Microbial ecology of the stratified water column of the Black Sea as revealed by a comprehensive biomarker study

Organic Geochemistry

Volumn 38, Issue 12, 2007, Pages 2070-2097

  Wakeham, Stuart G ^a   Amann, Rudi ^b   Freeman, Katherine H ^c   Hopmans, Ellen C ^d   Jørgensen, Bo Barker ^b   Putnam, Isabell F ^a   Schouten, Stefan ^d   Sinninghe Damsté, Jaap S ^d   Talbot, Helen M ^e   Woebken, Dagmar ^b  

^a SKIDAWAY INSTITUTE OF OCEANOGRAPHY   (United States)

^b MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY   (Germany)

^c PENNSYLVANIA STATE UNIVERSITY   (United States)

^d ROYAL NETHERLANDS INSTITUTE FOR SEA RESEARCH   (Netherlands)

^e NEWCASTLE UNIVERSITY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

MICROBIAL COMMUNITIES; MICROBIAL ECOLOGY; PARTICULATE MATTER; STRATIFIED WATER COLUMN;

BACTERIA; BIOGEOCHEMISTRY; BIOMARKERS; ECOLOGY; LIPIDS; OXIDATION;

WATER ANALYSIS;

BACTERIOPLANKTON; BIOGEOCHEMISTRY; BIOMARKER; LIPID; MICROBIAL COMMUNITY; MICROBIAL ECOLOGY; OXIDATION; PARTICULATE MATTER; PROKARYOTE; SULFATE-REDUCING BACTERIUM; WATER COLUMN;

BLACK SEA; EURASIA;

ARCHAEA; BACTERIA (MICROORGANISMS); CRENARCHAEOTA; EPSILONPROTEOBACTERIA; EURYARCHAEOTA; PROKARYOTA;

EID: 36148976101     PISSN: 01466380     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.orggeochem.2007.08.003     Document Type: Article

References (190)

1. Albert D.B., Taylor C., and Martens C.S. Sulfate reduction rates and low molecular weight fatty acid concentrations in the water column and surficial sediments of the Black Sea. Deep-Sea Research 42 (1995) 1239-1260
2. Amann R.I., Binder B.J., Olsen R.J., Chisolm S.W., Devereux R., and Stahl D.A. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Applied and Environmental Microbiology 56 (1990) 1919-1925
3. Amann R.I., Ludwig W., and Schleifer K.-H. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbial Reviews 59 (1995) 143-169
4. Beedle A.S., Munday K.A., and Wilton D.C. Studies on the biosynthesis of tetrahymanol in Tetrahymena pyriformis. The mechanism of inhibition by cholesterol. Biochemistry Journal 142 (1974) 57-64
5. Belt S.T., Allard W.G., Massé G., Robert J.-M., and Rowland S.J. Highly branched isoprenoids (HBIs): identification of the most common and abundant sedimentary isomers. Geochimica et Cosmochimica Acta 64 (2000) 3839-3851
6. 30 highly branched isoprenoid alkenes (rhizenes) in the marine diatom Rhizosolenia setigera. Tetrahedron Letters 42 (2001) 5583-5585
7. Benli, A.H., 1987. Investigation of plankton distribution in the southern Black Sea and its effect on particle flux. SCOPE/UNEP Sonderband Heft 62, Mitteilungen aus dem Geologische-Palaeontologischen Institute der Universitaet Hamburg, pp. 77-87.
8. Bian, L., Hinrichs, K.-U., Xie, T., Brassell, S.C., Iversen, N., Fossing, H., Jørgensen, B.B., Hayes, J.M., 2001. Algal and archaeal polyisoprenoids in a recent marine sediment: molecular isotopic evidence for anaerobic oxidation of methane. Geochemistry Geophysics Geosystems, 2, Paper number 2000GC000112.
9. Bird D.F., and Karl D.M. Microbial biomass and population diversity in the upper water column of the Black Sea. Deep-Sea Research 38 Suppl. 2 (1991) S1069-S1082
10. Bisseret P., Zundel M., and Rohmer M. Prokaryotic triterpenoids 2. 2β-Methylhopanoids from Methylobacterium organophilum and Nostoc muscorum, a new series of prokaryotic triterpenoids. European Journal of Biochemistry 150 (1985) 29-34
11. Blumenberg M., Seifert R., Reitner J., Pape T., and Michaelis W. Membrane lipid patterns typify distinct anaerobic methanotrophic consortia. Proceedings National Academy of Sciences 30 (2004) 11111-11116
12. Blumenberg M., Krüger M., Nauhaus K., Talbot H.M., Oppermann B.I., Seifert R., Pape T., and Michaelis W. Biosynthesis of hopanoids by sulfate-reducing bacteria (genus Desulfovibrio). Environmental Microbiology 8 (2006) 1220-1227
13. Blumenberg M., Seifert R., and Michaelis W. Aerobic methanotrophy in the oxic anoxic transition zone of the Black Sea water column. Organic Geochemistry 38 (2007) 84-91
14. Boetius A., Ravenschlag K., Schubert C.J., Rickert D., Widdel F., Gieseke A., Amann R., Jørgensen B.B., Witte U., and Pfannkuche O. A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature 407 (2000) 623-626
15. Bowman J.P., Skerratt J.H., Nichols P.D., and Sly L.I. Phospholipid fatty acids and lipopolysaccharide fatty acid signature lipids in methane-oxidizing bacteria. FEMS Microbial Ecology 85 (1991) 15-22
16. Brassell S.C., Wardroper A.M.K., Thomson I.D., Maxwell J.R., and Eglinton G. Specific acyclic isoprenoids as biological markers of methanogenic bacteria in marine sediments. Nature 290 (1981) 693-696
17. Bravo J.-M., Perzel M., Härtner T., Kannenberg E.L., and Rohmer M. Novel methylated triterpenoids of the gammacerane series from the nitrogen-fixing bacterium Bradyrhizobium japonicum USDA 110. European Journal of Biochemistry 268 (2001) 1323-1331
18. Conner R.L., Landry J.R., Burns C.H., and Mallory F.B. Cholesterol inhibition of pentacyclic triterpenoid biosynthesis in Tetrahymena pyriformis. Journal of Protozoology 15 (1968) 600-605
19. Coolen M.J.L., Abbas B., van Bleiswijk J., Hopmans E.C., Kuypers M.M., Wakeham S.G., and Sinninghe Damsté J.S. Putative ammonia-oxidizing Crenarchaeota thrive in suboxic waters of the Black Sea: a basin-wide ecological study using 16S ribosomal and functional genes and membrane lipids. Environmental Microbiology 9 (2007) 1001-1016
20. Cvejic J.H., Bodrossy L., Kovács K.L., and Rohmer M. Bacterial triterpenoids of the hopane series from the methanotrophic bacteria Methylocaldum spp.: phylogenetic implications and first evidence for an unsaturated aminobacteriohopanepolyol. FEMS Microbiology Letters 182 (2000) 361-365
21. Cvejic J.H., Rosa Putra S., El-Beltagy A., Hattori R., Hattori T., and Rohmer M. Bacterial triterpenoids of the hopane series as biomarkers for the chemotaxonomy of Burkholderia, Pseudomonas and Ralstonia spp. FEMS Microbiology Letters 183 (2000) 295-299
22. Daims H., Brühl A., Amann R., Schleifer K.-H., and Wagner M. The domain-specific probe EUB338 is insufficient for the detection of all Bacteria: development and evaluation of a more comprehensive probe set. Systematic and Applied Microbiology 22 (1999) 434-444
23. 2 production by the anammox reaction in the anoxic water column of Gulfo Dulce, Costa Rica. Nature 422 (2003) 606-608
24. DeLong E.F., Taylor L.T., Marsh T.L., and Preston C.M. Visualization and enumeration of marine planktonic archaea and bacteria using polyribonucleotide probes and fluorescent in situ hybridization. Applied and Environmental Microbiology 65 (1999) 5554-5563
25. De Rosa M., and Gambacorta A. The lipids of archaebacteria. Progress in Lipid Research 27 (1988) 153-175
26. Devol A.H. Solution to a marine mystery. Nature 422 (2003) 575-576
27. Dickman M., and Artuz I. Mass mortality of photosynthetic bacteria as a mechanism for dark lamina formation in sediments of the Black Sea. Nature 275 (1978) 191-193
28. Dowling N.J.E., Widdel F., and White D.C. Phospholipid ester-linked fatty acid biomarkers of acetate-oxidizing sulfate-reducers and other sulfide-forming bacteria. Journal of General Microbiology 132 (1986) 1815-1825
29. Dunkelblum E., Tan S.H., and Silk P.J. Double-bond location in monounsaturated fatty acids by dimethyl disulfide derivatization and mass spectrometry: application to analysis of fatty acids in pheromone glands of four Lepidoptera. Journal of Chemical Ecology 11 (1985) 265-277
30. Durisch-Kaiser E., Klauser L., Wehrli B., and Schubert C. Evidence of intense archaeal and bacterial methanotrophic activity in the Black Sea water column. Applied and Environmental Microbiology 71 (2005) 8099-8106
31. 25 irregular isoprenoids. Naturwissenschaften 86 (1999) 295-300
32. Elvert M., Whiticar M.J., and Suess E. Diploptene in varved sediments of Saanich Inlet: indicator of increasing bacterial activity under anaerobic conditions during the Holocene. Marine Geology 174 (2001) 371-383
33. Elvert M., Boetius A., Knittel K., and Jørgensen B.B. Characterization of specific membrane fatty acids as chemotaxonomic markers for sulfate-reducing bacteria involved in anaerobic oxidation of methane. Geomicrobiology Journal 20 (2003) 403-419
34. Elvert M., Hopmans E.C., Treude T., Boetius A., and Suess E. Spatial variations of methanogenic consortia at cold methane seeps: implications from high-resolution molecular and isotopic approach. Geobiology 3 (2005) 195-209
35. Fenchel T., and Finlay B.J. The biology of free-living anaerobic ciliates. European Journal of Protistology 26 (1991) 201-215
36. Fisher W.W., Summons R.E., and Pearson A. Targeted genomic detection of biosynthetic pathways; anaerobic production of hopanoid biomarkers by a common sedimentary microbe. Geobiology 3 (2005) 33-40
37. Francis C.A., Roberts K.J., Beman J.M., Santoro A.F., and Oakley B.B. Ubiquity and diversity of ammonium-oxidizing archaea in water columns and sediments of the ocean. Proceedings of the National Academy of Sciences 102 (2005) 14683-14688
38. Freeman K.H., and Wakeham S.G. Variations in the distributions and isotopic compositions of alkenones in Black Sea particles and sediments. In: Eckardt C.B., Maxwell J.R., Larter S.R., and Manning D.A.C. (Eds). Advances in Organic Geochemistry 1991. Organic Geochemistry vol. 19 (1992), Pergamon Press 277-285
39. Fuchs B.M., Woebken D., Zubkov M.V., Burkill P., and Amann R. Molecular identification of picoplankton populations in contrasting waters of the Arabian Sea. Aquatic Microbial Ecology 39 (2005) 145-157
40. Gal'chenko V.F., Abranochkina F.N., Bezukova L.V., Sokolova E.N., and Ivanov M.V. Species composition of the aerobic methanotrophic microflora of the Black Sea. Microbiology (Translated from Mikrobiologiya) 57 (1988) 305-311
41. Glazer B.T., Luther III G.W., Konovalov S.K., Friederich G.E., Trouwborst R.F., and Romanov A.S. Spatial and temporal variability of the Black Sea suboxic zone. Deep-Sea Research II 53 (2006) 1756-1768
42. Guckert J.B., Ringelberg D.B., White D.C., Hanson R.S., and Bratina B.J. Membrane fatty acids as phenotypic markers in the polyphasic taxonomy of methylotrophs within the proteobacteria. Journal General Microbiology 137 (1991) 2631-2641
43. Guhl B.E., and Finlay B.J. Anaerobic predatory ciliates track seasonal migrations of planktonic photosynthetic bacteria. FEMS Microbiology Letters 107 (1993) 313-316
44. Hallam S.J., Mincer T.J., Preston C.M., Roberts K., Richardson P.M., and Delong E.F. Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota. PLoS Biology 4 (2006) 520-536 e95
45. Hamersley M.R., Lavik G., Woebken D., Rattray J.E., Lam P., Hopmans E., Sinninghe Damsté J.S., Krüger S., Graco M., Gutiérrez D., and Kuypers M.M.M. Anaerobic ammonium oxidation in the Peruvian oxygen minimum zone. Limnology and Oceanography 52 (2007) 923-933
46. Härtner T., Straub K.L., and Kannenberg E. Occurrence of hopanoid lipids in anaerobic Geobacter species. FEMS Microbiology Letters 243 (2005) 59-64
47. Harvey H.R., and McManus G.B. Marine ciliates as a widespread source of tetrahymanol and hopan-3β-ol in sediments. Geochimica et Cosmochimica Acta 55 (1991) 3387-3390
48. Harvey H.R., Fallon R.D., and Patton J.S. The effect of organic matter and oxygen on the degradation of bacterial membrane lipids in marine sediments. Geochimica et Cosmochimica Acta 50 (1986) 795-804
49. Hebting Y., Schaeffer P., Behrens A., Adam P., Schmitt G., Schneckenburger P., Bernasconi S.M., and Albrecht P. Biomarker evidence for a major preservation pathway of sedimentary organic carbon. Science 312 (2006) 1627-1631
50. Hedges J.I., and Stern J.H. Carbon and nitrogen determinations of carbonate-containing solids. Limnology and Oceanography 29 (1984) 657-663
51. Herndl G.J., Reinthaler T., Teira F., van Aken H., Veth C., Pernthaler A., and Pernthaler J. Contribution of Archaea to total prokaryotic production in the deep Atlantic Ocean. Applied and Environmental Microbiology 71 (2005) 2303-2309
52. Hinrichs K.-U., and Boetius A. The anaerobic oxidation of methane: new insights in microbial ecology and biogeochemistry. In: Wefer G., Billett D., Hebbeln D., Jørgensen B., Schlüter M., and Van Weering T. (Eds). Ocean Margin Systems (2002), Springer-Verlag, Berlin 457-477
53. Hinrichs K.-U., Summons R.E., Orphan V., Sylva S.P., and Hayes J.M. Molecular and isotopic analysis of anaerobic methane-oxidizing communities in marine sediments. Organic Geochemistry 31 (2000) 1685-1701
54. Holler S., Pfennig N., Nuenlist S., and Rohmer M. Effect of a non-methanogenic symbiont and exogenous stigmasterol on the viability and tetrahymanol content of an anaerobic ciliate Tetrahymena compressum. European Journal Protistology 29 (1993) 42-48
55. Holzer G., Oró J., and Tornabene T.G. Gas chromatographic-mass spectrometric analysis of neutral lipids from methanogenic and thermoacidophilic bacteria. Journal of Chromatography 18 (1979) 795-809
56. Hopmans E.C., Schouten S., Pancost R.D., van der Meer M.T.J., and Sinninghe Damsté J.S. Analysis of intact tetraether lipids in archaeal cell material and sediments by high performance liquid chromatography/atmospheric pressure chemical ionization mass spectrometry. Rapid Communications in Mass Spectrometry 14 (2000) 585-589
57. Hopmans E.C., Kienhuis M.V.M., Rattray J.E., Jaeschke A., Schouten S., and Sinninghe Damsté J.S. Improved analysis of ladderane lipids in biomass and sediments using high-performance liquid chromatography/atmospheric pressure chemical ionization tandem mass spectrometry. Rapid Communications in Mass Spectrometry 20 (2006) 2099-2103
58. Hulth S., Aller R.C., and Gilbert F. Coupled anoxic nitrification/manganese reduction in marine sediments. Geochemica et Cosmochimica Acta 63 (1999) 49-66
59. Imhoff J.F. Taxonomy, phylogeny and general ecology of anoxygenic phototrophic bacteria. In: Mann N.H., and Carr N.G. (Eds). Photosynthetic Prokaryotes (1992), Plenum Press, New York 53-85
60. Ingalls A.E., Shah S.R., Hansman R.L., Aluwihare L.I., Santos G.M., Druffel E.R.M., and Pearson A. Quantifying archaeal community autotrophy in the mesopelagic ocean using natural radiocarbon. Proceedings of the National Academy of Sciences 103 (2006) 6442-6447
61. Jaeschke A., Hopmans E.C., Wakeham S.G., Schouten S., and Sinninghe Damsté J.S. The presence of ladderane lipids in the oxygen minimum zone of the Arabian Sea indicates nitrogen loss thought anammox. Limnology and Oceanography 52 (2007) 780-786
62. Jannasch H.W., Wirsen C.O., and Molyneaux S. Chemoautotropic sulfur oxidizing bacteria from the Black Sea. Deep-Sea Research 38 Suppl. 2 (1991) S1105-S1120
63. Jørgensen B.B., Fossing H., Wirsen C.O., and Jannasch H.W. Sulfide oxidation in the anoxic Black Sea chemocline. Deep-Sea Research 38 Suppl. 2 (1991) S1083-S1103
64. Kaneda T. Iso- and anteiso-fatty acids in bacteria - Biosynthesis, function, and taxonomic significance. Microbiology Reviews 55 (1991) 288-302
65. Karl D.M., and Knauer G.A. Microbial production and particle flux in the upper 350 m of the Black Sea. Deep-Sea Research 38 Suppl. 2 (1991) S921-S942
66. Karner M.B., DeLong E.F., and Karl D.M. Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature 409 (2001) 507-510
67. Kartal B., Kuypers M.M.M., Lavik G., Schalk J., Op den Camp H.J.M., Jetten M.S.M., and Strous M. Anammox bacteria disguised as denitrifiers: nitrate reduction to dinitrogen gas via nitrite and ammonium. Environmental Microbiology 9 (2007) 635-642
68. Kempe S., Diercks A.R., Liebezeit G., and Prange A. Geochemical and structural aspects of the pycnocline in the Black Sea. In: Izdar E., and Murray J.W. (Eds). Black Sea Oceanography (1991), Kluwer 89-110
69. 4) distributions in the water columns of the Black Sea and Cariaco Basin. Global Biogeochemical Cycles 20 GB4004, doi:10.1029/2005TGB002571.
70. Kessler J.D., Reeburgh W.S., Southon J., Seifert R., Michaelis W., and Tyler S.C. Basin-wide estimates of the input of methane from seeps and clathrates to the Black Sea. Earth and Planetary Letters 243 (2006) 366-375
71. Kimble B.J., Maxwell J.R., Philp P.R., Eglinton G., Albrecht P., Ensminger A., Arpino P., and Ourrison G. Tri- and tetraterpenoid hydrocarbons in the Messel Shale. Geochimica et Cosmochimica Acta 38 (1974) 1165-1181
72. Kirkpatrick J., Oakley B., Fuchsman C., Srinivasan S., Staley J.T., and Murray J.W. Diversity and distribution of Planctomycetes and related bacteria in the suboxic zone of the Black Sea. Applied and Environmental Microbiology 72 (2006) 3079-3083
73. Kleeman G., Poralla K., Englert G., Kjosen H., Liaaen-Jansen N., Nuenlist S., and Rohmer M. Tetrahyamanol from phototrophic bacterium Rhodopseudomonas palustris: first report of a gammacerane triterpenoid from a prokaryote. Journal of General Microbiology 136 (1990) 2551-2553
74. Knani M., Corpe W.A., and Rohmer M. Bacterial hopanoids from the pink-pigmented facultative methylotrophs (PPFMs) and from green plant surfaces. Microbiology 140 (1994) 2755-2759
75. Knoblauch C., Sahm K., and Jørgensen B.B. Psychrophilic sulfate-reducing bacteria silated from permanently cold arctic marine sediments: description of Desulfofrigus oceanense gen. nov., sp. nov., Desulfofirgis fragile sp. nov., Desulfofaba gelida gen. nov. sp. nov., Desulfotalea psychrophilia gen. nov. sp. nov. and Desulfotalea arctica sp. nov. International Journal of Sysematic Bacteriology 49 (1999) 1631-1643
76. Koenneke M., Bernhard A.E., de la Torre J.R., Walker C.B., Waterbury J.B., and Stahl D.A. Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437 (2005) 543-546
77. Koga Y., Nishihara M., Morii H., and Akagawa-Matsushita M. Ether polar lipids of methanogenic bacteria: structures and comparative aspects, and biosynthesis. Microbiology Reviews 57 (1993) 164-182
78. Konovalov S.K., Murray J.W., Luther G.W., Buesseler K.O., Friederich G., Tebo B.M., Samodurov A.S., Gregoire M., Ivanov L.I., Romanov A.S., Clement B., and Murray K. Oxygen fluxes, redox processes and the suboxic zone in the Black Sea. Presented at Second International Conference on Oceanography of Eastern Mediterranean and the Black Sea, 14-18 October 2002, Ankara, Turkey. In: Aysen Yilmaz A. (Ed). Oceanography of the Eastern Mediterranean and Black Sea (2003), TUBITAK Publishers, Turkey 566-577
79. Konovalov S.K., Murray J.W., and Luther III G.W. Basic processes of Black Sea biogeochemistry. Oceanography 18 (2005) 24-35
80. Kuypers M.M., Sliekers A.O., Lavik G., Schmid M., Jørgensen B.B., Sinninghe Damsté J.S., Strous M., and Jetten M.S.M. Anaerobic ammonium oxidation by anammox bacteria in the Black Sea. Nature 422 (2003) 608-611
81. Kuypers M.M.M., Lavik G., Woebken D., Schmid M., Fuchs B., Amann R., Jørgensen B.B., and Jettin M.S.M. Massive nitrogen loss from the Benguela upwelling system through anaerobic ammonium oxidation. Proceedings National Academy Science 102 (2005) 6478-6483
82. Kuypers M.M.M., Lavik G., and Thamdrup B. Anaerobic ammonium oxidation in the marine environment. In: Neretin L.N. (Ed). Past and Present Water Column Anoxia (2006), Springer 311-335
83. Lam, P., Jansen, M.M., Lavik, G., McGinnis, D.F., Müller, B., Schubert, C., Amann, R., Thamdrup, B., Kuypers, M.M.M., 2007. Linking crenarchaeal and bacterial nitrification to anammox in the Black Sea. Proceedings of the National Academy of Sciences doi:10.1073/pnas.o611081104.
84. Lewis B.L., and Landing W.M. The biogeochemistry of manganese and iron in the Black Sea. Deep-Sea Research 38 Suppl. 2 (1991) S773-S803
85. Lin X., Wakeham S.G., Putnam I.F., Astor Y.M., Scranton M.I., Chistoserdov A.Y., and Taylor G.T. Vertical distributions of prokaryotic assemblages in the anoxic Cariaco Basin and Black Sea compared using fluorescence in situ hybridization (FISH) techniques. Applied and Environmental Microbiology 72 (2006) 2679-2690
86. Londry K.L., and Des Marais D.J. Stable carbon isotope fractionation by sulfate-reducing bacteria. Applied and Environmental Microbiology 69 (2003) 2942-2949
87. Londry K.L., Jahnke L.L., and Des Marais D.J. Stable carbon isotope ratios of lipid biomarkers of sulfate-reducing bacteria. Applied and Environmental Microbiology 70 (2004) 745-751
88. Lovely D.R., Giovannoni S.J., White D.C., Champine J.E., Phillips E.J.P., Gorby Y.A., and Goodwin S. Geobacter metallireducens gen. nov., a microorganism capable of coupling the complete oxidation of organic compounds to the reduction of iron and other metals. Archives of Microbiology 159 (1993) 336-344
89. Luther III G.W., Sunby B., Lewis B.L., Brendel P.J., and Silverberg N. Interactions of manganese with the nitrogen cycle: alternative pathways to dinitrogen. Geochemica et Cosmochimica Acta 61 (1997) 4043-4052
90. Madrid V.M., Taylor G.T., Scranton M.I., and Chistoserdov A.Y. Phylogenetic diversity of bacterial and archaeal communities in the anoxic zone of the Cariaco Basin. Applied and Environmental Microbiology 67 (2001) 1663-1674
91. Makula R.A. Phospholipid composition of methane-oxidizing bacteria. Journal of Bacteriology 134 (1978) 771-777
92. Manske A.K., Glaeser J.M., Kuypers M.M.M., and Overmann J. Physiology and phylogeny of green sulfur bacteria forming a monospecific phototrophic assemblage at a depth of 100 m in the Black Sea. Applied Environmental Microbiology 71 (2005) 8049-8060
93. Manz W., Eisenbrecher M., Neu T.R., and Szewzyk U. Abundance and spatial organization of gram negative sulfate-reducing bacteria in activated sludge investigated by in situ probing with specific 16S rRNA targeted oligonucleotides. FEMS Microbial Ecology 25 (1998) 43-61
94. Massana R., Murray A.E., Preston C.M., and DeLong E.F. Vertical distribution and phylogenetic characterization of marine planktonic Archaea in the Santa Barbara Channel. Applied and Environmental Microbiology 63 (1997) 50-56
95. Massana R., DeLong E.F., and Pedrós-Alió C. A few cosmopolitan phylotypes dominate planktonic archaeal assemblages in widely different oceanic provinces. Applied and Environmental Microbiology 66 (2000) 1777-1787
96. Massé G., Belt S.T., Allard W.G., Lewis C.A., Wakeham S.G., and Rowland S.J. Occurrence of novel monocyclic alkenes from diatoms in marine particulate matter and sediments. Organic Geochemistry 35 (2004) 813-822
97. McCaffrey M.A., Farrington J.W., and Repeta D.J. Geochemical implication of the lipid composition of Thioploca spp. from the Peru upwelling region - 15°S. Organic Geochemistry 14 (1989) 61-68
98. 2 fixation. Autotrophic Bacteria (1989), Springer, New York 351-364
99. Michaelis W., Seifert R., Nauhaus K., Treude T., Thiel V., Blumenberg M., Knittel K., Gieseke A., Peterknecht K., Pape T., Boetius A., Amann R., Jørgensen B.B., Widdel F., Peckmann J., Pimenov N.V., and Gulin M.B. Microbial reefs in the Black Sea fueled by anaerobic oxidation of methane. Science 297 (2002) 1013-1015
100. Muole A.L., and Wilkinson S.G. Polar lipids, fatty acids, and isoprenoid quinones of Atleromonas putrefaciens (Shewanella putrefaciens). Systematic and Applied Microbiology 9 (1978) 192-198
101. Murray J.W., and Yakushev E. The suboxic transition zone in the Black Sea. In: Neretin L.N. (Ed). Past and Present Water Column Anoxia (2006), Springer 105-138
102. Murray J.W., Codispoti L.A., and Friederich G.E. Oxidation-reduction environments: the suboxic zone in the Black Sea. Aquatic Chemistry: Interfacial and Interspecies Processes. ACS Advances in Chemistry Series vol. 244 (1995), Oxford University Press, New York, NY 157-176
103. Murray J.W., Fuchsman C., Kirkpatrick J., Paul B., and Konovalov S.K. Species and signatures of nitrogen transformation in the suboxic zone of the Black Sea. Oceanography 18 (2005) 36-47
104. Neef A., Amann R., Schlesner H., and Schleifer K.-H. Monitoring a widespread bacterial group: in situ detection of planctomycetes with 16S rRNA-targeted probes. Microbiology 144 (1998) 3257-3266
105. Neunlist S., and Rohmer M. The hopanoids of "Methylosinus trichosporium": aminobacteriohopanetriol and aminobacteriohopanetetrol. Journal of General Microbiology 131 (1985) 1363-1367
106. Neunlist S., and Rohmer M. Novel hopanoids from the methylotrophic bacteria Methylococcus capsulatus and Methylomonas methanica (22S)-35-aminobacteriohopane-30,31,32,33,34-pentol and (22S)-35-amino-3β-methylbacteriohopane-30,31,32,33,34-pentol. Biochemical Journal 231 (1985) 635-639
107. Neunlist S., Holst O., and Rohmer M. Prokaryotic triterpenoids: the hopanoids of the purple non-sulphur bacterium Rhodomicrobium vannielii: an aminotriol and its aminoacyl derivatives, N-tryptophanyl and N-ornithinyl aminotriol. European Journal of Biochemistry 147 (1985) 561-568
108. Neunlist S., Bisseret P., and Rohmer M. The hopanoids of the purple non-sulfur bacteria Rhodopseudomonas palustris and Rhodopseudomonas acidophila. European Journal of Biochemistry 171 (1988) 245-252
109. Nichols P.D., Guckert J.B., and White D.C. Determination of monounsaturated fatty acid double-bond position and geometry for microbial monocultures and complex consortia by capillary GC-MS of their dimethyl disulphide derivatives. Journal of Microbiological Methods 5 (1986) 49-55
110. Op den Camp H.J.M., Kartal B., Guven D., van Niftrik L.A.M.P., Haaijer S.C.M., van der Star W.R.L., van de Pas-Schoonen K.T., Cabezas A., Ying Z., Schmid M.C., Kuypers M.M.M., van de Vossenberg J., Harhangi H.R., Picioreanu C., van Loosdrecht M.C.M., Kuenen J.G., Strous M., and Jetten M.S.M. Global impact and application of their anaerobic ammonium-oxidizing (anammox) bacteria. Biochemical Society Transactions 34 (2006) 174-178
111. Ourisson G., Rohmer M., and Poralla K. Prokaryotic hopanoids and other polyterpeniod sterol surrogates. Annual Review of Microbiology 41 (1987) 301-333
112. Ourisson G., and Rohmer M. Hopanoids 2. Biohopanoids: a novel class of bacterial lipids. Accounts of Chemical Research 25 (1992) 403-408
113. Ouverney C.C., and Fuhrman J.A. Marine planktonic archaea take up amino acids. Applied and Environmental Microbiology 66 (2000) 4829-4833
114. Pancost R.D., Hopmans E.C., Sinninghe Damsté J.S., and MEDINAUT Shipboard Scientific Party. Archaeal lipids in Mediterranean cold seeps: molecular proxies for anaerobic methane oxidation. Geochimica et Cosmochimica Acta 65 (2001) 1611-1627
115. Pancost R.D., Zhang C.L., Tavacoli J., Talbot H.M., Farrimond P., Schouten S., Sinninghe Damsté J.S., and Sassen R. Lipid biomarkers preserved in hydrate-associated authigenic carbonate rocks of the Gulf of Mexico. Paleogeography, Paleoclimatology, Paleoecology 227 (2005) 48-66
116. 14C analysis. Geochimica et Cosmochimica Acta 65 (2001) 3123-3137
117. Pernthaler A., Preston C.M., Pernthaler J., DeLong E.F., and Amann R. Comparison of fluorescently labeled oligonucleotide and polynucleotide probes for the detection of pelagic marine bacteria and archaea. Applied and Environmental Microbiology 68 (2002) 661-667
118. Pernthaler A., Pernthaler J., and Amann R. Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria. Applied and Environmental Microbiology 68 (2002) 3094-3101
119. Pimenov N.V., and Neretin L.N. Composition and activities of microbial communities involved in carbon, sulfur, nitrogen and manganese cycling in the oxic/anoxic interface of the Black Sea. In: Neretin L.N. (Ed). Past and Present Water Column Anoxia (2006), Springer 501-521
120. 2 fixation pathways. Zeitschrift fur Naturforschungen 44c (1989) 397-402
121. Raederstorff D., and Rohmer M. Polyisoprenoids as cholesterol and tetrahymanol surrogates in the ciliate Tetrahymena pyriformis. Biochimica et Biophysica Acta 960 (1988) 190-199
122. Reeburgh W.S. Oceanic methane biogeochemistry. Chemical Reviews 107 (2007) 486-513
123. Reeburgh W.S., Ward B.B., Whalen S.C., Sandbeck K.A., Kilpatrick K.A., and Kerkhof L.J. Black Sea methane geochemistry. Deep-Sea Research 38 Suppl. 2 (1991) S1189-S1210
124. Renoux J.M., and Rohmer M. Prokaryotic triterpenoids. New bacteriohopanetetrol cyclitol ethers from the methylotrophic bacterium Methylobacterium organophilum. European Journal of Biochemistry 151 (1985) 405-410
125. Repeta D.J., and Simpson D.J. The distribution and recycling of chlorophyll, bacteriochlorophyll and carotenoids in the Black Sea. Deep-Sea Research 38 Suppl. 2 (1991) S969-S984
126. Repeta D.J., Simpson D.J., Jørgensen B.B., and Jannasch H.W. Evidence for anoxygenic photosynthesis from the distribution of bacteriochlorophylls in the Black Sea. Nature 342 (1989) 69-72
127. Risatti J.B., Rowland S.J., Yon D.A., and Maxwell J.R. Stereochemical studies of acyclic isoprenoid-XII. Lipids of methanogenic bacteria and possible contributions to sediments. In: Schenck P.A., de Leeuw J.W., and Ljimbach G.W.M. (Eds). Advances in Organic Geochemistry 1983. Organic Geochemistry 6 (1984) 93-104
128. Rohmer M.P., Bouvier-Nave P., and Ourisson G. Distribution of hopanoid triterprenes in prokaryotes. Journal of General Microbiology 130 (1984) 1137-1150
129. Rossello-Mora R.A., Caccavo Jr. F., Osterlehner K., Springer N., Spring S., Schuler D., Ludwig W., Amann R., Vanncanneyt M., and Schleifer K.H. Isolation and taxonomic characterization of a halotolerant, facultatively iron-reducing bacterium. Systematic and Applied Microbiology 17 (1994) 569-573
130. Rütters H., Sass H., Cypionka H., and Rullkötter J. Monoalkylether phospholipids in the sulfate-reducing bacteria Desulfosarcina variabilis and Desulforhabdus amnifenus. Archives of Microbiology 176 (2001) 435-442
131. Sass A., Rütters H., Cypionka H., and Sass H. Desulfobulbus mediterraneus sp. nov., a sulfate-reducing bacterium growing on mono- and di-sacchsarides. Archives of Microbiology 177 (2002) 468-474
132. Schoell M., Hwang R.J., Carlson R.M.K., and Welton J.E. Carbon isotope composition of individual biomarkers in gilsonites (Utah). Organic Geochemistry 21 (1994) 683-763
133. Schouten S., van der Maarel M.J.E.C., Huber R., and Sinninghe Damsté J.S. 2,6,10,15,19-Pentamethylicosenes in Methanolobus bombayensis, a marine methanogenic archaeon, and in Methanosarcina mazei. Organic Geochemistry 26 (1997) 409-414
134. Schouten S., Strous M., Kuypers M.M.M., Rijpstra W.I.C., Baas M., Schubert C.J., Jetten M.S.M., and Sinninghe Damsté J.S. Stable carbon isotope fractionations associated with inorganic carbon fixation by anaerobic ammonium-oxidizing bacteria. Applied and Environmental Microbiology 70 (2004) 3785-3788
135. 86 paleothermometry by high pressure liquid chromatography/atmospheric pressure chemical ionization-mass spectrometry. Analytical Chemistry 79 (2007) 2940-2944
136. Schubert C.J., Coolen M.J.L., Neretin L.N., Schippers A., Abbas B., Durisch-Kaiser E., Wehrli B., Hopmans E.C., Sinninghe Damsté J.S., Wakeham S.G., and Kuypers M.M.M. Aerobic and anaerobic methanotrophs in the Black Sea water column. Environmental Microbiology (2006) 10.1111/j.1462-2920.2006.01079x
137. Sekar R., Fuchs B.M., Amann R., and Pernthaler J. Flow sorting of marine bacterioplankton after fluorescence in situ hybridization. Applied and Environmental Microbiology 70 (2003) 6210-6219
138. Sinninghe Damsté J.S., Wakeham S.G., Kohnen M.E.L., Hayes J.M., and de Leeuw J.W. A 6,000-year sedimentary record of chemocline excursions in the Black Sea. Nature 362 (1993) 827-829
139. Sinninghe Damsté J.S., Kenig F., Koopmans M.P., Köster J., Schouten S., Hayes J.M., and de Leeuw J.W. Evidence for gammacerane as an indicator of water column stratification. Geochimica et Cosmochimica Acta 59 (1995) 1895-1900
140. 25 highly branched isoprenoid pentaene in the marine diatom Rhizosolenia setigera. Organic Geochemistry 30 (1999) 1581-1583
141. Sinninghe Damsté J.S., Strous M., Rijpstra W.I.C., Hopmans E.C., Geenevasen J.A.J., van Duin A.C.T., van Niftrik L.A., and Jetten M.S.M. Linearly-concatenated cyclobutane lipids form a dense bacterial membrane. Nature 419 (2002) 708-712
142. Sinninghe Damsté J.S., Hopmans E.C., Schouten S., van Duin A.C.T., and Geenevasen J.A.J. Crenarchaeol: the characteristic core glycerol dibiphytanyl glycerol tetraether membrane lipid of cosmopolitan pelagic crenarchaeota. Journal of Lipid Research 43 (2002) 1641-1651
143. Sinninghe Damsté J.S., Rijpstra W.I.C., Hopmans E.C., Prahl F.G., Wakeham S.G., and Schouten S. Distribution of membrane lipids of planktonic crenarchaeota in the Arabian Sea. Applied and Environmental Microbiology 68 (2002) 2997-3002
144. Sinninghe Damsté J.S., Rijpstra W.I.C., Schouten S., Fuerst J.A., Jetten M.S.M., and Strous M. The occurrence of hopanoids in planctomycetes: implications for the sedimentary biomarker record. Organic Geochemistry 35 (2004) 561-566
145. Sinninghe Damsté J.S., Rijpstra W.I.C., Geenevasen J.A.J., Strous M., and Jetten M.S.M. Structural identification of ladderane and other membrane lipids of planctomycetes capable of anaerobic ammonium oxidation (anammox). FEBS Journal 272 (2005) 4270
146. Sorokin Y.I. The Black Sea Ecology and Oceanography (2002), Backhuys Publishers, Leiden, The Netherlands
147. Sorokin Y.I., Sorokin P.Y., Audeev D.Y., Sorokin D.Y., and Ilchenko S.V. Biomass, production and activity of bacteria in the Black Sea with special reference to chemosynthesis and the sulfur cycle. Hydrobiologia 308 (1995) 61-76
148. Stahl D.A., and Amann R. Development and application of nucleic acid probes. In: Stackebrandt E., and Goodfellow M. (Eds). Nucleic Acid Techniques in Bacterial Systematics (1991), John Wiley & Sons, Chichester, England 205-248
149. Summons R.E., and Jahnke L.L. Hopenes and hopanes methylated in ring-A: a correlation of the hopanoids from extant methylotrophic bacteria with their fossil analogs. In: Moldowan J.M., Albrecht P., and Philp R.P. (Eds). Biology Markers in Sediments and Petroleum (1992), Prentice Hall, New York 182-200
150. Summons R.E., Jahnke L.L., and Roksandic Z. Carbon isotopic fractionation in lipids from methanotrophic bacteria: relevance for interpretation of the geochemical record of biomarkers. Geochimica et Cosmochimica Acta 58 (1994) 2853-2863
151. Summons R.E., Franzmann P.D., and Nichols P.D. Carbon isotopic fractionation associated with methylotrophic methanogenesis. Organic Geochemistry 28 (1998) 465-475
152. Summons R.E., Jahnke L.L., Hope J.M., and Logan G.A. 2-Methylhopanoids as biomarkers for cyanobacterial oxygenic photosynthesis. Nature 400 (1999) 554-557
153. Summons R.E., Bradley A.S., Jahnke L.L., and Waldbauer J.R. Steroids, triterpenoids and molecular oxygen. Philosophical Transactions of the Royal Society B 361 (2006) 951-968 10.1098/rstb.2006.1837
154. Talbot H.M., Watson D.F., Murrell J.C., Carter J.F., and Farrimond P. Analysis of intact bacteriohopanepolyols from methylotrophic bacteria by reversed-phase high-performance liquid chromatography-atmospheric pressure chemical ionisation mass spectrometry. Journal of Chromatography A 921 (2001) 175-185
155. Talbot H.M., Summons R., Jahnke L.L., and Farrimond P. Characteristic fragmentation of bacteriohopanepolyols during atmospheric pressure chemical ionisation liquid chromatography/ion trap mass spectrometry. Rapid Communications in Mass Spectrometry 17 (2003) 2788-2796
156. Talbot H.M., Squier A.H., Keely B.J., and Farrimond P. Atmospheric pressure chemical ionisation reversed-phase liquid chromatography/ion trap mass spectrometry of intact bacteriohopanepolyols. Rapid Communications in Mass Spectrometry 17 (2003) 728-737
157. Talbot H.M., Watson D.F., Pearson E.J., and Farrimond P. Diverse biohopanoid compositions of non-marine sediments. Organic Geochemistry 34 (2003) 1353-1371
158. Talbot H.M., Farrimond P., Schaeffer P., and Pancost R.D. Bacteriohopanepolyols in hydrothermal vent biogenic silicates. Organic Geochemistry 36 (2005) 663-672
159. Talbot H.M., Rohmer M., and Farrimond P. Rapid structural elucidation of composite bacterial hopanoids by atmospheric pressure chemical ionisation liquid chromatography/ion trap mass spectrometry. Rapid Communications in Mass Spectrometry 21 (2007) 880-892
160. Talbot H.M., Rohmer M., and Farrimond P. Structural characterisation of unsaturated bacterial hopanoids by atmospheric pressure chemical ionisation liquid chromatography/ion trap mass spectrometry. Rapid Communications in Mass Spectrometry 21 (2007) 1613-1622
161. Taylor J., and Parkes R.J. Cellular fatty acids of the sulphate-reducing bacteria, Desulfobacter sp., Desulfolobus sp., and Desulfovibrio desulfuricans. Journal of General Microbiology 129 (1985) 3303-3309
162. Teece M.A., Fogel M.L., Dollhopf M.E., and Nealson K.H. Isotope fractionation associated with biosynthesis of fatty acids by a marine bacterium under oxic and anoxic conditions. Organic Geochemistry 30 (1999) 1571-1579
163. Teira E., Reinthaler T., Pernthaler A., Pernthaler J., and Herndl G.J. Combining catalyzed reporter deposition-fluorescence in situ hybridization and microautoradiography to detect substrate utilization by Bacteria and Archaea in the deep ocean. Applied and Environmental Microbiology 70 (2004) 4411-4414
164. ten Haven H.L., Rohmer M., Rullkötter J., and Bisseret P. Tetrahymanol, the most likely precursor of gammacerane, occurs ubiquotously in marine sediments. Geochimica et Cosmochimica Acta 53 (1989) 3073-3079
165. Thamdrup B., Dalsgaard T., Jensen M.M., Ulloa O., Fari{dotless}́as L., and Escribano R. Anaerobic ammonium oxidation in the oxygen-deficient waters off northern Chile. Limnology and Oceanography 51 (2006) 2145-2156
166. Thiel V., Peckmann J., Seifert R., Wehrung P., Reitner J., and Michaelis W. Highly isotopically depleted isoprenoids: molecular markers for ancient methane venting. Geochimica et Cosmochimica Acta 63 (1999) 3959-3966
167. Thiel V., Bumenberg M., Pape T., Siefert R., and Michaelis W. Unexpected occurrence of hopanoids at gas seeps in the Black Sea. Organic Geochemistry 34 (2003) 81-87
168. Tornabene T.G., and Langworthy T.A. Diphytanyl and diphytanyl glycerol ether lipids of methanogenic Archaebacteria. Science 203 (1979) 51-53
169. Vandamme P., and De Lay J. Proposal for a new family, Campylobacteraceae. International Journal of Systematic Bacterioliology 41 (1992) 451-455
170. 13C contents of bacterial lipids. Organic Geochemistry 28 (1998) 527-533
171. Venkatesan M.I. Tetrahymanol: its widespread occurrence and geochemical significance. Geochimica et Cosmochimica Acta 53 (1989) 3095-3101
172. Vetriani C., Tran H.V., and Kerkhof L.J. Fingerprinting microbial assemblages from the oxic/anoxic chemocline of the Black Sea. Applied and Environmental Microbiology 69 (2003) 6481-6488
173. 30 highly branched isoprenoid alkenes in laboratory cultures of marine diatoms. Organic Geochemistry 21 (1994) 407-414
174. Wakeham S.G. Reduction of stenols to stanols in particulate matter at oxic-anoxic boundaries in seawater. Nature 342 (1989) 787-790
175. Wakeham S.G., and Beier J.A. Fatty acid and sterol biomarkers as indicators of particulate organic matter source and alteration processes in the water column of the Black Sea. Deep-Sea Research 38 Suppl. 2 (1991) S943-S968
176. Wakeham S.G., and Canuel E.A. Organic geochemistry of particulate matter in the eastern tropical North Pacific Ocean: implications for particle dynamics. Journal of Marine Research 46 (1988) 183-213
177. Wakeham S.G., Freeman K.H., Pease T.K., and Hayes J.M. A photoautotrophic source for lycopane in marine water columns and sediments. Geochimica et Cosmochimica Acta 57 (1993) 159-165
178. Wakeham S.G., Lewis C.M., Hopmans E.C., Schouten S., and Sinninghe Damsté J.S. Archaea mediate anaerobic oxidation of methane in deep euxinic waters of the Black Sea. Geochimica Cosmochimica Acta 67 (2003) 1359-1374
179. Wallner G., Amann R., and Beisker W. Optimizing fluorescent in situ-hybridization with rRNA-targeted oligonucleotide probes for flow cytometric identification of microorganisms. Cytometry 14 (1993) 136-143
180. Ward B.B., and Kilpatrick K.A. Nitrogen transformations in the oxic layer of permanent anoxic basins: the Black Sea and the Cariaco Trench. In: Izdar E., and Murray J.W. (Eds). Black Sea Oceanography (1991), Kluwer Academic Publishers 111-124
181. White D.C. In situ measurement of microbial biomass, community structure and nutritional status. Philosophical Transactions of the Royal Society London Series A 344 (1993) 59-67
182. 25 isoprenoids in axenic cultures of Haslea ostrearia. Phytochemistry 51 (1999) 69-73
183. Wuchter C., Schouten S., Boschker H.T.S., and Sinninghe Damsté J.S. Bicarbonate uptake by marine Crenarchaeota. FEMS Microbiology Letters 219 (2003) 203-207
184. Wuchter C., Abbas B., Coolen M.J.L., Herfort L., van Bleijswijk J., Timmers P., Strous M., Teira E., Herndl G.J., Middelburg J.J., Schouten S., and Sinninghe Damsté J.S. Archaeal nitrification in the ocean. Proceedings of the National Academy of Sciences 103 (2006) 12317-12322
185. Yilmaz A., Çoban-Yildis Y., Telli-Karakoç F., and Bologa A. Surface and mid-water sources of organic carbon by photoautotrophic and chemoautotrophic production in the Black Sea. Deep-Sea Research II 53 (2006) 1988-2004
186. Zander J.M., Greig J.B., and Caspi E. Tetrahymanol biosynthesis: studies in vitro on squalene cyclization. Journal of Biological Chemistry 245 (1970) 1247-1254
187. Zhang C.L., Li Y., Ye Q., Fong J., Peacock A.D., Blunt E., Fang J., Lovley D.R., and White D.C. Carbon isotope signatures of fatty acids in Geobacter metallireducens and Shewanella algae. Organic Geochemistry 19 (2003) 17-28
188. Zhang C.I., Huang Z., Cantu J., Pancost R.D., Brigmon R.L., Lyons T.W., and Sassen R. Lipid biomarkers and carbon isotope signatures of a microbial (Beggiatoa) mat associated with gas hydrates in the Gulf of Mexico. Applied and Environmental Microbiology 71 (2005) 2106-2112
189. Zubkov M.V., Sazhin A.F., and Flint M.V. The microplankton organisms at the oxic-anoxic interface in the pelagial of the Black Sea. FEMS Microbial Ecology 101 (1992) 245-250
190. Zundel M., and Rohmer M. Hopanoids of the methylotrophic bacteria Methylococcus capsulatus and Methylomonas sp. as possible precursors for the C29 and C30 hopanoid chemical fossils. FEMS Microbiological Letters 28 (1985) 61-64