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Chapter 2 : From Geocycles to Genomes and Back

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Abstract:

This chapter discusses the ways a budding geomicrobiologist might embark on the quest to understand how microbial communities affect environment and to predict how they will respond in the face of environmental change. It introduces various methods geomicrobiologists have at their disposal to achieve this goal, including both traditional nonmolecular and molecular methods. It focuses on iron, which is one of the most ubiquitous and biogeochemically relevant metals in the environment. The chapter provides a brief review of the (bio)geochemistry of this element and describes Lake Matano, an iron-rich environment that is geochemically fascinating with respect to metal cycling. It presents the known-facts about Lake Matano and discusses how the traditional and the molecular microbiological approaches described can be used to gain insight into the manner in which microorganisms affect the biogeochemical cycling of iron and other elements in the environment. Once whole genomes of novel organisms from this environment would become available, bioinformatics provides powerful additional tools to search for metabolic key components that contribute to the biogeochemical cycling of iron and other elements in this environment.

Citation: Bose A, Kopf S, Newman D. 2011. From Geocycles to Genomes and Back, p 13-38. In Stolz J, Oremland R (ed), Microbial Metal and Metalloid Metabolism. ASM Press, Washington, DC. doi: 10.1128/9781555817190.ch2

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Environmental Microbiology
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Bacteria and Archaea
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Restriction Fragment Length Polymorphism
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Denaturing Gradient Gel Electrophoresis
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Restriction Fragment Length Polymorphism
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Denaturing Gradient Gel Electrophoresis
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Image of FIGURE 1
FIGURE 1

TEM and SEM of strain SW2 grown photoferrotrophically. (A) TEM image of strain SW2 grown photoferrotrophically for 5 days. Arrows indicate Fe(III) precipitates. Image previously published as Figure 4B in . (B) SEM of strain SW2 grown photoferrotrophically for 4 weeks showing the crystalline, regularly shaped Fe(III) precipitates. 10.1128/9781555817190.ch2.f1

Citation: Bose A, Kopf S, Newman D. 2011. From Geocycles to Genomes and Back, p 13-38. In Stolz J, Oremland R (ed), Microbial Metal and Metalloid Metabolism. ASM Press, Washington, DC. doi: 10.1128/9781555817190.ch2
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Image of FIGURE 2
FIGURE 2

Simplified illustration of the coupling of the biogeochemical cycling of iron with the carbon, nitrogen, and sulfur cycles. Shown are interactions of the element cycles during mineral formation and dissolution (left column: arrows indicate precipitation, parentheses provide examples of mineral species), redox cycling (center column: arrows illustrate redox transformations coupled to iron oxidation/reduction, parentheses provide examples of the reduced and oxidized species involved), and enzymatic catalysis (right column: arrows indicate examples of iron-dependent metabolic processes for sulfur, carbon, and nitrogen, respectively). 10.1128/9781555817190.ch2.f2

Citation: Bose A, Kopf S, Newman D. 2011. From Geocycles to Genomes and Back, p 13-38. In Stolz J, Oremland R (ed), Microbial Metal and Metalloid Metabolism. ASM Press, Washington, DC. doi: 10.1128/9781555817190.ch2
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Image of FIGURE 3
FIGURE 3

Simplified schematic illustrating the interactions of the iron cycle with other element cycles in Lake Matano. The oxic surface waters are shown with a white background, the anoxic monimolimion is shown in light grey. Penetration of sunlight and phototrophic transformations are indicated with dotted lines, nonphototrophic microbial transformations are indicated with solid lines, and precipitation and diffusion are shown by dashed lines. Coupled arrows, such as organic matter oxidation to carbon dioxide (<CHO> to CO) with sulfate reduction to hydrogen sulfide (SO to HS), illustrate closely linked redox transformations. Several hypothesized, but still insufficiently investigated potential processes in Lake Matano, such as photoferrotrophy and iron-dependent anaerobic methane oxidation, are highlighted with a question mark. 10.1128/9781555817190.ch2.f3

Citation: Bose A, Kopf S, Newman D. 2011. From Geocycles to Genomes and Back, p 13-38. In Stolz J, Oremland R (ed), Microbial Metal and Metalloid Metabolism. ASM Press, Washington, DC. doi: 10.1128/9781555817190.ch2
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References

/content/book/10.1128/9781555817190.ch02
1. Adamczyk, J.,, M. Hesselsoe,, N. Iversen,, M. Horn,, A. Lehner,, P. H. Nielsen,, M. Schloter,, P. Roslev, and, M. Wagner. 2003. The isotope array, a new tool that employs substrate-mediated labeling of rRNA for determination of microbial community structure and function. Appl. Environ. Microbiol. 69:68756887.
2. Allen, E. E.,, and J. F. Banfield. 2005. Community genomics in microbial ecology and evolution. Nat. Rev. Microbiol. 3:489498.
3. Amann, R.,, and B. M. Fuchs. 2008. Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques. Nat. Rev. Microbiol. 6:339348.
4. Amann, R. I.,, L. Krumholz, and, D. A. Stahl. 1990. Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. J. Bacteriol. 172:762770.
5. Amann, R. I.,, W. Ludwig, and, K. H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Mol. Biol. Rev. 59:143169.
6. Anbar, A. D.,, and A. H. Knoll. 2002. Proterozoic ocean chemistry and evolution: a bioinorganic bridge? Science 297:11371142.
7. Baker, B. J.,, and J. F. Banfield. 2003. Microbial communities in acid mine drainage. FEMS Microbiol. Ecol. 44:139152.
8. Baker, W. W.,, and J. F. Banfield. 1998. Zones of chemical and physical interaction at interfaces between microbial communities and minerals: a model. Geomicrobiol. J. 15:223244.
9. Beal, E. J.,, C. H. House, and, V. J. Orphan. 2009. Manganese-and iron-dependent marine methane oxidation. Science 325:184187.
10. Beja, O.,, L. Aravind,, E. V. Koonin,, M. T. Suzuki,, A. Hadd,, L. P. Nguyen,, S. B. Jovanovich,, C. M. Gates,, R. A. Feldman,, J. L. Spudich,, E. N. Spudich, and, E. F. DeLong. 2000. Bacterial rhodopsin: evidence for a new type of photo-trophy in the sea. Science 289:19021906.
11. Berner, R. A.,, and K. A. Maasch. 1996. Chemical weathering and controls on atmospheric O2 and CO2: fundamental principles were enunciated by J. J. Ebelmen in 1845. Geochim. Cosmochim. Acta 60:16331637.
12. Beukes, N. J.,, and J. Gutzmer. 2008. Origin and paleoenvironmental significance of major iron formations at the Archean-Paleoproterozoic boundary, p. 5–47. In S. Hagemann,, C. Rosiere,, J. Gutzmer, and, N. J. Beukes (ed.), Reviews in Economic Geology, vol. 15. Banded Iron Formation-Related High-Grade Iron Ore. Society of Economic Geologists, Denver, CO.
13. Boetius, A.,, K. Ravenschlag,, C. J. Schubert,, D. Rickert,, F. Widdel,, A. Gieseke,, R. Amann,, B. B. Jorgensen,, U. Witte, and, O. Pfannkuche. 2000. A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature 407:623626.
14. Brock, T. D. 1978. Thermophilic Microorganisms and Life at High Temperatures. Springer-Verlag, New York, NY.
15. Brooks, J. L. 1950. Speciation in ancient lakes. Q. Rev. Biol. 25:131176.
16. Burdige, D. J.,, and P. E. Kepkay. 1983. Determination of bacterial manganese oxidation rates in sediments using an in situ dialysis technique. I. Laboratory studies. Geochim. Cosmochim. Acta 47:19071916.
17. Canfield, D. E.,, K. S. Habicht and, B. Thamdrup. 2000. The Archean sulfur cycle and the early history of atmospheric oxygen. Science 288:658661.
18. Canfield, D. E.,, B. Thamdrup, and, J. W. Hansen. 1993. The anaerobic degradation of organic matter in Danish coastal sediments: iron reduction, manganese reduction, and sulfate reduction. Geochim. Cosmochim. Acta 57:38673883.
19. Canfield, D. E.,, E. Kristensen, and, B. Thamdrup. 2005. Aquatic Geomicrobiology. Elsevier, San Diego, CA.
20. Canfield, D. E.,, R. Raiswell, and, S. Bottrell. 1992. The reactivity of sedimentary iron minerals toward sulfide. Am. J. Sci. 292:659683.
21. Capone, D. G.,, and R. P. Kiene. 1988. Comparison of microbial dynamics in marine and fresh water sediments: contrasts in anaerobic carbon catabolism. Limnol. Oceanogr. 33:725749.
22. Clement, B. G.,, L. E. Kehl,, K. L. DeBord, and, C. L. Kitts. 1998. Terminal restriction fragment patterns (TRFPs), a rapid, PCR-based method for the comparison of complex bacterial communities. J. Microbiol. Methods 31:135142.
23. Cohan, F. M. 2002. What are bacterial species? Annu. Rev. Microbiol. 56:457487.
24. Croal, L. R.,, Y. Jiao, and, D. K. Newman. 2007. The fox operon from Rhodobacter strain SW2 promotes phototrophic Fe(II) oxidation in Rhodobacter capsulatus SB1003. J. Bacteriol. 189:17741782.
25. Crowe, S. A.,, S. Katsev,, K. Leslie,, A. Sturm,, C. Magen,, S. Nomosatryo,, M. A. Pack,, J. D. Kessler,, W. S. Reeburgh,, J. A. Roberts,, L. Gonzáles,, G. D. Haffner,, A. Mucci,, B. Sundby, and, D. A. Fowle. 2010. The methane cycle in ferruginous Lake Matano. Geobiology 9(1):6178. http://dx.doi.org/10.1111/j.1472-4669.2010.00257.x.
26. Crowe, S. A.,, C. Jones,, S. Katsev,, C. Magen,, A. H. O‘Neill,, A. Sturm,, D. E. Canfield,, G. D. Haffner,, A. Mucci,, B. Sundby, and, D. A. Fowle. 2008a. Photoferrotrophs thrive in an Archean Ocean analogue. Proc. Natl. Acad. Sci. USA 105:1593815943.
27. Crowe, S. A.,, A. H. O’Neill,, S. Katsev,, P. Hehanussa,, G. D. Haffner,, B. Sundby,, A. Mucci, and, D. A. Fowle. 2008b. The biogeochemistry of tropical lakes: a case study from Lake Matano, Indonesia. Limnol. Oceanogr. 53:319331.
28. Delsuc, F.,, H. Brinkmann, and, H. Philippe. 2005. Phylogenomics and the reconstruction of the tree of life. Nat. Rev. Genet. 6:361375.
29. Doolittle, W. F. 2000. Uprooting the tree of life. Sci. Am. 282:9095.
30. Duan, Y.,, L. Zhou,, D. G. Hall,, W. Li,, H. Doddapaneni,, H. Lin,, L. Liu,, C. M. Vahling,, D. W. Gabriel,, K. P. Williams,, A. Dickerman,, Y. Sun, and, T. Gottwald. 2009. Complete genome sequence of citrus huanglongbing bacterium, ‘Candidatus Liberibacter asiaticus’ obtained through metagenomics. Mol. Plant-Microbe Interact. 22:10111020.
31. Dumont, M. G.,, and J. C. Murrell. 2005. Stable isotope probing—linking microbial identity to function. Nat. Rev. Microbiol. 3:499504.
32. Dunbar, J.,, L. O. Ticknor, and, C. R. Kuske. 2001. Phylogenetic specificity and reproducibility and new method for analysis of terminal restriction fragment profiles of 16S rRNA genes from bacterial communities. Appl. Environ. Microbiol. 67:190197.
33. Edwards, K. J.,, P. L. Bond,, T. M. Gihring, and, J. F. Banfield. 2000. An archaeal iron-oxidizing extreme acidophile important in acid mine drainage. Science 287:17961799.
34. Edwards, K. J.,, B. M. Goebel,, T. M. Rodgers,, M. O. Schrenk,, T. M. Gihring,, M. M. Cardona,, B. Hu,, M. M. McGuire,, R. J. Hamers,, N. R. Pace, and, J. F. Banfield. 1999. Geomicrobiology of pyrite (FeS2) dissolution: case study at Iron Mountain, California. Geomicrobiol. J. 16:155179.
35. Ehrlich, H. L.,, and D. K. Newman. 2009a. Molecular methods in geomicrobiology, p. 139–156. In H. L. Ehrlich and, D. K. Newman (ed.), Geomicrobiology. CRC Press, Boca Raton, FL.
36. Ehrlich, H. L.,, and D. K. Newman. 2009b. Non-molecular methods in geomicrobiology, p. 117–138. In H. L. Ehrlich and, D. K. Newman (ed.), Geomicrobiology. CRC Press, Boca Raton, FL.
37. Eilers, H.,, J. Pernthaler,, F. O. Glockner, and, R. Amann. 2000. Culturability and in situ abundance of pelagic bacteria from the North Sea. Appl. Environ. Microbiol. 66:30443051.
38. Emerson, D.,, and J. V. Weiss. 2004. Bacterial iron oxidation in circumneutral freshwater habitats: findings from the field and the laboratory. Geomicrobiol. J. 21:405414.
39. Falkowski, P. G.,, R. T. Barber, and, V. Smetacek. 1998. Biogeochemical controls and feedbacks on ocean primary production. Science 281:200206.
40. Fraústo da Silva, J. J. R.,, and R. J. P. Williams. 2001. The Biological Chemistry of the Elements: the Inorganic Chemistry of Life. Oxford University Press, New York, NY.
41. Garrels, R. M.,, and A. Lerman. 1981. Phanerozoic cycles of sedimentary carbon and sulfur. Proc. Natl. Acad. Sci. USA 78:46524656.
42. Gentry, T. J.,, G. S. Wickham,, C. W. Schadt,, Z. He, and, J. Zhou. 2006. Microarray applications in microbial ecology research. Microb. Ecol. 52:159175.
43. Ghiorse, W. C.,, and D. L. Balkwill. 1983. Enumeration and morphological characterization of bacteria indigenous to subsurface environments. Dev. Ind. Microbiol. 24:213224.
44. Giovannoni, S. J.,, E. F. Delong,, G. J. Olsen, and, N. R. Pace. 1988. Phylogenetic group-specific oligonucleotide probes for identification of single microbial cells. J. Bacteriol. 170:720726.
45. Glass, J. B.,, F. Wolfe-Simon, and, A. D. Anbar. 2009. Coevolution of metal availability and nitrogen assimilation in cyanobacteria and algae. Geobiology 7:100123.
46. Guss, A. M.,, B. Mukhopadhyay,, J. K. Zhang, and, W. W. Metcalf. 2005. Genetic analysis of mch mutants in two Methanosarcina species demonstrates multiple roles for the methanopterin-dependent C-1 oxidation/reduction pathway and differences in H2 metabolism between closely related species. Mol. Microbiol. 55:16711680.
47. Guyer, R. L.,, and D. E. Koshland, Jr. 1989. The molecule of the year. Science 246:15431546.
48. Herbert, D.,, R. Elsworth, and, R. C. Telling. 1956. The continuous culture of bacteria; a theoretical and experimental study. J. Gen. Microbiol. 14:601622.
49. Hesselsoe, M.,, S. Fureder,, M. Schloter,, L. Bodrossy,, N. Iversen,, P. Roslev,, P. H. Nielsen,, M. Wagner, and, A. Loy. 2009. Isotope array analysis of Rhodocyclales uncovers functional redundancy and versatility in an activated sludge. ISME J. 3:13491364.
50. Hoff, K. J.,, M. Tech,, T. Lingner,, R. Daniel,, B. Morgenstern, and, P. Meinicke. 2008. Gene prediction in metagenomic fragments: a large scale machine learning approach. BMC Bioinf. 9:217231.
51. Hughes, J. B.,, J. J. Hellmann,, T. H. Ricketts, and, B. J. Bohannan. 2001. Counting the uncountable: statistical approaches to estimating microbial diversity. Appl. Environ. Microbiol. 67:43994406.
52. Isley, A. E.,, and D. H. Abbott. 1999. Plume- related mafic volcanism and the deposition of banded iron formations. J. Geophys. Res. Solid Earth 104:1546115477.
53. Ivanov, M. V. 1968. Microbiological Processes in the Formation of Sulfur Deposits. U.S. Department of Agriculture and the National Science Foundation (Israel Program for Scientific Translations), Washington, DC.
54. Jannasch, H. W. 1967. Growth of marine bacteria at limiting concentration of organic carbon in seawater. Limnol. Oceanogr. 12:264271.
55. Jannasch, H. W. 1969. Estimations of bacterial growth in natural waters. J. Bacteriol. 99:156160.
56. Jannasch, H. W.,, and C. O. Wirsen. 1981. Morphological survey of microbial mats near deep-sea thermal vents. Appl. Environ. Microbiol. 41:528538.
57. Jargeat, P.,, C. Cosseau,, B. Ola’h,, A. Jauneau,, P. Bonfante,, J. Batut, and, G. Becard. 2004. Isolation, free-living capacities, and genome structure of “Candidatus Glomeribacter gigasporarum,” the endocellular bacterium of the mycorrhizal fungus Gigaspora margarita. J. Bacteriol. 186:68766884.
58. Kaeberlein, T.,, K. Lewis, and, S. S. Epstein. 2002. Isolating “uncultivable” microorganisms in pure culture in a simulated natural environment. Science 296:11271129.
59. Kappler, A.,, C. Pasquero,, K. O. Konhauser, and, D. K. Newman. 2005. Deposition of banded iron formations by anoxygenic phototrophic Fe(II)-oxidizing bacteria. Geology 33:865868.
60. Kappler, A.,, and K. L. Straub. 2005. Geomicro-biological cycling of iron. Rev. Mineral. Geochem. 59:85108.
61. Klaassens, E. S.,, W. M. de Vos, and, E. E. Vaughan. 2007. Metaproteomics approach to study the functionality of the microbiota in the human infant gastrointestinal tract. Appl. Environ. Microbiol. 73:13881392.
62. Klappenbach, J. A.,, P. R. Saxman,, J. R. Cole, and, T. M. Schmidt. 2001. rrndb: the ribosomal RNA operon copy number database. Nucleic Acids Res. 29:181184.
63. Konhauser, K. O.,, L. Amskold,, S. V. Lalonde,, N. R. Posth,, A. Kappler, and, A. D. Anbar. 2007. Decoupling photochemical Fe(II) oxidation from shallow-water BIF deposition. Earth Planet. Sci. Lett. 258:87100.
64. Kraemer, S. 2004. Iron oxide dissolution and solubility in the presence of siderophores. Aquat. Sci. 66:318.
65. Kraemer, S. M.,, A. Butler,, P. Borer, and, J. Cervini-Silva. 2005. Siderophores and the dissolution of iron-bearing minerals in marine systems. Rev. Mineral. Geochem. 59:5384.
66. Lawrence, J. R.,, D. R. Korber,, G. M. Wolfaardt, and, D. E. Caldwell. 1997. Analytical imaging and microscopy techniques. In C. J. Hurst,, G. R. Knudsen,, M. J. McInerney,, L. D. Stetzenbach, and, M. V. Walter (ed.), Manual of Environmental Microbiology. ASM Press, Washington, DC.
67. Lee, N.,, P. H. Nielsen,, K. H. Andreasen,, S. Juretschko,, J. L. Nielsen,, K. H. Schleifer, and, M. Wagner. 1999. Combination of fluorescent in situ hybridization and microautoradiography-a new tool for structure-function analyses in microbial ecology. Appl. Environ. Microbiol. 65:12891297.
68. Liu, W. T.,, T. L. Marsh,, H. Cheng, and, L. J. Forney. 1997. Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl. Environ. Microbiol. 63:45164522.
69. Lovley, D. R.,, D. E. Holmes, and, K. P. Nevin. 2004. Dissimilatory Fe(III) and Mn(IV) reduction. Adv. Microb. Physiol. 49:219286.
70. Luther, G. W.,, P. J. Brendel,, B. L. Lewis,, B. Sundby,, L. Lefrancois,, N. Silverberg, and, D. B. Nuzzio. 1998. Simultaneous measurement of O2, Mn, Fe, I-, and S(-II) in marine pore waters with a solid-state voltammetric microelectrode. Limnol. Oceanogr. 43:325333.
71. Luther, G. W.,, B. T. Glazer,, L. Hohmann,, J. I. Popp,, M. Taillefert,, T. F. Rozan,, P. J. Brendel,, S. M. Theberge, and, D. B. Nuzzio. 2001. Sulfur speciation monitored in situ with solid state gold amalgam voltammetric microelectrodes: polysulfides as a special case in sediments, microbial mats and hydrothermal vent waters. J. Environ. Monit. 3:6166.
72. Maloy, S. R.,, and J. E. Cronan. 1994. Microbial Genetics. Jones and Bartlett Publishers, Sudbury, MA.
73. Maron, P. A.,, L. Ranjard,, C. Mougel, and, P. Lemanceau. 2007. Metaproteomics: a new approach for studying functional microbial ecology. Microb. Ecol. 53:486493.
74. Martinez, A.,, A. S. Bradley,, J. R. Waldbauer,, R. E. Summons, and, E. F. DeLong. 2007. Proteorhodopsin photosystem gene expression enables photophosphorylation in a heterologous host. Proc. Natl. Acad. Sci. USA 104:55905595.
75. McArthur, J. V. 2006. Microbial Ecology: An Evolutionary Approach. Academic Press, San Diego, CA.
76. Miller, F. D.,, and C. L. Hershberger. 1984. A quantitative beta-galactosidase alpha-complementation assay for fusion proteins containing human insulin B-chain peptides. Gene 29:247250.
77. Morel, F. M. M. 2003. The biogeochemical cycles of trace metals in the oceans. Science 300:944947.
78. Morgan, J. W.,, and E. Anders. 1980. Chemical composition of Earth, Venus, and Mercury. Proc. Natl. Acad. Sci. USA 77:69736977.
79. Muyzer, G.,, E. C. de Waal, and, A. G. Uitterlinden. 1993. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59:695700.
80. Myers, N.,, R. A. Mittermeier,, C. G. Mittermeier,, G. A. da Fonseca, and, J. Kent. 2000. Biodiversity hotspots for conservation priorities. Nature 403:853858.
81. Novick, A. 1955. Growth of bacteria. Annu. Rev. Microbiol. 9:97110.
82. Olsen, G. J.,, and C. R. Woese. 1993. Ribosomal RNA: a key to phylogeny. FASEB J. 7:113123.
83. Orphan, V. J.,, C. H. House,, K. U. Hinrichs,, K. D. McKeegan, and, E. F. DeLong. 2001. Methane-consuming archaea revealed by directly coupled isotopic and phylogenetic analysis. Science 293:484487.
84. Ottesen, E. A.,, J. W. Hong,, S. R. Quake, and, J. R. Leadbetter. 2006. Microfluidic digital PCR enables multigene analysis of individual environmental bacteria. Science 314:14641467.
85. Ouverney, C. C.,, and J. A. Fuhrman. 1999. Combined microautoradiography-16S rRNA probe technique for determination of radio-isotope uptake by specific microbial cell types in situ. Appl. Environ. Microbiol. 65:17461752.
86. Pelletier, E.,, A. Kreimeyer,, S. Bocs,, Z. Rouy,, G. Gyapay,, R. Chouari,, D. Riviere,, A. Ganesan,, P. Daegelen,, A. Sghir,, G. N. Cohen,, C. Medigue,, J. Weissenbach, and, D. Le Paslier. 2008. “Candidatus Cloacamonas acidaminovorans”: genome sequence reconstruction provides a first glimpse of a new bacterial division. J. Bacteriol. 190:25722579.
87. Perfil’ev, B. V.,, and D. R. Gabe. 1969. Capillary Methods for Studying Microorganisms. University of Toronto Press, Toronto, Canada.
88. Pernthaler, A.,, A. E. Dekas,, C. T. Brown,, S. K. Goffredi,, T. Embaye, and, V. J. Orphan. 2008. Diverse syntrophic partnerships from deep-sea methane vents revealed by direct cell capture and metagenomics. Proc. Natl. Acad. Sci. USA 105:70527057.
89. Pernthaler, A.,, J. Pernthaler, and, R. Amann. 2002. Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria. Appl. Environ. Microbiol. 68:30943101.
90. Petsch, S. T.,, K. J. Edwards, and, T. I. Eglinton. 2003. Abundance, distribution and delta C-13 analysis of microbial phospholipid-derived fatty acids in a black shale weathering profile. Org. Geochem. 34:731743.
91. Philippe, H.,, and J. Laurent. 1998. How good are deep phylogenetic trees? Curr. Opin. Genet. Dev. 8:616623.
92. Posth, N. R.,, F. Hegler,, K. O. Konhauser, and, A. Kappler. 2008. Alternating Si and Fe deposition caused by temperature fluctuations in Precambrian oceans. Nat. Geosci. 1:703708.
93. Pritchett, M. A.,, J. K. Zhang, and, W. W. Metcalf. 2004. Development of a markerless genetic exchange method for Methanosarcina acetivorans C2A and its use in construction of new genetic tools for methanogenic archaea. Appl. Environ. Microbiol. 70:14251433.
94. Radajewski, S.,, P. Ineson,, N. R. Parekh, and, J. C. Murrell. 2000. Stable-isotope probing as a tool in microbial ecology. Nature 403:646649.
95. Raghoebarsing, A. A.,, A. Pol,, K. T. van de Pas-Schoonen,, A. J. P. Smolders,, K. F. Ettwig,, W. I. C. Rijpstra,, S. Schouten,, J. S. S. Damste,, H. J. M. Op den Camp,, M. S. M. Jetten, and, M. Strous. 2006. A microbial consortium couples anaerobic methane oxidation to denitrification. Nature 440:918921.
96. Rankama, K.,, and T. Georg Sahama. 1950. Geochemistry. University of Chicago Press, Chicago, IL.
97. Rappe, M. S.,, S. A. Connon,, K. L. Vergin, and, S. J. Giovannoni. 2002. Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418:630633.
98. Reeburgh, W. S. 2007. Oceanic methane biogeochemistry. Chem. Rev. 107:486513.
99. Riesenfeld, C. S.,, P. D. Schloss, and, J. Handelsman. 2004. Metagenomics: genomic analysis of microbial communities. Annu. Rev. Genet. 38:525552.
100. Rokas, A.,, and P. W. Holland. 2000. Rare genomic changes as a tool for phylogenetics. Trends Ecol. Evol. 15:454459.
101. Rother, M.,, and W. W. Metcalf. 2005. Genetic technologies for Archaea. Curr. Opin. Microbiol. 8:745751.
102. Sabo, E.,, D. Roy,, P. B. Hamilton,, P. E. Hehanussa,, R. McNeely, and, G. D. Haffner. 2008. The plankton community of Lake Matano: factors regulating plankton composition and relative abundance in an ancient, tropical lake of Indonesia. Hydrobiologia 615:225235. http://dx.doi.org/10.1007/s10750-008-9560-4.
103. Saito, M. A.,, D. M. Sigman, and, F. M. M. Morel. 2003. The bioinorganic chemistry of the ancient ocean: the co-evolution of cyanobacterial metal requirements and biogeochemical cycles at the Archean-Proterozoic boundary? Inorg. Chim. Acta 356:308318.
104. Salyers, A. A.,, G. Bonheyo, and, N. B. Shoemaker. 2000. Starting a new genetic system: lessons from bacteroides. Methods 20:3546.
105. Schlegel, H. G. 1993. General Microbiology. Cambridge University Press, New York City, Ny.
106. Seeber, F.,, and J. C. Boothroyd. 1996. Escherichia coli beta-galactosidase as an in vitro and in vivo reporter enzyme and stable transfection marker in the intracellular protozoan parasite Toxoplasma gondii. Gene 169:3945.
107. Shi, Y.,, G. W. Tyson, and, E. F. DeLong. 2009. Metatranscriptomics reveals unique microbial small RNAs in the ocean’s water column. Nature 459:266269.
108. Sieburth, J. M. 1975. Microbial Seascapes. A Pictorial Essay on Marine Microorganism and Their Environments. University Park Press, Baltimore, MD.
109. Stackebrandt, E.,, and B. M. Goebel. 1994. A place for DNA : DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int. J. Syst. Bacteriol. 44:846849.
110. Stahl, D. A. 1997. Molecular approaches for the measurement of density, diversity and phylogeny, p. 102–114. In C. J. Hurst,, G. R. Knudsen,, M. J. McInerney,, L. D. Stetzenbach, and, M. V. Walter (ed.), Manual of Environmental Microbiology. ASM Press, Washington, DC.
111. Staley, J. T. 2003. Speciation and bacterial phylospecies, p. 40–48. In A. T. Bull (ed.), Microbial Diversity and Bioprospecting. ASM Press, Washington, DC.
112. Staley, J. T.,, and A. Konopka. 1985. Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Annu. Rev. Microbiol. 39:321346.
113. Stumm, W.,, and J. J. Morgan. 1995. Aquatic Chemistry: Chemical Equilibria and Rates in Natural Waters. Wiley, New York, NY.
114. Svensson, E.,, A. Skoog, and, J. P. Amend. 2004. Concentration and distribution of dissolved amino acids in a shallow hydrothermal system, Vulcano Island (Italy). Org. Geochem. 35:10011014.
115. Tran-Nguyen, L. T.,, M. Kube,, B. Schneider,, R. Reinhardt, and, K. S. Gibb. 2008. Comparative genome analysis of “Candidatus Phytoplasma australiense” (subgroup tuf-Australia I; rp-A) and “Ca. Phytoplasma asteris” strains OY-M And AY-WB. J. Bacteriol. 190:39793991.
116. Ussher, S. J.,, E. P. Achterberg, and, P. J. Worsfold. 2004. Marine biogeochemistry of iron. Environ. Chem. 1:6780.
117. Valdivia, R. H.,, B. P. Cormack, and, S. Falkow. 2006. The uses of green fluorescent protein in prokaryotes. Methods Biochem. Anal. 47:163178.
118. Ward, D. M.,, M. M. Bateson,, R. Weller, and, A. L. Ruffroberts. 1992. Ribosomal-RNA analysis of microorganisms as they occur in nature. Adv. Microb. Ecol. 12:219286.
119. Ward, D. M.,, M. J. Ferris,, S. C. Nold, and, M. M. Bateson. 1998. A natural view of microbial biodiversity within hot spring cyanobacterial mat communities. Microbiol. Mol. Biol. Rev. 62:13531370.
120. Ward, D. M.,, R. Weller, and, M. M. Bateson. 1990. 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 345:6365.
121. Warnecke, F.,, and M. Hess. 2009. A perspective: metatranscriptomics as a tool for the discovery of novel biocatalysts. J. Biotechnol. 142:9195.
122. Weber, K. A.,, J. Pollock,, K. A. Cole,, S. M. O’Connor,, L. A. Achenbach, and, J. D. Coates. 2006. Anaerobic nitrate-dependent iron(II) bio-oxidation by a novel lithoautotrophic beta-proteobacterium, strain 2002. Appl. Environ. Microbiol. 72:686694.
123. Wernegreen, J. J.,, A. B. Lazarus, and, P. H. Degnan. 2002. Small genome of Candidatus Bloch-mannia, the bacterial endosymbiont of Camponotus, implies irreversible specialization to an intracellular lifestyle. Microbiology 148:25512556.
124. White, D. 2000. The Physiology and Biochemistry of Prokaryotes. Oxford Unversity Press, New York, NY.
125. Whiteley, A. S.,, M. Manefield, and, T. Lueders. 2006. Unlocking the ‘microbial black box’ using RNA-based stable isotope probing technologies. Curr. Opin. Biotechnol. 17:6771.
126. Widdel, F.,, S. Schnell,, S. Heising,, A. Ehrenreich,, B. Assmus, and, B. Schink. 1993. Ferrous iron oxidation by anoxygenic phototrophic bacteria. Nature 362:834836.
127. Wilmes, P.,, and P. L. Bond. 2006. Metaproteomics: studying functional gene expression in microbial ecosystems. Trends Microbiol. 14:9297.
128. Wilmes, P.,, S. L. Simmons,, V. J. Denef, and, J. F. Banfield. 2009. The dynamic genetic repertoire of microbial communities. FEMS Microbiol. Rev. 33:109132.
129. Wilmes, P.,, M. Wexler, and, P. L. Bond. 2008. Metaproteomics provides functional insight into activated sludge wastewater treatment. PLoS One 3:e1778.
130. Woyke, T.,, G. Xie,, A. Copeland,, J. M. Gonzalez,, C. Han,, H. Kiss,, J. H. Saw,, P. Senin,, C. Yang,, S. Chatterji,, J. F. Cheng,, J. A. Eisen,, M. E. Sieracki, and, R. Stepanauskas. 2009. Assembling the marine metagenome, one cell at a time. PLoS One 4:e5299.
131. Wu, L. Y.,, X. Liu,, C. W. Schadt, and, J. Z. Zhou. 2006. Microarray-based analysis of subnanogram quantities of microbial community DNAs by using whole-community genome amplification. Appl. Environ. Microbiol. 72:49314941.
132. Zengler, K.,, G. Toledo,, M. Rappe,, J. Elkins,, E. J. Mathur,, J. M. Short, and, M. Keller. 2002. Cultivating the uncultured. Proc. Natl. Acad. Sci. USA 99:1568115686.

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