid or integrated by non-homologous recombination. However, the importance of homologous recombination and horizontal transfer varies widely among well-studied bacterial species, and perhaps even more so among the uncultured masses in the environment. This heterogeneity is one reason why we are still far from a consensus on the nature of bacterial species, as revealed at a recent Royal Society discussion meeting 9 .

A consequence of gene transfer is that the bacterial genome is thought to consist of two distinct parts, the core genome and the accessory genome 10 . The core genome comprises genes that are essential in most circumstances and might form the basis for Mayrian species that maintain coherence through homologous recombination. The accessory genome encodes special ecological adaptations in genes that are readily gained and lost. Strains that belong to the same species, as defined by their core genome, can differ in the presence and absence of hundreds of accessory genes, and consequently can have different ecological capabilities. According to this view, Cohans ecotypes are merely temporary lineages with particular constellations of accessory genes, and the ecological niche cannot explain the apparent cohesion of species that are defined by the phylogeny of core genes 11 . Surveys of 16S ribosomal RNA (rRNA) gene sequences have demonstrated the huge diversity of bacterial communities, but if much of the interesting ecological adaptation is conferred by the accessory genome then the true ecological diversity exists in the

rich brew of catabolic plasmids, resistance transposons and pathogenesis islands. These can be shared among disparate bacteria in an environment that favours them, but can be absent in the same bacterial species growing elsewhere. The methods of evolutionary ecology have been applied to the interaction between these accessory elements and their host bacteria. For example, Bergstrom and Ecological species concepts Most ecological theory depends on a concept of species: population ecology counts individuals within species whereas community ecology and macroecology count the number of species. Species are most commonly defined through the biological species concept promoted by Mayr 4 . This is a genetic definition that envisages a species as a group of interbreeding individuals that is isolated from other such groups by barriers to recombination. If genetic exchange within a species is sufficiently extensive, and that between species is sufficiently low, species will be relatively homogeneous in themselves and ecologically distinct from other species. Unfortunately, prokaryotes (and some eukaryotes) are asexual, thereby violating these assumptions, and do not form species in this genetic way. An

alternative, the ecological species concept, defines a species as a set of individuals that can be considered to be identical in all relevant ecological properties. Cohan 5 has argued that bacteria have ecological species (ecotypes). He postulates that bacteria occupy discrete niches and that periodic selection will purge genetic variation