Microbial diversity under extreme euxinia: Mahoney Lake, Canada

Geobiology

Volumn 10, Issue 3, 2012, Pages 223-235

  Klepac Ceraj, V ^a,b   Hayes, C A ^c   Gilhooly, W P ^d   Lyons, T W ^e   Kolter, R ^b   Pearson, A ^c  

^a FORSYTH INSTITUTE   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c HARVARD UNIVERSITY   (United States)

^d WASHINGTON UNIVERSITY   (United States)

^e UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEAL DNA; ARCHAEAL RNA; BACTERIAL DNA; BACTERIAL RNA; FRESH WATER; RIBOSOME DNA; RNA 16S;

ANOXIC CONDITIONS; BACTERIUM; GEOMICROBIOLOGY; HYPOLIMNION; LACUSTRINE DEPOSIT; METABOLISM; MICROBIAL ACTIVITY; MICROBIAL COMMUNITY; PHOTOAUTOTROPHY; SALINE LAKE; SULFUR CYCLE;

ARCHAEON; ARTICLE; BACTERIUM; BIOTA; CANADA; CHEMISTRY; CLASSIFICATION; CLUSTER ANALYSIS; DNA SEQUENCE; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; PHYLOGENY; RNA GENE; SEDIMENT; SEQUENCE HOMOLOGY;

ARCHAEA; BACTERIA; BIOTA; BRITISH COLUMBIA; CLUSTER ANALYSIS; DNA, ARCHAEAL; DNA, BACTERIAL; DNA, RIBOSOMAL; FRESH WATER; GENES, RRNA; GEOLOGIC SEDIMENTS; PHYLOGENY; RNA, ARCHAEAL; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID;

BRITISH COLUMBIA; CANADA; MAHONEY LAKE;

ACTINOBACTERIA; ALPHAPROTEOBACTERIA; BACTERIA (MICROORGANISMS); CHROMATIACEAE; CRENARCHAEOTA; DELTAPROTEOBACTERIA; EPSILONPROTEOBACTERIA; GAMMAPROTEOBACTERIA; NATRONOANAEROBIUM; VERRUCOMICROBIA;

EID: 84859443094     PISSN: 14724677     EISSN: 14724669     Source Type: Journal    
DOI: 10.1111/j.1472-4669.2012.00317.x     Document Type: Article

References (101)

1. Acinas SG, Sarma-Rupavtarm R, Klepac-Ceraj V, Polz MF (2005) PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample. Applied and Environmental Microbiology 71, 8966-8969.
2. Alain K, Olagnon M, Desbruyeres D, Page A, Barbier G, Juniper SK, Querellou J, Cambon-Bonavita MA (2002) Phylogenetic characterization of the bacterial assemblage associated with mucous secretions of the hydrothermal vent polychaete Paralvinella palmiformis. FEMS (Federation of European Microbiological Societies) Microbiology - Ecology 42, 463-476.
3. Amend JP, Shock EL (2001) Energetics of overall metabolic reactions of thermophilic and hyperthermophilic Archaea and bacteria. FEMS (Federation of European Microbiological Societies) Microbiology Reviews 25, 175-243.
4. Armbrust EV, Bowen JD, Olson RJ, Chisholm SW (1989) Effect of light on the cell cycle of a marine synechococcus strain. Applied and Environmental Microbiology 55, 425-432.
5. Arthur MA, Dean WE, Pratt LM (1988) Geochemical and climatic effects of increased marine organic-carbon burial at the cenomanian turonian boundary. Nature 335, 714-717.
6. Banciu H, Sorokin DY, Galinski EA, Muyzer G, Kleerebezem R, Kuenen JG (2004) Thialkalivibrio halophilus sp. nov., a novel obligately chemolithoautotrophic, facultatively alkaliphilic, and extremely salt-tolerant, sulfur-oxidizing bacterium from a hypersaline alkaline lake. Extremophiles 8, 325-334.
7. Barberan A, Casamayor EO (2010) Global phylogenetic community structure and beta-diversity patterns in surface bacterioplankton metacommunities. Aquatic Microbial Ecology 59, 217-228.
8. Barberan A, Casamayor EO (2011) Euxinic freshwater hypolimnia promote bacterial endemicity in continental areas. Microbial Ecology 61, 465-472.
9. Bray JR, Curtis JT (1957) An ordination of the upland forest communities of southern wisconsin. Ecological Monographs 27, 326-349.
10. Brochier-Armanet C, Boussau B, Gribaldo S, Forterre P (2008) Mesophilic Crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota. Nature Reviews. Microbiology 6, 245-252.
11. Brocks JJ, Love GD, Summons RE, Knoll AH, Logan GA, Bowden SA (2005) Biomarker evidence for green and purple sulphur bacteria in a stratified Palaeoproterozoic sea. Nature 437, 866-870.
12. Brodie EL, Desantis TZ, Joyner DC, Baek SM, Larsen JT, Andersen GL, Hazen TC, Richardson PM, Herman DJ, Tokunaga TK, Wan JMM, Firestone MK (2006) Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation. Applied and Environmental Microbiology 72, 6288-6298.
13. Brodie EL, Desantis TZ, Parker JPM, Zubietta IX, Piceno YM, Andersen GL (2007) Urban aerosols harbor diverse and dynamic bacterial populations. Proceedings of the National Academy of Sciences of the United States of America 104, 299-304.
14. Brunskill GJ, Ludlam SD (1969) Fayetteville Green Lake, New York. I. Physical and chemical limnology. Limnology and Oceanography 14, 817-829.
15. Canfield DE (1998) A new model for Proterozoic ocean chemistry. Nature 396, 450-453.
16. Chang HW, Nam YD, Kwon HY, Park JR, Lee JS, Yoon JH, An KG, Bae JW (2007) Marinobacterium halophilum sp. nov., a marine bacterium isolated from the Yellow Sea. International Journal of Systematic and Evolutionary Microbiology 57, 77-80.
17. Chao A (1987) Estimating the population size for capture-recapture data with unequal catchability. Biometrics 43, 783-791.
18. Coates JD, Ellis DJ, Gaw CV, Lovley DR (1999) Geothrix fermentans gen. nov., sp. nov., a novel Fe(III)-reducing bacterium from a hydrocarbon-contaminated aquifer. International Journal of Systematic Bacteriology 49(Pt 4), 1615-1622.
19. Cole JR, Chai B, Farris RJ, Wang Q, Kulam-Syed-Mohideen AS, Mcgarrell DM, Bandela AM, Cardenas E, Garrity GM, Tiedje JM (2007) The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data. Nucleic Acids Research 35, D169-D172.
20. Colwell RK (2009) EstimateS: statistical estimation of species richness and shared species from samples. Version 8.2. User's Guide and application published at:
21. Coolen MJL, Overmann J (1998) Analysis of subfossil molecular remains of purple sulfur bacteria in a lake sediment. Applied and Environmental Microbiology 64, 4513-4521.
22. Cottrell MT, Waidner LA, Yu L, Kirchman DL (2005) Bacterial diversity of metagenomic and PCR libraries from the Delaware River. Environmental Microbiology 7, 1883-1895.
23. Damste JS, Rijpstra WI, Hopmans EC, Weijers JW, Foesel BU, Overmann J, Dedysh SN (2011) 13, 16-Dimethyl octacosanedioic acid (iso-diabolic acid), a common membrane-spanning lipid of Acidobacteria subdivisions 1 and 3. Applied and Environmental Microbiology 77, 4147-4154.
24. Dekas AE, Poretsky RS, Orphan VJ (2009) Deep-sea archaea fix and share nitrogen in methane-consuming microbial consortia. Science 326, 422-426.
25. Delong EF (1992) Archaea in coastal marine environments. Proceedings of the National Academy of Sciences of the United States of America 89, 5685-5689.
26. Delong EF, Karl DM (2005) Genomic perspectives in microbial oceanography. Nature 437, 336-342.
27. Desantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL (2006a) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Applied and Environmental Microbiology 72, 5069-5072.
28. Desantis TZ Jr, Hugenholtz P, Keller K, Brodie EL, Larsen N, Piceno YM, Phan R, Andersen GL (2006b) NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Research 34, W394-W399.
29. Desantis TZ, Brodie EL, Moberg JP, Zubieta IX, Piceno YM, Andersen GL (2007) High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment. Microbial Ecology 53, 371-383.
30. Donachie SP, Bowman JP, On SL, Alam M (2005) Arcobacter halophilus sp. nov., the first obligate halophile in the genus Arcobacter. International Journal of Systematic and Evolutionary Microbiology 55, 1271-1277.
31. Eisenmann E, Beuerle J, Sulger K, Kroneck P, Schumacher W (1995) Lithotrophic growth of Sulfurospirillum deleyianum; with sulfide as electron donor coupled to respiratory reduction of nitrate to ammonia. Archives of Microbiology 164, 180-185.
32. Feingersch R, Suzuki MT, Shmoish M, Sharon I, Sabehi G, Partensky F, Beja O (2010) Microbial community genomics in eastern Mediterranean Sea surface waters. International Society for Microbial Ecology 4, 78-87.
33. Flanagan JL, Brodie EL, Weng L, Lynch SV, Garcia O, Brown R, Hugenholtz P, Desantis TZ, Andersen GL, Wiener-Kronish JP, Bristow J (2007) Loss of bacterial diversity during antibiotic treatment of intubated patients colonized with Pseudomonas aeruginosa. Journal of Clinical Microbiology 45, 1954-1962.
34. Francis CA, Beman JM, Kuypers MM (2007) New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation. International Society for Microbial Ecology 1, 19-27.
35. Freitag TE, Prosser JI (2003) Community structure of ammonia-oxidizing bacteria within anoxic marine sediments. Applied and Environmental Microbiology 69, 1359-1371.
36. Fuhrman JA, Mccallum K, Davis AA (1992) Novel major archaebacterial group from marine plankton. Nature 356, 148-149.
37. Grice K, Cao CQ, Love GD, Bottcher ME, Twitchett RJ, Grosjean E, Summons RE, Turgeon SC, Dunning W, Jin YG (2005) Photic zone euxinia during the Permian-Triassic superanoxic event. Science 307, 706-709.
38. Grossart H-P, Dziallas C, Tang KW (2009) Bacterial diversity associated with freshwater zooplankton. Environmental Microbiology Reports 1, 50-55.
39. Hall KJ, Northcote TG (1986) Conductivity-temperature standardization and dissolved solids estimation in a meromictic saline lake. Canadian Journal of Fisheries and Aquatic Sciences, 43, 2450-2454.
40. Huber T, Faulkner G, Hugenholtz P (2004) Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20, 2317-2319.
41. Hughes JB, Hellmann JJ, Ricketts TH, Bohannan BJM (2001) Counting the uncountable: statistical approaches to estimating microbial diversity. Applied and Environmental Microbiology 67, 4399-4406.
42. Humayoun SB, Bano N, Hollibaugh JT (2003) Depth distribution of microbial diversity in Mono Lake, a meromictic soda lake in California. Applied and Environmental Microbiology 69, 1030-1042.
43. Imhoff JF (2001) Transfer of Pfennigia purpurea tindall 1999 (Amoebobacter purpureus Eichler and Pfennig 1988) to the genus Lamprocystis as Lamprocystis purpurea comb. nov. International Journal of Systematic and Evolutionary Microbiology 51, 1699-1701.
44. Jehmlich N, Schmidt F, Hartwich M, Von Bergen M, Richnow HH, Vogt C (2008) Incorporation of carbon and nitrogen atoms into proteins measured by protein-based stable isotope probing (Protein-SIP). Rapid Communications in Mass Spectrometry 22, 2889-2897.
45. Jorgensen BB, Kuenen JG, Cohen Y (1979) Microbial transformations of sulfur-compounds in a stratified lake (Solar Lake, Sinai). Limnology and Oceanography 24, 799-822.
46. Jung S, Zeikus JG, Hollingsworth RI (1994) A new family of very long chain alpha, omega-dicarboxylic acids is a major structural fatty acyl component of the membrane lipids of Thermoanaerobacter ethanolicus 39E. Journal of Lipid Research 35, 1057-1065.
47. Klepac-Ceraj V, Lemon KP, Martin TR, Allgaier M, Kembel SW, Knapp AA, Lory S, Brodie EL, Lynch SV, Bohannan BJ, Green JL, Maurer BA, Kolter R (2010) Relationship between cystic fibrosis respiratory tract bacterial communities and age, genotype, antibiotics and Pseudomonas aeruginosa. Environmental Microbiology 12, 1293-1303.
48. Konneke M, Bernhard AE, De La Torre JR, Walker CB, Waterbury JB, Stahl DA (2005) Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437, 543-546.
49. Koopmans MP, Koster J, Vankaampeters HME, Kenig F, Schouten S, Hartgers WA, Deleeuw JW, Damste JSS (1996) Diagenetic and catagenetic products of isorenieratene: molecular indicators for photic zone anoxia. Geochimica Et Cosmochimica Acta 60, 4467-4496.
50. Kuever J, Konneke M, Galushko A, Drzyzga O (2001) Reclassification of Desulfobacterium phenolicum as Desulfobacula phenolica comb. nov and description of strain Sax(T) as Desulfotignum balticum gen. nov., sp nov. International Journal of Systematic and Evolutionary Microbiology 51, 171-177.
51. Kuypers MMM, Blokker P, Erbacher J, Kinkel H, Pancost RD, Schouten S, Damste JSS (2001) Massive expansion of marine archaea during a mid-Cretaceous oceanic anoxic event. Science 293, 92-94.
52. Lane DJ (1991) 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics (eds Stackebrandt E, Goodfellow M). John Wiley and Sons, New York, NY, pp. 115-148.
53. Lemon KP, Klepac-Ceraj V, Schiffer HK, Brodie EL, Lynch SV, Kolter R (2010) Comparative analyses of the bacterial microbiota of the human nostril and oropharynx. American Society for Microbiology 1, pii: e00129-10.
54. Ley RE, Harris JK, Wilcox J, Spear JR, Miller SR, Bebout BM, Maresca JA, Bryant DA, Sogin ML, Pace NR (2006) Unexpected diversity and complexity of the Guerrero Negro hypersaline microbial mat. Applied and Environmental Microbiology 72, 3685-3695.
55. Liesack W, Bak F, Kreft JU, Stackebrandt E (1994) Holophaga foetida gen. nov., sp. nov., a new, homoacetogenic bacterium degrading methoxylated aromatic compounds. Archives of Microbiology 162, 85-90.
56. Lliros M, Casamayor EO, Borrego C (2008) High archaeal richness in the water column of a freshwater sulfurous karstic lake along an interannual study. FEMS (Federation of European Microbiological Societies) Microbiology - Ecology 66, 331-342.
57. Lloyd KG, Lapham L, Teske A (2006) An anaerobic methane-oxidizing community of ANME-1b archaea in hypersaline Gulf of Mexico sediments. Applied and Environmental Microbiology 72, 7218-7230.
58. Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar, Buchner A, Lai T, Steppi S, Jobb G, Forster W, Brettske I, Gerber S, Ginhart AW, Gross O, Grumann S, Hermann S, Jost R, Konig A, Liss T, Lussmann R, May M, Nonhoff B, Reichel B, Strehlow R, Stamatakis A, Stuckmann N, Vilbig A, Lenke M, Ludwig T, Bode A, Schleifer KH (2004) ARB: a software environment for sequence data. Nucleic Acids Research 32, 1363-1371.
59. Lyons TW, Anbar AD, Severmann S, Scott C, Gill BC (2009) Tracking euxinia in the ancient ocean: a multiproxy perspective and proterozoic case study. Annual Review of Earth and Planetary Sciences 37, 507-534.
60. Maidak BL, Cole JR, Lilburn TG, Parker CT Jr, Saxman PR, Farris RJ, Garrity GM, Olsen GJ, Schmidt TM, Tiedje JM (2001) The RDP-II (Ribosomal Database Project). Nucleic Acids Research 29, 173-174.
61. Moeseneder MM, Arrieta JM, Herndl GJ (2005) A comparison of DNA- and RNA-based clone libraries from the same marine bacterioplankton community. FEMS (Federation of European Microbiological Societies) Microbiology - Ecology 51, 341-352.
62. Nabbefeld B, Grice K, Twitchett RJ, Summons RE, Hays L, Bottcher ME, Asif M (2010) An integrated biomarker, isotopic and palaeoenvironmental study through the Late Permian event at Lusitaniadalen, Spitsbergen. Earth and Planetary Science Letters 291, 84-96.
63. Northcote TG, Hall KJ (1983) Limnological contrasts and anomalies in 2 adjacent saline lakes. Hydrobiologia 105, 179-194.
64. Not F, Del Campo J, Balague V, De Vargas C, Massana R (2009) New insights into the diversity of marine picoeukaryotes. PLoS One 4, e7143.
65. Overmann J, Beatty JT, Hall KJ, Pfennig N, Northcote TG (1991) Characterization of a dense, purple sulfur bacterial layer in a meromictic salt lake. Limnology and Oceanography 36, 846-859.
66. Overmann J, Sandmann G, Hall KJ, Northcote TG (1993) Fossil carotenoids and paleolimnology of meromictic Mahoney Lake, British-Columbia, Canada. Aquatic Sciences 55, 31-39.
67. Overmann J, Beatty JT, Hall KJ (1994) Photosynthetic activity and population-dynamics of amoebobacter-purpureus in a meromictic saline lake. FEMS (Federation of European Microbiological Societies) Microbiology - Ecology 15, 309-319.
68. Overmann J, Beatty JT, Hall KJ (1996a) Purple sulfur bacteria control the growth of aerobic heterotrophic bacterioplankton in a meromictic salt lake. Applied and Environmental Microbiology 62, 3251-3258.
69. Overmann J, Beatty JT, Krouse HR, Hall KJ (1996b) The sulfur cycle in the chemocline of a meromictic salt lake. Limnology and Oceanography 41, 147-156.
70. Pati A, Gronow S, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Lucas S, Tice H, Cheng JF, Han C, Chertkov O, Bruce D, Tapia R, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Detter JC, Rohde M, Goker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC (2010) Complete genome sequence of Arcobacter nitrofigilis type strain (CI). Standards in Genomic Sciences 2, 300-308.
71. Polz MF, Harbison C, Cavanaugh CM (1999) Diversity and heterogeneity of epibiotic bacterial communities on the marine nematode Eubostrichus dianae. Applied and Environmental Microbiology 65, 4271-4275.
72. Puchkova NN, Imhoff JF, Gorlenko VM (2000) Thiocapsa litoralis sp. nov., a new purple sulfur bacterium from microbial mats from the White Sea. International Journal of Systematic and Evolutionary Microbiology 50(Pt 4), 1441-1447.
73. Pukall R, Buntefuss D, Fruhling A, Rohde M, Kroppenstedt RM, Burghardt J, Lebaron P, Bernard L, Stackebrandt E (1999) Sulfitobacter mediterraneus sp. nov., a new sulfite-oxidizing member of the alpha-Proteobacteria. International Journal of Systematic Bacteriology 49(Pt 2), 513-519.
74. Quaiser A, Ochsenreiter T, Lanz C, Schuster SC, Treusch AH, Eck J, Schleper C (2003) Acidobacteria form a coherent but highly diverse group within the bacterial domain: evidence from environmental genomics. Molecular Microbiology 50, 563-575.
75. Rappe MS, Giovannoni SJ (2003) The uncultured microbial majority. Annual Review of Microbiology 57, 369-394.
76. Rathgeber C, Yurkova N, Stackebrandt E, Schumann P, Beatty JT, Yurkov V (2005) Roseicyclus mahoneyensis gen. nov., sp. nov., an aerobic phototrophic bacterium isolated from a meromictic lake. International Journal of Systematic and Evolutionary Microbiology 55, 1597-1603.
77. Rathgeber C, Yurkova N, Stackebrandt E, Schumann P, Humphrey E, Beatty JT, Yurkov V (2007) Porphyrobacter meromictius sp. nov., an appendaged bacterium, that produces Bacteriochlorophyll a. Current Microbiology 55, 356-361.
78. Repeta DJ (1993) A high-resolution historical record of holocene anoxygenic primary production in the black-sea. Geochimica Et Cosmochimica Acta 57, 4337-4342.
79. Schaeffer P, Adam P, Wehrung P, Albrecht P (1997) Novel aromatic carotenoid derivatives from sulfur photosynthetic bacteria in sediments. Tetrahedron Letters 38, 8413-8416.
80. Schatz MC, Phillippy AM, Gajer P, Desantis TZ, Andersen GL, Ravel J (2010) Integrated microbial survey analysis of prokaryotic communities for the PhyloChip microarray. Applied and Environmental Microbiology 76, 5636-5638.
81. Schlesner H, Jenkins C, Staley J (2006) The phylum verrucomicrobia: a phylogenetically heterogeneous bacterial group. In: The Prokaryotes (eds Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E). Springer, New York, NY, pp. 881-896.
82. Sievert SM, Wieringa EB, Wirsen CO, Taylor CD (2007) Growth and mechanism of filamentous-sulfur formation by Candidatus Arcobacter sulfidicus in opposing oxygen-sulfide gradients. Environmental Microbiology 9, 271-276.
83. Sikorski J, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Lucas S, Chen F, Tice H, Cheng JF, Saunders E, Bruce D, Goodwin L, Pitluck S, Ovchinnikova G, Pati A, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Chain P, Land M, Hauser L, Chang YJ, Jeffries CD, Brettin T, Detter JC, Han C, Rohde M, Lang E, Spring S, Goker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP (2010) Complete genome sequence of Sulfurospirillum deleyianum type strain (5175). Standards in Genomic Sciences 2, 149-157.
84. Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, Neal PR, Arrieta JM, Herndl GJ (2006) Microbial diversity in the deep sea and the underexplored "rare biosphere". Proceedings of the National Academy of Sciences of the United States of America 103, 12115-12120.
85. Sorokin DY, Muyzer G (2010) Bacterial dissimilatory MnO(2) reduction at extremely haloalkaline conditions. Extremophiles 14, 41-46.
86. Sorokin DY, Foti M, Pinkart HC, Muyzer G (2007) Sulfur-oxidizing bacteria in Soap Lake (Washington State), a meromictic, haloalkaline lake with an unprecedented high sulfide content. Applied and Environmental Microbiology 73, 451-455.
87. Stamatakis A, Hoover P, Rougemont J (2008) A rapid bootstrap algorithm for the RAxML Web servers. Systematic Biology 57, 758-771.
88. Teske A, Sorensen KB (2008) Uncultured archaea in deep marine subsurface sediments: have we caught them all? International Society for Microbial Ecology 2, 3-18.
89. Thrash JC, Coates JD (2011) Phylum XVII. Acidobacteria phyl. nov. In Bergey's Manual of Systematic Bacteriology (ed Whitman WB), Springer, New York, NY, 725-735.
90. Tokunaga TK, Wan JM, Kim YM, Daly RA, Brodie EL, Hazen TC, Herman D, Firestone MK (2008) Influences of organic carbon supply rate on uranium bioreduction in initially oxidizing, contaminated sediment. Environmental Science & Technology 42, 8901-8907.
91. Tonolla M, Demarta A, Peduzzi R, Hahn D (1999) In situ analysis of phototrophic sulfur bacteria in the chemocline of meromictic Lake Cadagno (Switzerland). Applied and Environmental Microbiology 65, 1325-1330.
92. Tonolla M, Demarta A, Peduzzi S, Hahn D, Peduzzi R (2000) In situ analysis of sulfate-reducing bacteria related to Desulfocapsa thiozymogenes in the chemocline of meromictic Lake Cadagno (Switzerland). Applied and Environmental Microbiology 66, 820-824.
93. Tonolla M, Peduzzi S, Hahn D, Peduzzi R (2003) Spatio-temporal distribution of phototrophic sulfur bacteria in the chemocline of meromictic Lake Cadagno (Switzerland). FEMS (Federation of European Microbiological Societies) Microbiology - Ecology 43, 89-98.
94. Treusch AH, Leininger S, Kletzin A, Schuster SC, Klenk HP, Schleper C (2005) Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling. Environmental Microbiology 7, 1985-1995.
95. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science, 304, 66-74.
96. Weijers JWH, Schouten S, Hopmans EC, Geenevasen JAJ, David ORP, Coleman JM, Pancost RD, Damste JSS (2006) Membrane lipids of mesophilic anaerobic bacteria thriving in peats have typical archaeal traits. Environmental Microbiology 8, 648-657.
97. Widdel F, Pfenning N (1982) Studies on dissimilatory sulfate-reducing bacteria that decompose fatty acids. II. Incomplete oxidation of propionate by Desulfobulbus propionicus gen. nov., sp. nov. Archives of Microbiology 131, 360-365.
98. Wirsen CO, Sievert SM, Cavanaugh CM, Molyneaux SJ, Ahmad A, Taylor LT, Delong EF, Taylor CD (2002) Characterization of an autotrophic sulfide-oxidizing marine Arcobacter sp. that produces filamentous sulfur. Applied and Environmental Microbiology 68, 316-325.
99. Wolfe RS, Penning N (1977) Reduction of sulfur by spirillum 5175 and syntrophism with Chlorobium. Applied and Environmental Microbiology 33, 427-433.
100. Wrighton KC, Agbo P, Warnecke F, Weber KA, Brodie EL, Desantis TZ, Hugenholtz P, Andersen GL, Coates JD (2008) A novel ecological role of the Firmicutes identified in thermophilic microbial fuel cells. International Society for Microbial Ecology 2, 1146-1156.
101. Yurkova N, Rathgeber C, Swiderski J, Stackebrandt E, Beatty JT, Hall KJ, Yurkov V (2002) Diversity, distribution and physiology of the aerobic phototrophic bacteria in the mixolimnion of a meromictic lake. FEMS (Federation of European Microbiological Societies) Microbiology - Ecology 40, 191-204.