Brock Biology of Microorganisms, 14th Edition (Chapter 15-17) PDF

C h ap t e r 14 Functional Diversity of Bacteria microbiologynow One Culture Away Microbiologists continue to discover novel microbial processes that impact the biosphere, and the newly discovered bacterium Methylomirabilis oxyfera is one such example. Biological methane (CH4) oxidation wa...

C h ap t e r 14 Functional Diversity of Bacteria microbiologynow One Culture Away Microbiologists continue to discover novel microbial processes that impact the biosphere, and the newly discovered bacterium Methylomirabilis oxyfera is one such example. Biological methane (CH4) oxidation was once thought to require oxygen (O2). Recently, however, methane oxidation has been observed in a variety of anoxic environments. Methane is a powerful greenhouse gas, and microbial consumption of methane has a major role in balancing the global methane cycle. The model for anaerobic methane oxidation was previously based on a known metabolic partnership between sulfate-reducing bacteria and methanogens able to reverse the pathway of methane production. The discovery of M. oxyfera, however, proves the adage that where there is energy, microorganisms will find a way to use it. M. oxyfera emerged from an anaerobic enrichment culture begun with anoxic sediment from a canal in the Netherlands (photo). The canal received runoff from agricultural fields and contained both nitrate and methane. The enrichment culture I Functional Diversity as a Concept 434 coupled the oxidation of methane to denitrification, a process II Diversity of Phototrophic Bacteria 435 that had never before been seen. Surprisingly, however, M. oxyfera, though growing anaerobically, was using the standard III Bacterial Diversity in the Sulfur aerobic pathway of methane oxidation! How is this possible? Cycle 447 M. oxyfera was found to use a novel pathway of denitrification IV Bacterial Diversity in the Nitrogen in which two molecules of nitric oxide (NO) are used to make Cycle 452 N2 and O2; the O2 is then used immediately as the electron acceptor for the oxidation of methane.1 Thus, O2 production is V Diversity of Other Distinctive central to the methane metabolism of M. oxyfera even though Chemotrophic Bacteria 456 the bacterium inhabits anoxic environments. M. oxyfera also has VI Morphological Diversity of Bacteria 466 a unique polyhedral morphology (photo inset) and belongs to a novel phylum of Bacteria, NC-10, from which no previous species had been isolated. The discovery of M. oxyfera shows that major discoveries in microbiology are often just “one culture away.” 1 Ettwig, K.F., et al. 2010. Nitrite-driven anaerobic methane oxidation by oxygenic bacteria. Nature 464: 543–550. 433 434 UNIT 3 Microbial Diversity The microbial world is one of immense diversity, in both form and In this and the next three chapters we focus on microbial diversity function. Microorganisms have been evolving for more than 3.8 itself, including that of Bacteria, Archaea, and Eukarya. billion years and have diversified to fill every available habitat on In the present chapter we consider the functional diversity of par- Earth. In Chapter 12 we considered the evolution of microbial life ticular groups of Bacteria. In particular we focus on organisms that and the phylogenetic tools that have revealed it. In Chapter 13 we share distinct physiological or ecological characteristics that do not examined the enormous metabolic diversity of microorganisms. necessarily affiliate with a single coherent phylogenetic group. I Functional Diversity as a Concept M icrobial diversity can be understood in terms of both phy- logenetic diversity and functional diversity. In Section 14.1 we define and contrast the concepts of phylogenetic diversity and its broadest, phylogenetic diversity encompasses the genetic and genomic diversity of evolutionary lineages and so can be defined on the basis of either genes or organisms ( Section 12.5). Most functional diversity. commonly, though, phylogenetic diversity is defined on the basis of ribosomal RNA gene phylogeny, which is thought to reflect the phylogenetic history of the entire organism ( Section 12.4). 14.1 Making Sense of Microbial Diversity Phylogenetic diversity is the overarching theme of our coverage Phylogenetic diversity is the component of microbial diversity that of microbial diversity in Chapters 15–17. deals with evolutionary relationships between microorganisms. Functional diversity is the component of microbial diver- Most fundamentally, phylogenetic diversity deals with the diver- sity that deals with diversity in form and function as it relates sity of evolutionary lineages such as phyla, genera, and species. At to microbial physiology and ecology. It is useful to consider Verru Cyanobacteria Lentisphaerae Ge Plan obact etes Firmic teria Chlamy mm De comic etes Fib ctom ere Th s utes s in Ba hloro haete Fusobac ati Sp ericute er oc r m ac tes mo loro mu oc od yc robia ria diae Ac cte bi ob de cu Ch he es C iroc na fle s te u s– Ten tin roi d Th lfob ia T ra ia ter pi cter s er m acte ac r s b xi A ot q og ia r tro ba teo ria Eur yar uific ae Ni cido npro bacte A silo oteo ia Tha uma cha ae Ep ltapr cter rcha ota e e o t e oba Cren e D hapr teria archa ota Alp roteobac eota e t a p acteria Nanoarc Z proteob haeota Gamma Korarchaeota Betaproteobacteria Hydrogen Oxidation Dissimilative Iron Oxidation Homoacetogens Dissimilative Iron Reduction Methylotrophy Dissimilative Sulfur Oxidation Nitrogen Fixation Dissimilative Sulfate Reduction Denitrification Dissimilative Sulfur Reduction Nitrification Oxygenic Phototrophy Anoxygenic Phototrophy Figure 14.1 Major functional traits mapped across major phyla of Bacteria and Archaea.The dendrogram shows relationships between microbial phyla as inferred by analysis of 16S ribosomal RNA gene sequences. Blue branches are used to denote phyla of Bacteria and red branches phyla of Archaea. Colored circles indicate phyla that contain at least one species with a functional trait indicated in the color key.  CHAPTER 14 Functional Diversity of Bacteria 435 microbial diversity in terms of functional groupings because of microorganisms. Physiological diversity is most commonly organisms with common traits and common genes often share described in terms of microbial metabolism and cellular bio- physiological characteristics and have similar ecological roles. chemistry (Chapter 13). Ecological diversity relates to relation- In many cases, functional traits align with phylogenetic groups ships between organisms and their environments. Organisms (for example, in Sections 14.3, 14.4, 14.6, 14.7, 14.20). Micro- with similar physiological characteristics can have different eco- bial functional diversity, however, often does not correspond logical strategies (Section 14.11). Causes and consequences of with phylogenetic diversity as defined by the 16S ribosomal ecological diversity will also be considered when we consider the RNA gene. We will see many examples in this chapter where science of microbial ecology in Chapter 19. Morphological diver- functional traits are widely distributed among the Bacteria and sity relates to the outward appearance of an organism (Sections Archaea (Figure 14.1). 14.20–14.24). In some cases, the morphology of a group is so dis- At least three reasons can be offered for why a functional trait tinctive that the group is essentially defined by this property, for is shared between divergent organisms with dissimilar 16S ribo- example, with the spirochetes (Section 14.22). somal RNA gene sequences. The first is gene loss, a situation The concepts of physiological, ecological, and morphological where a trait present in the common ancestor of several lineages diversity are often intertwined. The examples provided in this is subsequently lost in some lineages but retained in others which chapter are meant to be illustrative and not exhaustive, and we UNIT 3 over evolutionary time became quite divergent. The second is will consider other organisms with important ecological func- convergent evolution, in which a trait has evolved independently tions in Chapters 15–17 and 19–22. in two or more lineages and is not encoded by homologous genes shared by these lineages. The third is horizontal gene transfer MiniQuiz ( Sections 6.12 and 12.5), a situation where genes that con- Why is it necessary to consider microbial diversity in terms of fer a particular trait are homologous and have been exchanged phylogenetic diversity and functional diversity? between distantly related lineages. What are three reasons that functional traits might not Functional diversity can be further defined in terms of physi- correspond with distinct phylogenetic groups as defined by ological diversity, ecological diversity, and morphological diver- 16S ribosomal RNA gene sequences? sity. Physiological diversity relates to the functions and activities II Diversity of Phototrophic Bacteria I n this section we consider the diversity of phototrophic micro- organisms, those microorganisms that conserve energy from light. We will see that phototrophy is widespread within the to drive electron transfer reactions that ultimately result in the production of ATP ( Sections 13.1–13.4). Anoxygenic photo- trophic bacteria have either a type I or type II photosystem. The domain Bacteria and that several distinct types of phototrophs terms “type I” and “type II” refer to the structure of the photo- can be defined on the basis of their physiological traits. synthetic reaction center. Type I photosystems are most similar to photosystem I of oxygenic phototrophs while type II photosys- tems are most similar to photosystem II of oxygenic phototrophs. 14.2 Overview of Phototrophic Bacteria Both types of photosystems are present in cyanobacteria ( Sec- The ability to conserve energy from light evolved early in the tion 13.4), whereas only one type or the other is present in anoxy- history of life, when the Earth was anoxic ( Section 12.2). genic phototrophs. In some cases photosynthetic pigments are Photosynthesis originated within the Bacteria, and the first pho- found in the cytoplasmic membrane, but often they are present totrophic organisms were anoxygenic phototrophs, organisms that in intracellular photosynthetic membrane systems that originate do not generate O2 as a product of photosynthesis ( Section from invaginations of the cytoplasmic membrane. These internal 13.3). Instead of H2O, these early phototrophs likely used H2, membranes allow phototrophic bacteria to increase the amount ferrous iron, or H2S as the electron donor for photosynthesis. of pigment they contain for better use of light of low intensities. Anoxygenic photosynthesis is present in five bacterial phyla: the Many phototrophic bacteria couple light energy to carbon fixa- Proteobacteria, Chlorobi, Chloroflexi, Firmicutes, and Acidobacte- tion through a variety of different mechanisms ( Section 13.5), ria. Oxygenic photosynthesis is known only within the Cyanobac- but not all phototrophs fix CO2; some instead either prefer or teria (Figure 14.1). There is extensive metabolic diversity among require organic sources of carbon to support growth. We will see the anoxygenic phototrophs, which are found in a wide range of that many of the characteristics of phototrophic bacteria, includ- habitats. It is clear that horizontal gene exchange has had a major ing their membrane systems and photosynthetic pigments, have impact on the evolution of photosynthesis and on the distribution evolved as a result of niche adaptation for the light environment. of photosynthetic genes across the phylogenetic tree of Bacteria. Phototrophic bacteria have several common features. All pho- MiniQuiz totrophic bacteria use chlorophyll-like pigments and various What form of photosynthesis was most likely the first to appear accessory pigments to harvest energy from light and transfer this on Earth? energy to a membrane-bound reaction center where it is used 436 UNIT 3 Microbial Diversity 14.3 Cyanobacteria Table 14.1 Genera and grouping of cyanobacteria Key Genera: Prochlorococcus, Crocosphaera, Synechococcus, Group Genera Trichodesmium, Oscillatoria, Anabaena Group I, Chroococcales. Gloeothece (Figure 14.2a), Cyanobacteria comprise a large, morphologically and ecologically Unicellular or cell aggregates Gloeobacter, Synechococcus, heterogeneous group of oxygenic, phototrophic Bacteria. As we Cyanothece, Gloeocapsa, saw in Section 12.2, these organisms were the first oxygen-evolving Synechocystis, Chamaesiphon, phototrophic organisms on Earth, and over billions of years con- Merismopedia, Crocosphaera (Figure 14.7a), Prochlorococcus, verted the once anoxic atmosphere of Earth to the oxygenated Prochloron atmosphere we see today. Group II, Pleurocapsales. Pleurocapsa (Figure 14.2b), Reproduce by formation of Dermocarpa, Xenococcus, Phylogeny and Classification of Cyanobacteria small spherical cells called Dermocarpella, Myxosarcina, The morphological diversity of the Cyanobacteria is impressive baeocytes produced through Chroococcidiopsis multiple fission (Figure 14.2). Both unicellular and filamentous forms are known, Group III, Oscillatoriales. Lyngbya (Figure 14.2c), Spirulina and there is considerable variation within these morphological Undifferentiated filamentous (Figure 14.5), Arthrospira, types. Cyanobacterial cells range in size from 0.5 μm in diam- cells that divide by binary Oscillatoria (Figure 14.6a–b), eter to cells as large as 100 μm in diameter. Cyanobacteria can fission in a single plane Microcoleus, Pseudanabaena, be divided into five morphological groups: (1) Chroococcales are Trichodesmium (Figure 14.7b) unicellular, dividing by binary fission (Figure 14.2a); (2) Pleuro- Group IV, Nostocales. Nodularia (Figures 14.2d ), Nostoc, capsales are unicellular, dividing by multiple fission (colonial) Filamentous cells that produce Calothrix (Figure 14.8a–b), heterocysts Anabaena (Figure 14.6c), (Figure 14.2b); (3) Oscillatoriales are filamentous nonheterocys- Cylindrospermum, Scytonema, tous forms (Figure 14.2c); (4) Nostocales are filamentous, divide Richelia (Figure 14.7c) along a single axis, and are capable of cellular differentiation (Fig- Group V, Stigonematales. Cells Fischerella (Figures 14.2e, 14.8c, d ), ure 14.2d); and (5) Stigonematales are morphologically similar divide to form branches Stigonema, Chlorogloeopsis, to Nostocales except that cells divide in multiple planes forming Hapalosiphon branching filaments (Figure 14.2e). Finally, the prochlorophytes are a lineage of unique unicellular Cyanobacteria once thought to be distinct but now classified within the Chroococcales. Table 14.1 not (Figure 14.3). Species of Pleurocapsales form a coherent group lists some major genera currently recognized in each group. within the cyanobacteria, indicating that reproduction by mul- Some of the major morphological classifications of Cyanobac- tiple fission arose only once in the evolutionary history of cya- teria correspond to coherent phylogenetic groups, but others do nobacteria (Figure 14.3). Likewise, species of the Nostocales and Susan Barns and Norman Pace Daniel H. Buckley Daniel H. Buckley (a) (b) (c) Figure 14.2 Cyanobacteria: the five major morphological types of cyanobacteria. (a) Unicellular, Gloeothece; a single cell measures 5–6 μm in note to COMP: diameter; (b) colonial, Pleurocapsa; these structures contain hundreds of cells and are 7 50 Please put figure μm in diameter; (c) filamentous, Lyngbya; a single Daniel H. Buckley Daniel H. Buckley legend cell measures aboutin10 space in filamentous μm wide; (d) heterocystous, Nodularia; a single cell measures about lower 10 μm wide; left corner (e) filamentous branching, Fischerella; a cell is about 10 μm wide. See how morphological diversity relates to phylogenetic diversity in Figure 14.3. (d) (e)  CHAPTER 14 Functional Diversity of Bacteria 437 apsales Pleuroc Osc illat oria les Chroococcidiopsis sp. PCC6712 ale s s Syn Pleuro oplaste cc m No co ech aeu roo sto c a ps a oco Tric coleus chthon ythr 8 Pr ca Cr Ch 06 oc ccu Cy oc les hl r 81 me a or sp. PC o no CC s sp o. sp Pr a th oc miu m im ha.P hlo ec ar lis. PC tson 2 ax in bi era CC8 ro. e sp Ly hodes us C7319 m ia sp ma sp r e Stigo Micro ira ya C70 ii w Syn rin va.P.M rm a 80 ech us sp fo Ar ngb a oco. M IT95 sp en ctina Multiple Fission ro 02 3 un UNIT 3 ccu a ige th s sp ab c p nematale Syne IT 1 n p um Branching Filaments choc. WH 930 5 A os t o ia s occu 810 3 N dular jor Heterocyst Forming s elo ngat 2 No herella ma Filamentous Gloeobacter us F is c violaceus sis fritschii Nitrogen Fixing Chlorogloeop s Figure 14.3 Taxonomically informative traits mapped onto the phylogeny of Cyanobacteria. The dendrogram depicts phylogenetic relationships inferred from analysis of conserved protein families in cyanobacterial genomes. Colored circles are used to indicate species traits as indicated by the key. Color shading is used to indicate taxonomic groupings. “Prochloro.” is used to indicate Prochlorococcus, which is a distinct group within the Chroococcales. Note that the Chroococcales and Oscillatoriales are not monophyletic in origin, meaning that these traits have arisen independently on multiple occasions in the phylogeny. Stigonematales share a common ancestor and form a coherent ( Figure 13.10). The cell wall of cyanobacteria contains pep- phylogenetic group indicating a single origin of cellular differen- tidoglycan and is structurally similar to that of gram-negative tiation within the Cyanobacteria (Figure 14.3). All Stigonematales bacteria. Photosynthesis takes place in the thylakoid membrane, share a single ancestor within the clade composed of Nostocales a complex and multilayered photosynthetic membrane system and Stigonematales, indicating that the capacity to form branch- containing photopigments and proteins that mediate photosyn- ing filaments arose only once within the lineage of Cyanobacte­ thesis ( Sections 13.1 and 13.2). In most unicellular cyanobac- ria capable of cellular differentiation (Figure 14.3). In contrast, teria, the thylakoid membranes are arranged in regular concentric unicellular and simple filamentous Cyanobacteria (Chroococcales circles around the periphery of the cytoplasm (Figure 14.4). Cyano- and Oscillatoriales, respectively) are dispersed in the cyanobacte- bacteria produce chlorophyll a, and most also have characteristic rial phylogeny, and these morphological groups do not represent pigments called phycobilins ( Figure 13.10), which function as coherent evolutionary lineages (Figure 14.3). accessory pigments in photosynthesis. One class of phycobilins, phycocyanins, are blue and, together with the green chlorophyll a, Physiology and Photosynthetic Membranes are responsible for the blue-green color of most cyanobacteria. Cyanobacteria are oxygenic phototrophs and therefore have both Some cyanobacteria produce phycoerythrin, a red phycobilin, type I and type II photosystems. All species are able to fix CO2 and species producing phycoerythrin are red or brown. Photo- by the Calvin cycle, many can fix N2, and most can synthesize pigments are fluorescent and emit light when visualized using a their own vitamins. Cells harvest energy from light and fix CO2 during the day. During the night, cells generate energy by fermen- tation or aerobic respiration of carbon storage products such as glycogen. While CO2 is the predominant source of carbon for most species, some cyanobacteria can assimilate simple organic compounds such as glucose and acetate if light is present, a pro- cess called photoheterotrophy. A few cyanobacteria, mainly fila- mentous species, can also grow in the dark on glucose or sucrose, using the sugar as both carbon and energy source. Finally, when M. R. Edwards sulfide concentrations are high, some cyanobacteria are able to switch from oxygenic photosynthesis to anoxygenic photosynthe- sis using hydrogen sulfide rather than water as electron donor for photosynthesis ( Figure 13.15). Figure 14.4 Thylakoids in cyanobacteria. Electron micrograph of a thin section Cyanobacteria have specialized membrane systems called of the cyanobacterium Synechococcus lividus. A cell is about 5 μm in diameter. Note thylakoids that increase the ability of cells to harvest light energy thylakoid membranes running parallel to the cell wall. 438 UNIT 3 Microbial Diversity Separation of hormogonium T. D. Brock (a) Daniel H. Buckley Hormogonium Figure 14.5 Phycocyanin fluorescence in cyanobacteria. Fluorescence micrograph of Spirulina. Filaments consist of chains of helical cells with each cell approximately 5 μm wide. T. D. Brock fluorescence microscope (Figure 14.5). Prochlorophytes, such as Prochlorococcus and Prochloron, are unique among Cyanobacte­ (b) ria in that all members of this group contain chlorophyll a and b but do not contain phycobilins. Akinete Motility and Cellular Structures Cyanobacteria possess several mechanisms for motility. Many cyanobacteria exhibit gliding motility ( Section 2.18). Glid- ing occurs only when a cell or filament is in contact with a solid T. D. Brock surface or with another cell or filament. In some cyanobacteria, gliding is not a simple translational movement but is accompa- (c) nied by rotations, reversals, and flexing of filaments. Most gliding species exhibit directional movement toward light (phototaxis), Figure 14.6 Structural differentiation in filamentous cyanobacteria. (a) Initial and chemotaxis ( Section 2.19) may occur as well. Synechococ­ stage of hormogonium formation in Oscillatoria. Notice the empty spaces where cus exhibits an unusual form of swimming motility that does not the hormogonium is separating from the filament. (b) Hormogonium of a smaller require flagella or any other extracellular organelle. The cell sur- Oscillatoria species. Notice that the cells at both ends are rounded. Cells are about face of Synechococcus has specialized proteins that provide direct 10 μm wide. Differential interference contrast microscopy. (c) Akinete (resting spore) of Anabaena in a phase-contrast micrograph, cells about 5 μm wide. thrust through a mechanism that has yet to be resolved. Gas vesicles ( Section 2.15) are also found in a variety of aquatic cyanobacteria and are important in positioning cells in the water form a structure called cyanophycin. This structure is a copolymer column. The function of gas vesicles is to regulate cell buoyancy of aspartic acid and arginine and is a nitrogen storage product; such that cells can remain in a position in the water column where when nitrogen in the environment becomes deficient, cyanophy- light intensity is optimal for photosynthesis. cin is broken down and used as a cellular nitrogen source. Many Cyanobacteria are able to form a variety of structures associated species of the Nostocales and Stigonematales are also able to form with energy storage, reproduction, and survival. Many cyanobac- heterocysts, as discussed next. teria produce extensive mucilaginous envelopes, or sheaths, that bind groups of cells or filaments together (Figure 14.2a). Some fil- Heterocysts and Nitrogen Fixation amentous cyanobacteria can form hormogonia (Figure 14.6), short, Many cyanobacteria are capable of nitrogen fixation (Figure motile filaments that break off from longer filaments to facilitate 14.3). The nitrogenase enzyme, however, is inhibited by oxygen dispersal in times of stress. Some species also form resting struc- and thus nitrogen fixation cannot occur along with oxygenic tures called akinetes (Figure 14.6c), which protect the organism photosynthesis ( Section 3.17). Cyanobacteria have evolved during periods of darkness, desiccation, or cold. Akinetes are several regulatory mechanisms for separating nitrogenase activ- cells with thickened outer walls. When conditions improve, aki- ity from photosynthesis ( Section 7.13). For example, many netes germinate by breaking down their outer wall and initiat- unicellular cyanobacteria, such as Cyanothece and Crocosphaera ing growth of a new vegetative filament. Many cyanobacteria also (Figure 14.7a), fix nitrogen only at night when photosynthesis does  CHAPTER 14 Functional Diversity of Bacteria 439 Rachel Foster Angel White Angel White (a) (b) (c) Figure 14.7 Marine cyanobacteria that fix N2. (a) Unicellular Crocosphaera-like cells in the process of dividing; cells are approximately 5 μm diameter. (b) Colonial “tuft” of Trichodesmium. The tuft is composed of many attached undifferentiated UNIT 3 unbranching filaments and has a diameter of approximately 100 μm. (c) A diatom containing the cyanobacterial symbiont Richelia (scale in micrometers). The Richelia symbiont is an unbranching filament with a terminal heterocyst; cells are about 5 μm wide. not occur. In contrast, the filamentous cyanobacteria Trichodes­ occur in an anoxic environment. Heterocysts lack photosystem II mium (Figure 14.7b) fixes nitrogen only during the day through (Figure 14.8), the oxygen-evolving photosystem that generates a mechanism that remains somewhat unclear, but appears to reducing power from H2O ( Section 13.4). Without photosys- require transient suppression of photosynthetic activity within tem II, heterocysts are unable to fix CO2 and thus lack the nec- filaments. Finally, many filamentous cyanobacteria of the Nosto­ essary electron donor (pyruvate) for nitrogen fixation. However, cales and Stigonematales facilitate nitrogen fixation by forming heterocysts have intercellular connections with adjacent veg- specialized cells called heterocysts, either on the ends of fila- etative cells that allow for mutual exchange of materials between ments (Figure 14.8a, b) or along the filament (Figure 14.8c, d). these cells. Fixed carbon is imported by the heterocyst from Heterocysts arise from differentiation of vegetative cells and adjacent vegetative cells, and this is oxidized to yield electrons are the sites of nitrogen fixation in heterocystous cyanobacteria. for nitrogen fixation. The products of photosynthesis move from Heterocysts are surrounded by a thickened cell wall that slows the vegetative cells to heterocysts, and fixed nitrogen moves from diffusion of O2 into the cell and permits nitrogenase activity to heterocysts to vegetative cells ( Section 7.13 and Figure 7.28). Daniel H. Buckley Daniel H. Buckley (a) (b) Daniel H. Buckley Daniel H. Buckley (c) (d) Figure 14.8 Heterocysts. Differentiation of heterocysts causes the loss of photopigments and inability to carry out photosynthesis. (a) Phase-contrast micrograph of Calothrix with terminal heterocysts. (b) Fluorescence micrograph of the same Calothrix filaments; cells are about 10 μm wide. (c) Phase-contrast micrograph of Fischerella. (d) Fluorescence micrograph of the same Fischerella filaments; cells are about 10 μm wide. See how heterocyst formation is regulated at the genetic level in the well-studied cyanobacterium, Anabaena in Figure 7.28. 440 UNIT 3 Microbial Diversity Ecology of Cyanobacteria in late summer when temperatures are warmest ( Figures 19.1 Cyanobacteria are of central importance to the productivity of the and 19.17). A few cyanobacteria are symbionts of liverworts, oceans. Small unicellular cyanobacteria, such as Synechococcus ferns, and cycads, and a number are phototrophic components and Prochlorococcus ( Section 19.10), are the most abundant of lichens, a symbiosis between a phototroph and a fungus phototrophs in the oceans. Together these organisms contrib- ( Section 22.1). ute 80% of marine photosynthesis and 35% of all photosynthetic Several metabolic products of cyanobacteria are of consider- activity on Earth. able practical importance. Some cyanobacteria produce potent Cyanobacterial nitrogen fixation represents the dominant neurotoxins, and toxic blooms may form when massive accumu- input of new nitrogen into vast segments of Earth’s oceans, par- lations of cyanobacteria develop. Animals ingesting water con- ticularly in oligotrophic tropical and subtropical waters. Marine taining these toxic products may be killed. Many cyanobacteria nitrogen fixation is dominated by two groups of cyanobacteria, are also responsible for the production of earthy odors and flavors the unicellular species and the filamentous Trichodesmium. Cro- in some freshwater, and if such waters are used as drinking water cosphaera (Figure 14.7a) and relatives dominate nitrogen fixation sources, aesthetic problems may arise. The major compound pro- in most of the Pacific Ocean and are widespread in tropical and duced is geosmin, a substance also produced by many actinomy- subtropical habitats. Trichodesmium is the dominant nitrogen- cetes ( Section 15.12). fixer in the North Atlantic Ocean and parts of the Pacific where dissolved iron concentrations are elevated. Trichodesmium forms MiniQuiz macroscopically visible tufts of filaments (Figure 14.7b) and relies What are the differentiating properties of the five major on gas vesicles to remain suspended in the photic zone where it is morphological groups of Cyanobacteria? often observed in dense masses of cells called blooms. In addition, What is a heterocyst and what is its function? other marine nitrogen-fixers including species of Calothrix and Richelia form symbiotic associations with diatoms (Figure 14.7c); these symbiotic associations are often observed in tropical and subtropical oceans. Finally, heterocystous cyanobacteria such as Nodularia (Figure 14.2d) and Anabaena can sometimes dominate 14.4 Purple Sulfur Bacteria nitrogen fixation in cold waters of the Northern Hemisphere and Key Genera: Chromatium, Ectothiorhodospira are often observed in the Baltic Sea. Purple sulfur bacteria are anoxygenic phototrophs that use Cyanobacteria are also widely found in terrestrial and freshwa- hydrogen sulfide (H2S) as an electron donor for photosynthesis. ter environments. In general, they are more tolerant of environ- Purple sulfur bacteria are a phylogenetically coherent group found mental extremes, particularly extremes of desiccation, than are within the order Chromatiales in the Gammaproteobacteria. algae (eukaryotes). Cyanobacteria are often the dominant or sole Purple sulfur bacteria are generally found in illuminated anoxic oxygenic phototrophic organisms in hot springs, saline lakes, des- zones where H2S is present. Such habitats occur commonly in ert soils, and other extreme environments. In some of these envi- lakes, marine sediments, and “sulfur springs,” where H2S pro- ronments, cyanobacterial mats of variable thickness may form duced geochemically or biologically can support the growth of ( Figure 19.9). Freshwater lakes, especially those rich in inor- purple sulfur bacteria (Figure 14.9). Purple sulfur bacteria are also ganic nutrients, often develop blooms of cyanobacteria, especially commonly found in microbial mats ( Section 19.5) and in salt Douglas Caldwell Jörg Overmann T. D. Brock (a) (b) (c) Figure 14.9 Blooms of purple sulfur bacteria. (a) Lamprocystis roseopersicina, in a sulfide spring. The bacteria grow near the bottom of the spring pool and float to the top (by virtue of their gas vesicles) when disturbed. The green color is from cells of the eukaryotic alga Spirogyra. (b) Sample of water from a depth of 7 m in Lake Mahoney, British Columbia; the major phototroph is Amoebobacter purpureus. (c) Phase-contrast photomicrograph of layers of purple sulfur bacteria from a small, stratified lake in Michigan. The purple sulfur bacteria include Chromatium species (large rods) and Thiocystis (small cocci).  CHAPTER 14 Functional Diversity of Bacteria 441 Norbert Pfennig Norbert Pfennig C. C. Remsen (a) (b) UNIT 3 (a) Jeffrey C. Burnham and S. C. Conti Johannes F. Imhoff Norbert Pfennig (c) (d) (b) Figure 14.10 Bright-field and phase-contrast photomicrographs of purple sulfur bacteria. (a) Chromatium okenii; cells are about 5 μm wide. Note the globules Figure 14.11 Membrane systems of phototrophic purple bacteria as of elemental sulfur inside the cells. (b) Thiospirillum jenense, a very large, polarly revealed by transmission electron microscopy. (a) Ectothiorhodospira mobilis, flagellated spiral; cells are about 30 μm long. Note the sulfur globules. (c) Thiopedia showing the photosynthetic membranes in flat sheets (lamellae). (b) Allochromatium rosea; cells are about 1.5 μm wide. (d) Phase-contrast micrograph of cells of vinosum, showing the membranes as individual, spherical vesicles. Ectothiorhodospira mobilis  ; cells are about 0.8 μm wide. Note external sulfur globules (arrow). organisms are common in stratified lakes containing sulfide and in the anoxic sediments of salt marshes. Ectothiorhodospiraceae, marsh sediments. The characteristic color of purple sulfur bac- including the two main genera Ectothiorhodospira and Halo­ teria comes from their carotenoids, accessory pigments involved rhodospira, oxidize H2S to S0 that is deposited outside the cell in light harvesting ( Section 13.2). These bacteria use a (Figure 14.10d) and have lamellar intracellular photosynthetic type II photosystem ( Figure 13.3), contain either bacterio- membrane systems (Figure 14.11). These genera are also interest- chlorophyll a or b, and carry out CO2 fixation by the Calvin cycle ing because many species are extremely halophilic (salt-loving) ( Section 13.5). or alkaliphilic (alkalinity-loving) and are among the most During autotrophic growth of purple sulfur bacteria, H2S is oxi- extreme in these characteristics of all known Bacteria. These dized to elemental sulfur (S0), which is deposited as sulfur gran- organisms are typically found in saline lakes, soda lakes, and ules (Figure 14.10). When sulfide is limiting, the sulfur is used as an salterns, where abundant levels of SO42– support sulfate-reduc- electron donor for photosynthesis, resulting in the oxidation of S0 ing bacteria ( Section 20.4 and Section 14.9), the organisms to sulfate (SO42–). Many purple sulfur bacteria can also use other that produce H2S. reduced sulfur compounds as photosynthetic electron donors; for Purple sulfur bacteria are often observed in high density in example, thiosulfate (S2O32–) is commonly used to grow labora- meromictic (permanently stratified) lakes. Meromictic lakes form tory cultures. layers because they have denser (usually saline) water on the bot- The purple sulfur bacteria form two families: the Chromatia­ tom and less dense (usually freshwater) water nearer the surface. ceae and the Ectothiorhodospiraceae. Species of the two families If sufficient sulfate is present to support sulfate reduction, sulfide are readily distinguished by the location of sulfur granules and is produced in the sediments and diffuses upward into the anoxic by their photosynthetic membranes. Chromatiaceae, including bottom waters. The presence of sulfide and light in the anoxic the genera Chromatium and Thiocapsa, store S0 granules inside layers of the lake allow purple sulfur bacteria to form dense cell their cells (in the periplasmic space) and have vesicular intra- masses, usually in association with green phototrophic bacteria cellular photosynthetic membrane systems (Figure 14.11). These (Figure 14.9b). 442 UNIT 3 Microbial Diversity MiniQuiz What is the source of the purple color from which the purple sulfur bacteria get their name? Where would you expect to find purple sulfur bacteria? Norbert Pfennig Norbert Pfennig 14.5 Purple Nonsulfur Bacteria and Aerobic Anoxygenic Phototrophs (a) (b) Purple Nonsulfur Bacteria Key Genera: Rhodospirillum, Rhodoferax, Rhodobacter The purple nonsulfur bacteria are the most metabolically versa- tile of all microorganisms. Despite their name, they are not always purple; these organisms synthesize an array of carotenoids ( Section 13.2) that can lend them a variety of spectacular colors (Figure 14.12). Together, these pigments give purple bacteria their Norbert Pfennig Norbert Pfennig colors, usually purple, red, or orange. Purple nonsulfur bacteria are typically photoheterotrophs (a condition where light is the energy source and an organic compound is the carbon source), and spe- cies are able to use a wide range of carbon sources and electron (c) (d) donors for photosynthesis, including organic acids, amino acids, alcohols, sugars, and even aromatic compounds like benzoate or toluene. Like purple sulfur bacteria, purple nonsulfur bacteria use a type II photosystem, and contain either bacteriochlorophyll a or b. The purple nonsulfur bacteria are morphologically and phylo- genetically diverse (Figure 14.13) and reside within the Alphaproteo­ bacteria (e.g., Rhodospirillum, Rhodobacter, Rhodopseudomonas) Norbert Pfennig Peter Hirsch or Betaproteobacteria (e.g., Rubrivivax, Rhodoferax). Purple nonsulfur bacteria are able to conserve energy through a variety of metabolic processes. For example, some species can (e) (f) grow photoautotrophically using H2, low levels of H2S, or even ferrous iron (Fe2+) as the electron donor for photosynthesis with Figure 14.13 Representatives of several genera of purple nonsulfur bacteria. CO2 fixation carried out by the Calvin cycle. Most species are also (a) Phaeospirillum fulvum; cells are about 3 μm long. (b) Rhodoblastus acidophilus  ; able to grow in darkness by using aerobic respiration of organic or cells are about 4 μm long. (c) Rhodobacter sphaeroides; cells are about 1.5 μm wide. (d) Rhodopila globiformis; cells are about 1.6 μm wide. (e) Rhodocyclus purpureus; cells even some inorganic compounds; synthesis of the photosynthetic are about 0.7 μm in diameter. (f) Rhodomicrobium vannielii; cells are about 1.2 μm wide. machinery is typically repressed by O2. Finally, some species can also grow by fermentation or anaerobic respiration using a variety of electron donors and acceptors. Enrichment and isolation of purple nonsulfur bacteria is easy using a mineral salts medium supplemented with an organic acid as carbon source. Such media, inoculated with a mud, lake water, or sewage sample and incubated anaerobically in the light, invari- ably select for purple nonsulfur bacteria. Enrichment cultures can be made even more selective by omitting fixed nitrogen sources (for example, ammonia) or organic nitrogen sources (for example, yeast extract or peptone) from the medium and supplying a gas- eous headspace of N2. Virtually all purple nonsulfur bacteria can Norbert Pfennig fix N2 and will thrive under such conditions, rapidly outcompet- ing other bacteria. Aerobic Anoxygenic Phototrophs Figure 14.12 Photograph of liquid cultures of phototrophic purple bacteria showing the color of species with various carotenoid pigments. The blue Key Genera: Roseobacter, Erythrobacter culture is a carotenoidless mutant strain of Rhodospirillum rubrum showing that The aerobic anoxygenic phototrophs are obligatory aerobic het- bacteriochlorophyll a is actually blue. The bottle on the far right (Rhodobacter erotrophs that use light as a supplemental source of energy to sup- sphaeroides strain G) lacks one of the carotenoids of the wild type and thus is greener. port growth. Like purple nonsulfur bacteria, aerobic anoxygenic  CHAPTER 14 Functional Diversity of Bacteria 443 phototrophs are phylogenetically diverse and are Alphaproteo­ bacteria or Betaproteobacteria. The primary physiological differ- ence with the purple nonsulfur bacteria is that aerobic anoxygenic phototrophs are strict heterotrophs and employ anoxygenic pho- tosynthesis only under oxic conditions as a supplemental source of energy. Aerobic anoxygenic phototrophs contain bacteriochlo- rophyll a and a type II photosystem, but are unable to fix CO2 and F. Rudy Turner and Michael T. Madigan must rely on organic carbon for growth. Carotenoids of various types lend colors of yellow, orange, or pink to cultures. Aerobic anoxygenic phototrophs are only able to photosynthe- size when grown on a day/night cycle. Under these conditions, bacteriochlorophyll a is made only in the dark and then used to conserve energy by photophosphorylation when the light returns. Aerobic anoxygenic phototrophs can account for as much as a quarter of the microbial community inhabiting coastal marine Figure 14.15 The thermophilic green sulfur bacterium Chlorobaculum UNIT 3 waters and 5% of gross photosynthesis in such systems ( Sec- tepidum. Transmission electron micrograph. Note chlorosomes (arrow) in the cell tion 19.10). Common genera found in coastal marine habitats periphery. A cell is about 0.7 μm wide. include Roseobacter and Erythrobacter. unlike most purple sulfur bacteria, the S0 produced by green MiniQuiz sulfur bacteria is deposited only outside the cell (Figure 14.14a). What are some similarities between purple nonsulfur bacteria Autotrophy is supported not by the reactions of the Calvin cycle, and aerobic anoxygenic phototrophs? What are the differences as in purple bacteria, but instead by a reversal of steps in the citric between these two groups? acid cycle ( Section 13.5 and Figure 13.19a), a unique means of Where would you expect to find aerobic anoxygenic autotrophy in phototrophic bacteria. phototrophs? Pigments and Ecology Green sulfur bacteria contain bacteriochlorophyll c, d, or e and house these pigments in unique structures called chlorosomes 14.6 Green Sulfur Bacteria (Figure 14.15). A small amount of bacteriochlorophyll a is present in Key Genera: Chlorobium, Chlorobaculum, “Chlorochromatium” the reaction center and FMO protein, which connects the chloro- Green sulfur bacteria are a phylogenetically coherent group of some to the cytoplasmic membrane ( Figure 13.7b). Chlorosomes anoxygenic phototrophs that forms the phylum Chlorobi. Green are oblong bacteriochlorophyll-rich bodies bounded by a thin, sulfur bacteria have little metabolic versatility and they are typi- nonunit membrane and attached to the cytoplasmic membrane in cally nonmotile and strictly anaerobic anoxygenic phototrophic the periphery of the cell (Figure 14.15 and Figure 13.7). Chlo- bacteria. The group is also morphologically restricted and rosomes function to funnel energy into the photosystem, and this includes primarily short to long rods (Figure 14.14). eventually leads to ATP synthesis. Unlike purple anoxygenic photo- Like purple sulfur bacteria, green sulfur bacteria oxidize hydro- trophs, green sulfur bacteria use a type I photosystem. Both green- gen sulfide (H2S) as an electron donor for autotrophic growth, and brown-colored species of green sulfur bacteria are known, the oxidizing it first to sulfur (S0) and then to sulfate (SO42-). But brown-colored species containing bacteriochlorophyll e and carot- enoids that turn dense cell suspensions brown (Figure 14.16). (a) Norbert Pfennig Norbert Pfennig Deborah O. Jung (b) (a) (b) Figure 14.14 Phototrophic green sulfur bacteria. (a) Chlorobium limicola; cells Figure 14.16 Green and brown chlorobia. Tube cultures of (a) Chlorobaculum are about 0.8 μm wide. Note the spherical sulfur granules deposited extracellularly. tepidum and (b) Chlorobaculum phaeobacteroides. Cells of C. tepidum contain (b) Chlorobium clathratiforme, a bacterium forming a three-dimensional network; bacteriochlorophyll c and green carotenoids, and cells of C. phaeobacteroides cells are about 0.8 μm wide. contain bacteriochlorophyll e and isorenieratene, a brown carotenoid. 444 UNIT 3 Microbial Diversity Like purple sulfur bacteria (Section 14.4), green sulfur bacte- ria live in anoxic, sulfidic aquatic environments. However, the chlorosome is a very efficient light-harvesting structure, which allows green sulfur bacteria to grow at light intensities much lower than those required by other phototrophs. Green sulfur Douglas Caldwell Jörg Overmann Jörg Overmann bacteria also tend to have a greater tolerance of H2S than do other anoxygenic phototrophs. As a result, green sulfur bacte- ria are typically found at the greatest depths of all phototrophic microorganisms in lakes or microbial mats, where light intensi- (a) (b) (c) ties are low and H2S levels the highest. As an example, a species of green sulfur bacteria isolated from a deep-sea hydrothermal vent ( Section 19.13) was found to be growing phototrophi- cally on the weak glow of infrared radiation emitted from the geothermally heated rock. One species, Chlorobaculum tepi­ dum (Figure 14.15), is thermophilic and forms dense microbial mats in high-sulfide hot springs. C. tepidum also grows rapidly and is amenable to genetic manipulation by both conjugation and transformation. Because of these features, C. tepidum has become the model organism for studying the molecular biology of green sulfur bacteria. Green Sulfur Bacteria Consortia Certain species of green sulfur bacteria form an intimate two- Douglas Caldwell membered association, called a consortium, with a chemo- organotrophic bacterium. In the consortium, each organism benefits, and thus a variety of such consortia containing different (d) phototrophic and chemotrophic components probably exist in nature. The phototrophic component, called the epibiont, is phys- Figure 14.17 “Chlorochromatium aggregatum.” Consortia of green ically attached to the nonphototrophic central cell (Figure 14.17) sulfur bacteria and a chemoorganotroph. (a) In a phase-contrast micrograph, the and communicates with it in various ways ( Section 22.2). nonphototrophic central organism is lighter in color than the pigmented phototrophic The name “Chlorochromatium aggregatum” (not a formal bacteria. (b) Green carotenoids lend their color to the phototrophs in a differential interference contrast micrograph. (c) A fluorescence micrograph shows the cells name because this is a mixed culture) has been used to describe stained with a phylogenetic FISH probe specific for green sulfur bacteria. a commonly observed green-colored consortium that is green (d) Transmission electron micrograph of a cross section through a single consortium; because the epibionts are green sulfur bacteria that contain green- note the chlorosomes (arrows) in the epibionts. The entire consortium is about 3 μm colored carotenoids (Figure 14.17b). Evidence that the epibionts in diameter. are indeed green sulfur bacteria comes from pigment analyses, the presence of chlorosomes (Figure 14.17d), and phylogenetic staining (Figure 14.17c). A structurally similar consortium called bacteria. The remainder of the phylum contains metabolically “Pelochromatium roseum” is brown because its epibionts produce diverse organisms including both aerobic and anaerobic chemo- brown-colored carotenoids ( Figures 22.3 and 22.4). We exam- organotrophs as well as the Dehalococcoidetes, a group of deha- ine the symbiotic nature of the Chlorochromatium consortium in logenating bacteria that use halogenated organic compounds as more detail in Section 22.2. electron acceptors in anaerobic respiration ( Section 13.21). Analyses of 16S ribosomal RNA sequences from environmental MiniQuiz samples ( Section 18.5) indicate that species of the phylum Chloroflexi are widespread and that most species in the phylum Which pigments are present in the chlorosome? have yet to be cultivated in isolation; thus the metabolic diversity What evidence exists that the epibionts of green bacterial of this phylum remains poorly characterized. consortia are truly green sulfur bacteria? All cultured representatives of the green nonsulfur bacteria are filamentous bacteria that are capable of gliding motility. Chloro­ flexus, one of the most studied of the green nonsulfur bacteria, 14.7 Green Nonsulfur Bacteria forms thick microbial mats in neutral to alkaline hot springs along Key Genera: Chloroflexus, Heliothrix, Roseiflexus with thermophilic cyanobacteria (Figure 14.18; Figure 19.9b). Green nonsulfur bacteria are anoxygenic phototrophs of the Green nonsulfur bacteria grow best as photoheterotrophs using phylum Chloroflexi. The latter contains several distinct lineages, simple carbon sources as electron donors for photosynthesis. one of which, the class Chloroflexi, contains green nonsulfur However, growth also occurs photoautotrophically using H2 or  CHAPTER 14 Functional Diversity of Bacteria 445 OH — CH3 — OH (a) In Out OH OH — — V. M. Gorlenko M. T. Madigan CH3 H3C OH OH Membrane (a) (b) (b) Figure 14.19 The unusual lipids of Thermomicrobium. (a) Membrane lipids from Thermomicrobium roseum contain long-chain diols like the one shown here (13-methyl-1,2-nonadecanediol). Note that unlike the lipids of other Bacteria or UNIT 3 of Archaea, neither ester- nor ether-linked side chains are present. (b) To form a bilayer membrane, dialcohol molecules oppose each other at the methyl groups, and the —OH groups are the inner and outer hydrophilic surfaces. Small amounts of the diols have fatty acids esterified to the secondary —OH group (shown in red), whereas the primary —OH group (shown in green) can bond a hydrophilic molecule like phosphate. Other Chloroflexi In addition to Chloroflexus, other phototrophic green nonsul- fur bacteria include the thermophile Heliothrix and the large- celled mesophiles Oscillochloris (Figure 14.18b) and Chloronema (Figure 14.18c). Oscillochloris and Chloronema form rather large Charles A. Abella Deborah O. Jung cells, 2–5 μm wide and up to several hundred micrometers long (Figure 14.18c). Species of both genera inhabit freshwater lakes containing H2S. Roseiflexus and Heliothrix are similar to Chlo- (c) (d) roflexus in their filamentous morphology and thermophilic life- Figure 14.18 Green nonsulfur bacteria. (a) Phase-contrast micrograph of the style, but differ in a major photosynthetic property. Roseiflexus anoxygenic phototroph Chloroflexus aurantiacus; cells are about 1 μm in diameter. and Heliothrix lack bacteriochlorophyll c and chlorosomes and (b) Phase-contrast micrograph of the large phototroph Oscillochloris; cells are thus more closely resemble purple phototrophic bacteria (Sec- about 5 μm wide. The brightly contrasting material on the top is a holdfast, used for tions 14.4, 14.5) than Chloroflexus. This can be seen in cultures attachment. (c) Phase-contrast micrograph of filaments of a Chloronema species; of Roseiflexus that are yellow-orange instead of green from their the cells are wavy filaments and about 2.5 μm in diameter. (d) Tube cultures of extensive carotenoid pigments and lack of bacteriochlorophyll c C. aurantiacus (right) and Roseiflexus (left). Roseiflexus is yellow because it lacks bacteriochlorophyll c and chlorosomes. (Figure 14.18d). Thermomicrobium is a chemotrophic genus of Chloroflexi and a strictly aerobic, gram-negative rod, growing optimally in com- plex media at 75°C. Besides its phylogenetic properties, Ther- H2S as electron donors for photosynthesis. The hydroxypropionate momicrobium is also of interest because of its membrane lipids cycle, a pathway of CO2 incorporation unique to only a few Bacte- (Figure 14.19). Recall that the lipids of Bacteria and Eukarya con- ria and Archaea, supports autotrophic growth ( Section 13.5). tain fatty acids esterified to glycerol ( Section 2.7). By contrast, Most green nonsulfur bacteria also grow well in the dark by aero- the lipids of Thermomicrobium are formed on 1,2-dialcohols bic respiration of a wide variety of carbon sources. The photo- instead of glycerol, and have neither ester nor ether linkages (Fig- synthetic features of the green nonsulfur bacteria are a “hybrid”