Petermann H, Bleil U (1993) Detection of live magnetotactile bacteria
in South Atlantic deep-see sediments. Earth Planet Sci Lett
117:223–228
Pfennig N (1975) The phototrophic bacteria and their role in sulfur
cycle. Plant and Soil 43:1–16
Pfennig N (1989) Metabolic diversity among the dissimilatory sulfatereducing bacteria – Albert Jan Kluyver memorial lecture. Ant
Leeuw Int J G 56:127–138
Prentice IC et al (2001) The carbon cycle and atmospheric carbon
dioxide. In: Houghton J, Ding Y, Griggs DJ, Noguer N, van der
Linden PJ, Dai X (eds) Climate change 2001: the scientific basis.
Cambridge University Press, Cambridge, pp 183–239
Raghoebarsing AA et al (2006) A microbial consortium couples anaerobic methane oxidation to denitrification. Nature 440:918–921
Ranchou-Peyruse M, Monperrus M, Bridou R, Duran R, Amouroux D,
Salvado JC, Guyoneaud R (2009) Overview of mercury methylation
capacities among anaerobic bacteria including representatives of
the sulphate-reducers : implications for environmental studies.
Geomicrobiol J 26:1–8
Redfield AC (1934) On the proportions of organic derivatives in sea
water and their relation to the composition of plankton. In: Daniel
RJ (ed) James Johnstone memorial volume. University Press of
Liverpool, Liverpool, pp 177–192
Reeburgh WS (2007) Oceanic methane biogeochemistry. Chem Rev
107:486–513
Risgaard-Petersen N (2003) Coupled nitrification-denitrification in
autotrophic and heterotrophic estuarine sediments: on the influence
of benthic microalgae. Limnol Oceanogr 48:93–105
Robertson LA, Kuenen JG (2006) The colorless sulfur bacteria. In:
Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E
(eds) The prokaryotes. Springer, New York, pp 985–1011
Roesch LF et al (2007) Pyrosequencing enumerates and contrasts soil
microbial diversity. ISME J 1:283–290
Ruiz-Rueda O, Hallin S, Baneras L (2009) Structure and function of
denitrifying and nitrifying bacterial communities in relation to the
plant species in a constructed wetland. FEMS Microbiol Ecol
67:308–319
Samuel BS, Hansen EE, Manchester JK, Coutinho PM, Henrissat B,
Fulton R, Latreille P, Kim K, Wilson RK, Gordon JI (2007) Genomic and metabolic adaptations of Methanobrevibacter smithii to the
human gut. Proc Natl Acad Sci USA 104:10643–10648
Sarmiento JL, Gruber N (2006) Ocean biogeochemical dynamics.
Princeton University Press, Princeton
Satoh H, Nakamura Y, Okabe S (2007) Influences of infaunal burrows on
the community structure and activity of ammonia-oxidizing bacteria
in intertidal sediments. Appl Environ Microbiol 73:1341–1348
Schauss K et al (2009) Dynamics and functional relevance of ammoniaoxidizing Archaea in two agricultural soils. Environ Microbiol
11:446–456
Schloss PD, Handelsman J (2006) Toward a census of bacteria in soil.
Plos Comput Biol 2:786–793
Schmidt I, van Spanning RJ, Jetten MS (2004) Denitrification and
ammonia oxidation by Nitrosomonas europaea wild-type, and
NirK- and NorB-deficient mutants. Microbiology 150:4107–4114
Sieburth JM, Smetacek V, Lenz J (1978) Pelagic ecosystem structure:
heterotrophic compartments of the plankton and their relationship to
plankton size fractions. Limnol Oceanogr 23(6):1256–1263
Straub KL, Benz B, Schink B, Widdel F (1996) Anaerobic, nitratedependent microbial oxidation of ferrous iron. Appl Environ
Microbiol 62:1458–1460
Straub KL, Scho ¨nhuber WA, Buchholz-Cleven BEE, Schink B (2004)
Diversity of ferrous iron-oxidizing, nitrate-reducing bacteria and
their involvement in oxygen-independent iron cycling.
Geomicrobiol J 21:371–378
Strong A, Chisholm S, Miller C, Cullen J (2009) Iron fertilization: time
to move on. Nature 461:347–348
Strous M, Jetten SM (2004) Anaerobic oxidation of methane and
ammonium. Annu Rev Microbiol 58:99–117
Tabatabai MA (1974) Determination of sulfate in water samples. Sulphur Inst J 10:11–14
Tebo BM, Johson HA, McCarthy JK, Templeton AS (2005)
Geomicrobiology of manganese (II) oxidation. Trends Microbiol
13:421–428
Thamdrup B, Dalsgaard T (2002) Production of N 2 through anaerobic
ammonium oxidation coupled to nitrate reduction in marine
sediments. Appl Environ Microbiol 68:1312–1318
Thauer RK, Jungermann K, Deker K (1977) Energy conservation in
chemotrophic anaerobic bacteria. Microbiol Mol Biol Rev
41:100–180
Thingstad TF, Hagstrom A, Rassoulzadegan F (1997) Accumulation of
degradable DOC in surface waters: is it caused by a malfunctioning
microbial loop? Limnol Oceanogr 42:398–404
Thompson IA, Huber DM, Guest CA, Schulze DG (2005) Fungal
manganese oxidation in a reduced soil. Environ Microbiol
7:1480–1487
Tiedje JM, Sextone AJ, Myrold DD, Robinson JA (1982) Denitrification, ecological niches competition and survival. Ant Leeuw Int J G
48:569–583
Tre ´guer P, Nelson DM, Van Bennekom AJ, Demaster DJ, Que ´guiner B,
Leynaert A (1995) The silica budget of the World Ocean: a reestimate. Science 268:375–379
Trimmer M, Risgaard-Petersen N, Nicholls J-C, Engstrom P (2006)
Direct measurement of anaerobic ammonium oxidation (anammox)
and denitrification in intact sediment cores. Mar Ecol Prog Ser
326:37–47
Valentine DL, Reeburgh WS (2000) New perspectives on anaerobic
methane oxidation. Environ Microbiol 2:477–484
van Gemerden H (1993) Microbial mats, a joint venture. Mar Geol
113:3–25
van Herwijnen R, Laverye T, Poole J, Hodson ME, Hutchings TR
(2007) The effect of organic materials on the mobility and
toxicity of metals in contaminated soils. Appl Geochem
22:2422–2434
van Mooy BAS et al (2009) Phytoplankton in the ocean use nonphosphorus lipids in response to phosphorus scarcity. Nature
458:69–72
van Niftrik LA, Fuerst JA, Damste JSS, Kuenen JG, Jetten MSM,
Strous M (2004) The anammoxosome: an intracytoplasmic compartment in anammox bacteria. FEMS Microbiol Lett 233:7–13
van Wambeke F, Nedoma J, Duhamel S, Lebaron P (2008) Alkaline
phosphatase activity of marine bacteria studied with ELF97 phosphate: success and limits in P-limited Mediterranean Sea. Aquat
Microb Ecol 52:245–251
Vandecasteele J-P (2008) Petroleum microbiology, vols 1 and 2.
Editions Technip, Paris
Von Wolzogen Kur CAH, van der Vlugt IS (1934) De graphiteering
van gietijzer ais electrobiochemisch proces in anaerobe gronden.
Water 18:147–165
Wagner M, Loy A, Klein M, Lee N, Ramsing NB, Stahl DA, Friedrich
MW (2005) Functional marker genes for identification of sulfatereducing prokaryotes. Methods Enzymol 397:469–489
Waterbury JB, Watson SW, Guillard RRL, Brand LE (1979)
Widespread occurrence of a unicellular marine planktonic cyanobacterium. Nature 277:293–294
Weisskopf L, Fromin N, Tomasi N, Aragno M, Martinoia E (2005)
Secretion activity of white lupin’s cluster roots influences bacterial
abundance, function and community structure. Plant and Soil
268:181–194
616
J.-C. Bertrand et al.
in South Atlantic deep-see sediments. Earth Planet Sci Lett
117:223–228
Pfennig N (1975) The phototrophic bacteria and their role in sulfur
cycle. Plant and Soil 43:1–16
Pfennig N (1989) Metabolic diversity among the dissimilatory sulfatereducing bacteria – Albert Jan Kluyver memorial lecture. Ant
Leeuw Int J G 56:127–138
Prentice IC et al (2001) The carbon cycle and atmospheric carbon
dioxide. In: Houghton J, Ding Y, Griggs DJ, Noguer N, van der
Linden PJ, Dai X (eds) Climate change 2001: the scientific basis.
Cambridge University Press, Cambridge, pp 183–239
Raghoebarsing AA et al (2006) A microbial consortium couples anaerobic methane oxidation to denitrification. Nature 440:918–921
Ranchou-Peyruse M, Monperrus M, Bridou R, Duran R, Amouroux D,
Salvado JC, Guyoneaud R (2009) Overview of mercury methylation
capacities among anaerobic bacteria including representatives of
the sulphate-reducers : implications for environmental studies.
Geomicrobiol J 26:1–8
Redfield AC (1934) On the proportions of organic derivatives in sea
water and their relation to the composition of plankton. In: Daniel
RJ (ed) James Johnstone memorial volume. University Press of
Liverpool, Liverpool, pp 177–192
Reeburgh WS (2007) Oceanic methane biogeochemistry. Chem Rev
107:486–513
Risgaard-Petersen N (2003) Coupled nitrification-denitrification in
autotrophic and heterotrophic estuarine sediments: on the influence
of benthic microalgae. Limnol Oceanogr 48:93–105
Robertson LA, Kuenen JG (2006) The colorless sulfur bacteria. In:
Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E
(eds) The prokaryotes. Springer, New York, pp 985–1011
Roesch LF et al (2007) Pyrosequencing enumerates and contrasts soil
microbial diversity. ISME J 1:283–290
Ruiz-Rueda O, Hallin S, Baneras L (2009) Structure and function of
denitrifying and nitrifying bacterial communities in relation to the
plant species in a constructed wetland. FEMS Microbiol Ecol
67:308–319
Samuel BS, Hansen EE, Manchester JK, Coutinho PM, Henrissat B,
Fulton R, Latreille P, Kim K, Wilson RK, Gordon JI (2007) Genomic and metabolic adaptations of Methanobrevibacter smithii to the
human gut. Proc Natl Acad Sci USA 104:10643–10648
Sarmiento JL, Gruber N (2006) Ocean biogeochemical dynamics.
Princeton University Press, Princeton
Satoh H, Nakamura Y, Okabe S (2007) Influences of infaunal burrows on
the community structure and activity of ammonia-oxidizing bacteria
in intertidal sediments. Appl Environ Microbiol 73:1341–1348
Schauss K et al (2009) Dynamics and functional relevance of ammoniaoxidizing Archaea in two agricultural soils. Environ Microbiol
11:446–456
Schloss PD, Handelsman J (2006) Toward a census of bacteria in soil.
Plos Comput Biol 2:786–793
Schmidt I, van Spanning RJ, Jetten MS (2004) Denitrification and
ammonia oxidation by Nitrosomonas europaea wild-type, and
NirK- and NorB-deficient mutants. Microbiology 150:4107–4114
Sieburth JM, Smetacek V, Lenz J (1978) Pelagic ecosystem structure:
heterotrophic compartments of the plankton and their relationship to
plankton size fractions. Limnol Oceanogr 23(6):1256–1263
Straub KL, Benz B, Schink B, Widdel F (1996) Anaerobic, nitratedependent microbial oxidation of ferrous iron. Appl Environ
Microbiol 62:1458–1460
Straub KL, Scho ¨nhuber WA, Buchholz-Cleven BEE, Schink B (2004)
Diversity of ferrous iron-oxidizing, nitrate-reducing bacteria and
their involvement in oxygen-independent iron cycling.
Geomicrobiol J 21:371–378
Strong A, Chisholm S, Miller C, Cullen J (2009) Iron fertilization: time
to move on. Nature 461:347–348
Strous M, Jetten SM (2004) Anaerobic oxidation of methane and
ammonium. Annu Rev Microbiol 58:99–117
Tabatabai MA (1974) Determination of sulfate in water samples. Sulphur Inst J 10:11–14
Tebo BM, Johson HA, McCarthy JK, Templeton AS (2005)
Geomicrobiology of manganese (II) oxidation. Trends Microbiol
13:421–428
Thamdrup B, Dalsgaard T (2002) Production of N 2 through anaerobic
ammonium oxidation coupled to nitrate reduction in marine
sediments. Appl Environ Microbiol 68:1312–1318
Thauer RK, Jungermann K, Deker K (1977) Energy conservation in
chemotrophic anaerobic bacteria. Microbiol Mol Biol Rev
41:100–180
Thingstad TF, Hagstrom A, Rassoulzadegan F (1997) Accumulation of
degradable DOC in surface waters: is it caused by a malfunctioning
microbial loop? Limnol Oceanogr 42:398–404
Thompson IA, Huber DM, Guest CA, Schulze DG (2005) Fungal
manganese oxidation in a reduced soil. Environ Microbiol
7:1480–1487
Tiedje JM, Sextone AJ, Myrold DD, Robinson JA (1982) Denitrification, ecological niches competition and survival. Ant Leeuw Int J G
48:569–583
Tre ´guer P, Nelson DM, Van Bennekom AJ, Demaster DJ, Que ´guiner B,
Leynaert A (1995) The silica budget of the World Ocean: a reestimate. Science 268:375–379
Trimmer M, Risgaard-Petersen N, Nicholls J-C, Engstrom P (2006)
Direct measurement of anaerobic ammonium oxidation (anammox)
and denitrification in intact sediment cores. Mar Ecol Prog Ser
326:37–47
Valentine DL, Reeburgh WS (2000) New perspectives on anaerobic
methane oxidation. Environ Microbiol 2:477–484
van Gemerden H (1993) Microbial mats, a joint venture. Mar Geol
113:3–25
van Herwijnen R, Laverye T, Poole J, Hodson ME, Hutchings TR
(2007) The effect of organic materials on the mobility and
toxicity of metals in contaminated soils. Appl Geochem
22:2422–2434
van Mooy BAS et al (2009) Phytoplankton in the ocean use nonphosphorus lipids in response to phosphorus scarcity. Nature
458:69–72
van Niftrik LA, Fuerst JA, Damste JSS, Kuenen JG, Jetten MSM,
Strous M (2004) The anammoxosome: an intracytoplasmic compartment in anammox bacteria. FEMS Microbiol Lett 233:7–13
van Wambeke F, Nedoma J, Duhamel S, Lebaron P (2008) Alkaline
phosphatase activity of marine bacteria studied with ELF97 phosphate: success and limits in P-limited Mediterranean Sea. Aquat
Microb Ecol 52:245–251
Vandecasteele J-P (2008) Petroleum microbiology, vols 1 and 2.
Editions Technip, Paris
Von Wolzogen Kur CAH, van der Vlugt IS (1934) De graphiteering
van gietijzer ais electrobiochemisch proces in anaerobe gronden.
Water 18:147–165
Wagner M, Loy A, Klein M, Lee N, Ramsing NB, Stahl DA, Friedrich
MW (2005) Functional marker genes for identification of sulfatereducing prokaryotes. Methods Enzymol 397:469–489
Waterbury JB, Watson SW, Guillard RRL, Brand LE (1979)
Widespread occurrence of a unicellular marine planktonic cyanobacterium. Nature 277:293–294
Weisskopf L, Fromin N, Tomasi N, Aragno M, Martinoia E (2005)
Secretion activity of white lupin’s cluster roots influences bacterial
abundance, function and community structure. Plant and Soil
268:181–194
616
J.-C. Bertrand et al.