Bacteria, Archaea, Viruses, Protists and Fungi

Most of the life on Earth is invisible. Bacteria and archaea outnumber every other organism, protists drift through every drop of pond water and ocean, fungi thread through every handful of soil, and viruses, which are not even cells, outnumber them all. This chapter surveys these microscopic and mostly microscopic groups: how they are built, how they reproduce, how they obtain energy and why they matter for nutrient cycles, food, medicine and the infectious diseases that still shape human health.

Section 1Prokaryotic structure, diversity and metabolism

Small cells, enormous success

Prokaryotes are single celled organisms without a nucleus or other membrane bounded organelles. They belong to two of the three domains of life, Bacteria and Archaea. Most are 0.5 to 5 micrometers long, roughly a tenth to a hundredth the size of a typical eukaryotic cell. They were the first organisms on Earth and remain the most abundant: a gram of fertile soil can hold billions of cells, and the bacteria living in and on a human body are roughly as numerous as the body's own cells. Their success comes from small size, rapid reproduction, enormous metabolic diversity and the ability to exchange genes.

Prokaryotic cells come in three common shapes: spheres called cocci (singular coccus), rods called bacilli (singular bacillus) and spirals, including rigid spirilla and flexible, corkscrew spirochetes. Cocci that stay together in chains are streptococci; in grapelike clusters they are staphylococci.

Cell surface structures

Nearly all prokaryotes have a cell wall outside the plasma membrane. The wall maintains shape, protects the cell and prevents it from bursting in a hypotonic environment, where water rushes in by osmosis. Bacterial walls contain peptidoglycan, a network of sugar polymers cross linked by short polypeptides. Archaeal walls lack peptidoglycan and are built from other polysaccharides and proteins.

The Gram stain, developed in the 1880s, sorts bacteria into two groups by wall structure. Cells are stained with crystal violet, treated with iodine, rinsed with alcohol and counterstained with a red dye (safranin). Gram positive bacteria have a thick peptidoglycan layer that traps the crystal violet, so they stay purple. Gram negative bacteria have a thin peptidoglycan layer sandwiched between the plasma membrane and an outer membrane; the alcohol washes the violet out and they take the red counterstain. The outer membrane of gram negative bacteria contains lipopolysaccharide, whose lipid portion is toxic to animals, and it also blocks many drugs, so gram negative infections are often harder to treat. Penicillin and related antibiotics work by inhibiting peptidoglycan cross linking; because human cells have no peptidoglycan, these drugs harm bacteria with few direct effects on the patient.

Many prokaryotes secrete a sticky layer of polysaccharide or protein outside the wall: a dense, well defined capsule or a looser slime layer. These layers help cells adhere to surfaces, form biofilms (communities attached to surfaces such as teeth or medical catheters) and hide from the host's immune system. Some bacteria also form endospores, tough, dormant structures produced when essential nutrients run short. The cell copies its chromosome and surrounds one copy with a multilayered coat; the outer cell disintegrates, and the endospore can survive boiling, drying and disinfectants for centuries before germinating. Endospore formers include the bacteria that cause anthrax, tetanus and botulism, which is why canned foods must be heated under pressure to well above boiling.

Hairlike appendages called fimbriae allow prokaryotes to stick to surfaces or to each other. Longer pili (singular pilus), sometimes called sex pili, pull two cells together for DNA transfer. About half of prokaryotes are capable of directed movement, or taxis, toward or away from a stimulus such as food or light. The most common structure for movement is the flagellum. Bacterial flagella are entirely different from eukaryotic flagella: they are not covered by membrane and they rotate like propellers, driven by a motor in the cell envelope powered by the flow of hydrogen ions. The bacterial flagellum is a famous example of an evolved molecular machine: many of its proteins are related to proteins used in secretion systems, suggesting that it was assembled from preexisting parts.

Internal organization and genome

Prokaryotic cells lack the complex internal membranes of eukaryotes, although some carry out respiration or photosynthesis on infoldings of the plasma membrane. The genome usually consists of a single circular chromosome, with far fewer genes than a eukaryotic genome (a typical bacterium has a few thousand). The chromosome is concentrated in the nucleoid, a region without a membrane. Many cells also carry plasmids, small rings of DNA that replicate independently and often carry genes for antibiotic resistance, toxin production or the ability to use unusual nutrients. Prokaryotic ribosomes (70S) are smaller than eukaryotic ribosomes (80S) and differ in protein and RNA content, which allows antibiotics such as tetracycline and streptomycin to block bacterial protein synthesis selectively.

Reproduction and genetic variation

Prokaryotes reproduce asexually by binary fission: the chromosome is copied, the copies move apart, and the cell divides in two. Under ideal conditions some species divide every 20 minutes, although in nature growth is usually limited by nutrients. Three features generate great genetic diversity despite asexual reproduction: rapid reproduction, mutation and genetic recombination. Even a low mutation rate produces many new mutations in a population of billions of cells that reproduces several times a day, so prokaryotes can evolve within days, as the spread of drug resistance shows.

Genetic recombination in prokaryotes occurs through horizontal gene transfer by three mechanisms:

• Transformation: a cell takes up foreign DNA from its surroundings. In a classic experiment, harmless pneumococci acquired the ability to cause pneumonia by taking up DNA from heat killed virulent cells.
• Transduction: a bacteriophage (a virus that infects bacteria) accidentally packages a fragment of host DNA and carries it to a new host cell.
• Conjugation: DNA is transferred directly from one cell to another through a temporary connection. In E. coli, a donor cell carrying the F factor (fertility factor) on a plasmid forms a sex pilus, draws a recipient close and transfers a copy of the plasmid. R plasmids carry genes for resistance to antibiotics and can pass between different species, which is a major reason resistance spreads so quickly.

Metabolic diversity

Organisms are classified by how they obtain energy and carbon. Phototrophs get energy from light; chemotrophs get energy from chemicals. Autotrophs need only carbon dioxide as a carbon source; heterotrophs require at least one organic nutrient. Combining these gives four modes, and prokaryotes display all four, while eukaryotes use only two.

Prokaryotes also differ in their relationship to oxygen. Obligate aerobes require O2 for cellular respiration. Obligate anaerobes are poisoned by O2 and live by fermentation or by anaerobic respiration, in which a substance other than oxygen, such as nitrate or sulfate, accepts electrons at the end of the electron transport chain. Facultative anaerobes, such as E. coli, use O2 when it is present and switch to fermentation or anaerobic respiration when it is not.

Many prokaryotes perform nitrogen fixation, converting atmospheric N2 into ammonia (NH3), a form other organisms can use to build proteins and nucleic acids. Only prokaryotes can fix nitrogen. Some cyanobacteria, such as Anabaena, separate this oxygen sensitive process from photosynthesis by forming specialized cells called heterocysts, which fix nitrogen but do not produce O2. Cooperation also appears in biofilms and in metabolic partnerships among different species.

Diversity of Bacteria and Archaea

Molecular phylogenies have divided Bacteria into many clades. Proteobacteria are a large, diverse group of gram negative bacteria including nitrogen fixing Rhizobium, the gut bacterium E. coli, Salmonella, Helicobacter pylori (a cause of stomach ulcers) and the ancestors of mitochondria. Cyanobacteria are the only prokaryotes with plantlike oxygenic photosynthesis; an ancient cyanobacterium became the chloroplast. Gram positive bacteria include soil dwelling Streptomyces (the source of many antibiotics), Staphylococcus, Streptococcus, Bacillus and Clostridium, and the wall-less mycoplasmas, the smallest known cells. Spirochetes are helical heterotrophs that spin through their environment using internal flagella; they cause syphilis and Lyme disease. Chlamydias are parasites that live only inside animal cells and cause a common sexually transmitted infection and blinding trachoma.

The Archaea include many extremophiles. Extreme halophiles live in highly saline environments such as the Great Salt Lake and the Dead Sea; some require water several times saltier than seawater. Extreme thermophiles thrive in very hot environments: a strain of Pyrococcus and other vent archaea grow above 100°C, and one archaeon can reproduce at 121°C, the temperature of an autoclave. Methanogens release methane as a byproduct of using CO2 to oxidize H2. They are strict anaerobes found in swamps, marshes, the guts of cattle and termites and in sewage treatment, and they are important producers of methane, a powerful greenhouse gas. Many archaea are not extreme at all and are abundant in ordinary soils and oceans.

Section 2Viruses and their replication

What is a virus?

A virus is an infectious particle consisting of nucleic acid enclosed in a protein coat and, in some cases, a membranous envelope. Viruses are not cells. They have no ribosomes, no metabolism of their own and cannot reproduce outside a host cell. For this reason they are described as obligate intracellular parasites, and many biologists regard them as existing at the boundary between living and nonliving chemistry. They are, however, made of the same molecules as life, carry genes that evolve by natural selection, and have shaped the evolution of every lineage they infect. Most viruses are tiny, 20 to 300 nanometers across, far smaller than bacteria; they were first recognized because the agent of tobacco mosaic disease passed through filters that trapped bacteria.

Viral structure

The viral genome may be double stranded DNA, single stranded DNA, double stranded RNA or single stranded RNA, depending on the virus. It is usually linear or circular and may carry as few as four genes or as many as several hundred to over a thousand in "giant" viruses. The genome is enclosed in a protein shell, the capsid, built from many copies of a few kinds of protein subunits called capsomeres. Capsids may be rod shaped (helical), as in tobacco mosaic virus, or many sided (icosahedral), as in adenoviruses. Many animal viruses, including influenza, HIV and coronaviruses, have a viral envelope outside the capsid. The envelope is made from host cell membrane, studded with viral glycoproteins that bind to receptors on host cells. The most complex capsids belong to bacteriophages, or phages, viruses that infect bacteria. The T4 phage that infects E. coli has an icosahedral head holding its DNA, a protein tail sheath and tail fibers that attach to the host.

Each virus has a host range, the set of species, and often cell types, it can infect, determined largely by the fit between viral surface proteins and host receptor molecules. Some viruses are narrow: human cold viruses infect only cells lining the upper respiratory tract. Others, such as rabies and West Nile virus, infect many species. HIV binds the CD4 protein on helper T cells, which explains which cells it destroys.

The general pattern of viral replication

Every viral infection follows the same general logic. The virus binds to a host cell and its genome enters. The host's enzymes, ribosomes, tRNAs, amino acids and ATP are commandeered to copy the viral genome and make capsid proteins. The new genomes and capsid proteins then self assemble into new virus particles, which leave the cell. A single infected cell can release hundreds or thousands of new viruses.

Phage replication: the lytic and lysogenic cycles

Bacteriophages are the best understood viruses, and they illustrate two alternative strategies. In the lytic cycle, the phage replicates immediately and kills the host. A T4 phage attaches by its tail fibers, the tail sheath contracts and drives the DNA through the cell wall and membrane, and the phage DNA directs the host to destroy its own DNA and to make phage components. New phages assemble, and a phage encoded enzyme, lysozyme, digests the cell wall; the cell bursts (lyses) and releases about 100 to 200 phages. A phage that reproduces only this way is a virulent phage. Bacteria defend themselves: restriction enzymes cut foreign DNA at specific sequences while the cell's own DNA is protected by chemical modification, and the CRISPR-Cas system stores fragments of past phage DNA and uses them to target and cut matching invaders, a bacterial immune memory that was later adapted into a gene editing tool.

In the lysogenic cycle, the phage genome is replicated without destroying the host. A temperate phage, such as phage lambda, can use either cycle. After entering the cell, lambda DNA circularizes and may integrate into the bacterial chromosome at a specific site. The integrated viral DNA, called a prophage, is copied along with the chromosome each time the cell divides, so a single infection can produce a large population of bacteria carrying the virus in latent form. Most prophage genes are silent, held off by a repressor protein. An environmental signal, such as radiation or certain chemicals that damage DNA, can trigger the prophage to exit the chromosome and switch to the lytic cycle. Some prophage genes are expressed during lysogeny and change the host's properties: the bacteria that cause diphtheria, botulism and scarlet fever are harmful because prophage genes encode their toxins, and certain dangerous strains of E. coli carry a Shiga toxin gene from a prophage.

Animal viruses

Animal viruses enter cells by fusion of the envelope with the plasma membrane or by endocytosis. For an enveloped virus such as influenza, glycoproteins on the envelope bind host receptors, the capsid and genome enter the cell, and host enzymes remove the capsid. Viral genes are expressed, new genomes are copied, and capsid proteins are made by free ribosomes, while envelope glycoproteins are made in the endoplasmic reticulum and travel through the Golgi apparatus to the plasma membrane. New capsids wrapped around genomes then bud from the cell, taking a piece of membrane with them. Budding does not necessarily kill the host cell immediately, which is one reason some enveloped viruses cause chronic infections. Herpesviruses gain their envelope from the nuclear membrane and can remain latent as minichromosomes in nerve cells for years, reactivating under stress as cold sores or shingles.

RNA viruses must copy RNA from an RNA template, something host cells normally do not do, so most carry or encode an RNA dependent RNA polymerase. This enzyme lacks proofreading, so RNA viruses have high mutation rates, one reason influenza vaccines must be updated each year. In positive sense single stranded RNA viruses (such as poliovirus and coronaviruses), the genome itself acts as mRNA and is translated as soon as it enters the cell. Negative sense viruses (such as influenza, measles and rabies) carry a genome that is complementary to mRNA and must first be copied by the viral polymerase they bring along.

Retroviruses, such as HIV, have the most complicated cycle. They carry an enzyme, reverse transcriptase, that copies their RNA genome into DNA, reversing the usual flow of genetic information. The new viral DNA enters the nucleus and is inserted into a host chromosome by the viral enzyme integrase, becoming a provirus. Unlike a prophage, a provirus remains permanently in the host genome. Host RNA polymerase transcribes it into RNA that serves both as new genomes and as mRNA for viral proteins. HIV gradually destroys helper T cells, and untreated infection progresses to acquired immunodeficiency syndrome (AIDS). Combination drug therapy that blocks reverse transcriptase, integrase and the viral protease can hold the virus at undetectable levels, but it cannot remove proviruses already integrated into long lived cells. About 8 percent of the human genome consists of the remnants of ancient retroviral infections inherited from our ancestors.

Emerging viruses, viroids and prions

Viruses that suddenly appear or spread to new hosts are called emerging viruses. They arise in three main ways: mutation of existing viruses, as in new influenza strains; spread of an existing virus from a small, isolated human population; and, most commonly, spillover from animals into humans (zoonosis), as with HIV from chimpanzees, Ebola, the 2009 H1N1 influenza and SARS coronaviruses from bats. Influenza A is especially changeable because its genome is in eight separate RNA segments; when two strains infect the same cell, as can happen in pigs or birds, the segments can be reshuffled into a new combination. A disease that spreads widely within a population is an epidemic; one that spreads worldwide is a pandemic.

Two kinds of infectious agent are even simpler than viruses. Viroids are small, naked, circular RNA molecules, only a few hundred nucleotides long, that infect plants. They encode no proteins but disrupt the plant's gene regulation, stunting growth. Prions are misfolded forms of a normal brain protein. A prion converts normally folded versions of the protein into the misfolded shape, and the misfolded proteins aggregate, causing degenerative brain diseases such as scrapie in sheep, bovine spongiform encephalopathy ("mad cow disease") and Creutzfeldt-Jakob disease in humans. Prions act very slowly, with incubation periods of years, and resist heat and normal sterilization because they contain no nucleic acid to destroy.

Section 3Protist diversity and endosymbiosis

What is a protist?

Protists are eukaryotes that are not plants, animals or fungi. Most are unicellular, but there are colonial and multicellular forms, including giant kelps tens of meters long. The term is convenient rather than formal: protists do not form a clade, because some are more closely related to plants, animals or fungi than to other protists. The old kingdom Protista is therefore paraphyletic and has been abandoned, and protists are now distributed among several eukaryotic supergroups.

Protists are more structurally diverse than any other eukaryotic group, and a single cell must carry out every function of life. Their nutrition spans the full range. Photoautotrophs contain chloroplasts; heterotrophs absorb organic molecules or ingest food particles; and mixotrophs, such as Euglena, combine photosynthesis with heterotrophic nutrition. Photosynthetic protists are informally called algae, heterotrophs that move and ingest food are called protozoans, and absorptive forms resemble fungi, but these labels describe lifestyles, not relationships. Reproduction is equally varied: some protists reproduce only asexually, while others use meiosis and fertilization, and many alternate between the two.

Endosymbiosis: how eukaryotes got their organelles

Endosymbiosis is a relationship in which one organism lives inside the cells of another. According to the endosymbiont theory, mitochondria and plastids (chloroplasts and related organelles) descend from free living prokaryotes that were engulfed by a host cell and became permanent residents. Strong evidence supports it. Both organelles have two membranes, with inner membrane enzymes and transport systems similar to those of prokaryotes. They divide by a process like binary fission. They carry their own circular DNA without histones, and their own ribosomes, which resemble bacterial 70S ribosomes in size, sequence and sensitivity to antibiotics. Their genes are most similar to those of particular bacteria: mitochondria to alphaproteobacteria and plastids to cyanobacteria. Over time most endosymbiont genes moved to the host nucleus, so the organelles can no longer live on their own.

The mitochondrion came first: all known eukaryotes either have mitochondria or have reduced organelles derived from them, so the engulfment of an alphaproteobacterium by an archaeal host was probably part of the origin of eukaryotes themselves. Later, in primary endosymbiosis, a heterotrophic eukaryote that already had mitochondria engulfed a cyanobacterium. Its descendants gave rise to red algae and green algae (and, from green algae, land plants), whose plastids are surrounded by two membranes. Plastids then spread further through secondary endosymbiosis, in which a heterotrophic eukaryote engulfed a red or green alga and kept its plastid. These secondary plastids are wrapped in three or four membranes, the extra layers coming from the engulfed alga's plasma membrane and the host's food vacuole. In some species, such as chlorarachniophytes, a tiny vestigial nucleus of the engulfed alga, the nucleomorph, still sits between the membranes, a clear trace of the event.

The major protist groups

Current phylogenies place most protists into four supergroups, though their exact relationships are still debated.

Excavata is named for a feeding groove "excavated" into one side of the cell in many members. Diplomonads and parabasalids have reduced mitochondria and live in anaerobic environments. They include Giardia intestinalis, an intestinal parasite spread through water contaminated with feces, and Trichomonas vaginalis, a sexually transmitted parasite. Euglenozoans have a spiral or crystalline rod inside their flagella. They include kinetoplastids, with a single large mitochondrion holding a mass of DNA, such as Trypanosoma, which causes African sleeping sickness (spread by tsetse flies) and Chagas disease, and euglenids such as Euglena, which has a light sensing eyespot and is a mixotroph.

The SAR clade, named for its three subgroups, is united by DNA similarities. Stramenopiles usually have a "hairy" flagellum paired with a smooth one. They include diatoms, unicellular algae with glassy two part walls of silica that perform a large share of global photosynthesis and form diatomaceous earth; brown algae, the largest and most complex algae, including kelps with rootlike holdfasts, stemlike stipes and leaflike blades; and oomycetes (water molds), once mistaken for fungi, including the pathogen that caused the Irish potato famine. Alveolates have membrane bounded sacs (alveoli) under the plasma membrane. They include dinoflagellates, whose blooms cause toxic "red tides" and which live as symbionts in reef building corals; apicomplexans, parasites with an apical complex of organelles for penetrating host cells, such as Plasmodium, the cause of malaria; and ciliates, such as Paramecium, which move by cilia and carry two kinds of nuclei, a large macronucleus for everyday functions and small micronuclei used in conjugation, a sexual exchange of genes. Rhizarians are amoebas with threadlike pseudopodia, including forams, whose porous calcium carbonate shells build limestone deposits and serve as climate records, and radiolarians, with delicate silica skeletons.

Archaeplastida descends from the primary endosymbiosis and includes red algae, colored by the pigment phycoerythrin and able to live at greater depths than other algae (some are used as nori in sushi and as the source of agar), green algae, such as Chlamydomonas, Volvox and sea lettuce, and the land plants, which evolved from green algae called charophytes.

Unikonta includes the amoebozoans, amoebas with lobe or tube shaped pseudopodia, such as plasmodial slime molds (a single mass of cytoplasm with many nuclei that streams over forest litter), cellular slime molds such as Dictyostelium, whose cells aggregate into a multicellular slug when food runs short, and Entamoeba histolytica, which causes amoebic dysentery. Unikonta also includes the opisthokonts: animals, fungi and their closest protist relatives, the choanoflagellates (sister group of animals) and the nucleariids (close to fungi).

A protist life cycle: malaria

Plasmodium needs two hosts, mosquitoes and humans. When an infected Anopheles mosquito bites, it injects sporozoites that travel to the liver, multiply and then invade red blood cells. Inside red cells the parasite divides asexually, releasing merozoites that burst the cells and infect more of them in synchronized waves, causing cycles of chills and fever. Some merozoites become gametocytes that a biting mosquito takes up; fertilization and further development occur in the mosquito, which then carries new sporozoites to its salivary glands. The parasite changes its surface proteins and spends much of its time hidden inside host cells, which has made a vaccine hard to develop. Malaria still causes several hundred thousand deaths each year, mostly in young children.

Section 4Fungal structure, reproduction and diversity

Fungi are absorptive heterotrophs

Fungi are eukaryotes that include yeasts, molds, mushrooms and their relatives. Although they were once classified with plants, molecular evidence shows that fungi are more closely related to animals: both belong to the opisthokonts, and the two lineages diverged roughly a billion years ago. Like animals, fungi are heterotrophs, but they do not ingest food. Instead they feed by absorption: they secrete powerful hydrolytic enzymes into their surroundings, break down complex molecules outside the body and absorb the resulting small molecules. This mode of nutrition lets fungi digest almost any organic material, including wood, which few other organisms can break down. Fungi live as decomposers (saprobes) that feed on dead matter, as parasites that absorb nutrients from living hosts, or as mutualists that exchange nutrients with partners.

Body structure

Some fungi are single celled yeasts, but most grow as multicellular filaments. A fungal filament is a hypha (plural hyphae), a tube of cytoplasm surrounded by a plasma membrane and a cell wall of chitin, a strong, flexible nitrogen containing polysaccharide also found in insect exoskeletons. Hyphae branch and interweave to form a mycelium, the feeding network of the fungus. A mycelium maximizes surface area for absorption: a cubic centimeter of rich soil may contain a kilometer of hyphae. Mycelia grow rapidly at their tips, extending perhaps a kilometer of new hyphae a day in a large individual, and some are enormous: one honey mushroom mycelium in Oregon covers about 965 hectares and is estimated to be thousands of years old. Mushrooms and other visible structures are only the reproductive bodies of a much larger hidden mycelium.

Most fungi have hyphae divided into cells by cross walls called septa, which usually have pores large enough for ribosomes, mitochondria and even nuclei to flow between cells; these are septate hyphae. Some fungi lack septa and have coenocytic hyphae, continuous masses of cytoplasm containing hundreds or thousands of nuclei formed by repeated nuclear division without cytokinesis. Parasitic fungi often have specialized hyphae called haustoria that penetrate host cells and extract nutrients. Mutualistic fungi form mycorrhizae ("fungus roots"), associations with plant roots in which the fungus supplies phosphate and other minerals and receives sugars from the plant; nearly all vascular plants have them. In ectomycorrhizae, hyphae sheath the root and grow between root cells; in arbuscular mycorrhizae, hyphae penetrate root cell walls and form branched arbuscules against the plant cell membrane.

Sexual and asexual reproduction

Fungi reproduce by producing vast numbers of spores, sexually or asexually. Spores are carried by wind, water or animals, and any that land in a moist place with food germinate into new mycelia. A puffball can release trillions of them.

The nuclei of fungal hyphae and spores are usually haploid, though many species have genetically different nuclei sharing one mycelium. Sexual reproduction in fungi has an unusual two step fertilization. First, hyphae of two mycelia of different mating types, signaled by pheromones, fuse their cytoplasm in plasmogamy. The nuclei do not fuse right away; the mycelium contains coexisting haploid nuclei from both parents and is called a heterokaryon. In some fungi the paired nuclei divide in tandem, two to a cell, a condition called dikaryotic (n + n). Hours, days, or even centuries later, the haploid nuclei fuse in karyogamy, forming diploid nuclei. The diploid stage is brief: the zygote quickly undergoes meiosis, producing genetically varied haploid spores. Thus the diploid zygote is the only diploid stage in most fungal life cycles.

Many fungi also reproduce asexually. Molds produce haploid spores by mitosis on specialized hyphae, often called conidia when made at the tips of hyphae. Yeasts reproduce by simple cell division or by budding of a small cell from a parent. Many fungi have no known sexual stage and were once grouped as "imperfect fungi" or deuteromycetes; DNA comparisons now place most of them in the ascomycetes.

The diversity of fungi

Fungi probably evolved from a single celled, flagellated ancestor in water. The earliest diverging lineages are still mostly aquatic. Mycologists recognize about 100,000 described species, but estimates of the true number run to several million.

• Chytrids are found in lakes, soil and animal guts and are the only fungi with flagellated spores, called zoospores, a trait inherited from the common ancestor of fungi. One chytrid, Batrachochytrium dendrobatidis, has caused catastrophic declines and extinctions of amphibians worldwide by infecting their skin.
• Zygomycetes (zygote fungi) include fast growing molds on bread and fruit, such as black bread mold, Rhizopus stolonifer, with coenocytic hyphae. Their sexual stage forms a tough, resistant zygosporangium that can survive harsh conditions, then undergo meiosis to release spores.
• Glomeromycetes form arbuscular mycorrhizae with the roots of most plants. They reproduce asexually and have been central to plant life since plants first colonized land.
• Ascomycetes (sac fungi) form sexual spores in saclike asci (singular ascus), usually housed in a fruiting body called an ascocarp. They range from unicellular yeasts to cup fungi and morels, and include Penicillium (source of penicillin and flavor in blue cheese), baker's and brewer's yeast Saccharomyces cerevisiae, Neurospora (a genetics model) and many plant pathogens. Many ascomycetes form lichens.
• Basidiomycetes (club fungi) form spores on club shaped cells called basidia, usually in a basidiocarp such as a mushroom. Their long lived dikaryotic mycelia produce mushrooms quickly, sometimes overnight, by absorbing water. The group includes mushrooms, puffballs, shelf fungi, rusts and smuts, and the important wood decomposers that break down lignin.

Section 5Microbes in ecosystems and human health

Decomposers and chemical recycling

Without microbes, the chemical elements of life would be locked in dead bodies and wastes. Bacteria, archaea and fungi are the principal decomposers: they break down dead organisms and wastes and return carbon, nitrogen, phosphorus and other elements to the soil, water and air in inorganic forms that plants and other producers can reuse. Fungi are especially important for decomposing wood because their enzymes can attack lignin and cellulose. Prokaryotes also drive steps of nutrient cycles that no other organisms perform. Photosynthetic cyanobacteria and protists, including diatoms and dinoflagellates, generate a large share of Earth's oxygen and form the base of aquatic food webs as phytoplankton.

The nitrogen cycle

Nitrogen is essential for amino acids and nucleotides, and air is about 78 percent N2. But the triple bond of N2 makes it unusable for most organisms, so the availability of fixed nitrogen often limits plant growth. Prokaryotes carry out every key conversion in the nitrogen cycle:

• Nitrogen fixation: nitrogen fixing bacteria and archaea, using the enzyme nitrogenase, convert N2 to ammonia (NH3), which picks up a hydrogen ion in soil to become ammonium (NH4+). Rhizobium lives in root nodules of legumes such as peas, beans and clover; cyanobacteria fix nitrogen in water and in rice paddies.
• Ammonification: decomposers release ammonium from the proteins and nucleic acids of dead organisms and wastes.
• Nitrification: chemoautotrophic bacteria oxidize ammonium to nitrite (NO2-) and then nitrite to nitrate (NO3-), gaining energy at each step. Nitrate is the form most plants absorb.
• Denitrification: under low oxygen conditions, some bacteria use nitrate in anaerobic respiration and release N2 back to the atmosphere.

Symbiosis

An ecological relationship in which two species live in close contact is a symbiosis. The larger organism is the host and the smaller the symbiont. In mutualism both partners benefit; in commensalism one benefits and the other is neither helped nor harmed; in parasitism the parasite benefits at the host's expense. Parasites that cause disease are pathogens.

Microbial mutualisms are everywhere. Bacteria in the root nodules of legumes fix nitrogen in exchange for sugars. Bacteria and protists in the rumen of cattle and the gut of termites digest cellulose that the animals cannot break down alone. Lichens are symbiotic associations of a fungus (usually an ascomycete) with millions of photosynthetic green algae or cyanobacteria held in its hyphae; the photosynthetic partner provides carbon compounds (and fixed nitrogen if it is a cyanobacterium), while the fungus provides a protective environment, water and minerals. Lichens can colonize bare rock, where their acids help begin soil formation, and because they absorb pollutants from the air they are used to monitor air quality. Fungal endophytes live inside leaves of nearly all plants without causing harm, and some make toxins that deter herbivores or improve drought tolerance. Leaf cutter ants farm fungi in underground gardens, feeding them chewed leaves and eating the fungal growth.

The human body hosts a dense community of microbes, the microbiome, numbering trillions of cells of hundreds of species, most in the large intestine. These microbes digest fiber into short chain fatty acids that nourish the colon lining, synthesize vitamins such as vitamin K and some B vitamins, train the immune system and occupy space that would otherwise be open to pathogens. Disruption of the microbiome, for example by broad spectrum antibiotics, can let the toxin producing bacterium Clostridioides difficile overgrow and cause severe diarrhea; transplants of stool from healthy donors can restore the community and cure many such infections.

Microbes as pathogens

Only a small fraction of microbes cause disease, but those few have had enormous effects on human history. To prove that a particular microbe causes a disease, researchers traditionally use Koch's postulates: (1) the pathogen must be found in every case of the disease; (2) it must be isolated and grown in pure culture; (3) the cultured pathogen must cause the disease when introduced into a healthy host; and (4) the same pathogen must be isolated again from the experimentally infected host. Some pathogens, such as viruses and bacteria that cannot be grown outside cells, cannot satisfy every postulate, and molecular methods are now used as well.

Bacteria typically cause illness by producing toxins. Exotoxins are proteins secreted by bacteria, often by gram positive species, that can cause disease even when the bacteria are not present. They are among the most potent poisons known: botulinum toxin from Clostridium botulinum blocks release of acetylcholine and causes paralysis, and cholera toxin causes massive loss of water and salts into the intestine. Endotoxins are the lipid portions of lipopolysaccharide in the outer membrane of gram negative bacteria, released when the bacteria die and break apart; they cause fever, inflammation and, in large amounts, septic shock, as in Salmonella infections.

Fungal pathogens cause athlete's foot and ringworm, vaginal yeast infections by Candida, and dangerous lung infections in people with weakened immunity. Fungi devastate crops: rusts, smuts and molds can destroy harvests, and ergot, a fungus on rye, produces toxins that caused historic outbreaks of poisoning. Protist pathogens include the agents of malaria, sleeping sickness, giardiasis and amoebic dysentery.

Antibiotic resistance

An antibiotic is a compound that kills bacteria or inhibits their growth, often by targeting structures absent in human cells, such as peptidoglycan walls or 70S ribosomes. Antibiotics have no effect on viruses. Resistance evolves by natural selection: within a large bacterial population, a few cells may carry a mutation or plasmid gene that lets them survive a drug. Antibiotic exposure kills the susceptible cells, the resistant survivors multiply, and R plasmids can then pass resistance genes horizontally to other cells and species. Overprescription, stopping treatment early, and routine use of antibiotics in livestock all accelerate this process. Strains such as methicillin resistant Staphylococcus aureus (MRSA) and multidrug resistant tuberculosis now cause infections that are difficult or impossible to treat with standard drugs.

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