Fossing H, Jørgensen BB (1989) Measurement of bacterial sulfate
reduction in sediments: evaluation of single step chromium reduction method. Biogeochemistry 8:205–222
Francis CA, Co EM, Tebo BM (2001) Enzymaticmanganese(II) oxidation by a marine alpha-proteobacterium. Appl Environ Microbiol
67:4024–4029
Frontier S, et Pichot-Viale D (1998) Ecosyste `mes: Structure,
fonctionnement, e ´volution, 2e e ´dition. Dunod, Paris
Fung I, John J, Lerner J, Matthews E, Prather M, Steele LP, Fraser PJ
(1991) Three-dimensional model synthesis of the global methane
cycle. J Phys Res 96(D7):13033–13065
Galloway JN, Aber JD, Erisman JW, Seitzinger SP, Howarth RW,
Cowling EB, Cosby BJ (2003) The nitrogen cascade. Bioscience
53:341–356
Gans J, Wolinsky M, Dunbar J (2005) Computational improvements
reveal great bacterial diversity and high metal toxicity in soil.
Science 309:1387–1390
Garcia J-L, Patel BKC, Ollivier B (2000) Taxonomic, phylogenetic,
and ecological diversity of methanogenic Archaea. Anaerobe
6:205–226
Gilbert F, Bonin P, Stora G (1995) Effect of bioturbation on denitrification in a marine sediment from the West Mediterranean littoral.
Hydrobiologia 304:49–58
Goevert D, Conrad R (2009) Effect of substrate concentration on
carbon isotope fractionation during acetoclastic methanogenesis
by Methanosarcina barkeri and M. acetivorans and in rice field
soil. Appl Environ Microbiol 75:2605–2612
Graham JW, Cooper SC (1959) Biological origin of manganese-rich
deposits of the sea floor. Nature 183:1050–1051
Grossi V, Cuny P, Caradec S, Nerini D, Pancost R, Gilbert F (2006)
Impact of feeding by Arenicola marina (L.) and ageing of faecal
material on fatty acid distribution and bacterial community structure in marine sediments: an expe ´rimental approach. J Exp Mar Biol
Ecol 336:54–64
Hanson RS, Hanson TE (1996) Methanotrophic bacteria. Microbiol
Rev 60:439–471
Haroon MF et al (2013) Anaerobic oxidation of methane coupled
to nitrate reduction in a novel archaeal lineage. Nature
500:567–570
Hauck RD, Bouldin DR (1961) Distribution of isotopic nitrogen gas
during denitrification. Nature 191:871–872
Hegler F, Popsth NR, Jiang J, Kappler A (2008) Physiology
of phototrophic iron (II)-oxidizing bacteria: implications for
modern and ancient environments. FEMS Microbiol Ecol
66:250–260
Herbert RA (1999) Nitrogen cycling in coastal marine ecosystems.
FEMS Microbiol Rev 23:563–590
Hernesmaa A, Bjorklof K, Kiikkila O, Fritze H, Haahtela K,
Romantschuk M (2005) Structure and function of microbial
communities in the rhizosphere of Scots pine after tree-felling.
Soil Biol Biochem 37:777–785
Hinrichs K-U, Hayes JM, Sylva SP, Brewer PG, De Long EF (1999)
Methane-consuming archaebacteria in marine sediments. Nature
398:802–805
Hinrichs K-U, Summons RE, Orphan V, Sylva SP, Jayes JM (2000)
Molecular and isotopic analysis of anaerobic methane-oxidizing
communities in marine sediments. Org Geochem 31:1685–1701
Hoeler TM, Alperin MJ, Albert DB, Martens CS (1994) Field and
laboratory studies of methane oxidation in an anoxic marine sediment: evidence for a methanogen-sulfate reducer consortium. Glob
Biogeochem Cycle 8:451–463
Houghton JT, Ding Y, Griggs DJ, Noguer M, van der Linden PJ, Dai X,
Maskell K, Johnson CA (2004) Climate change 2001: the scientific
basis. Contribution of working group I to the third assessment report
of the Intergovernmental Panel on Climate Change. Cambridge
University Press, Cambridge
Hu S, Zeng RJ, Burow LC, Lant P, Keller J, Yuan Z (2009) Enrichment
of denitrifying anaerobic methane oxidizing microorganisms. Environ Microbiol Rep 1:377–384
Hutsch BW, Augustin J, Merbach W (2002) Plant rhizodeposition – an
important source for carbon turnover in soils. J Plant Nut Soil Sci
165:397–407
IPCC (1995) Greenhouse gas inventory reference manual. IPCC
Guidelines for National Greenhouse Gas Inventories. United
Nations Environment Programme (UNEP), the Organisation for
Economic Co-operation and Development (OECD), the International Energy Agency (IEA) and the Intergovernmental Panel on
Climate Change (IPCC), Bracknell
IPCC (2007) Climate change 2007: the physical science basis. Contribution of working group I to the fourth assessment report IPCC. In:
Solomon S, Qin D, Manning M, Chen Z, Marquis M, Averyt KB,
Tignor M, Mille HL (eds). Cambridge University Press, Cambridge/
New York
Jahn MK, Haderlein SB, Meckenstock RU (2005) Anaerobic degradation of benzene, toluene, ethylbenzene, and o-xylene in sedimentfree iron-reducing enrichment cultures. Appl Environ Microbiol
71:3355–3358
Jannasch HW, Mottl MJ (1985) Geomicrobiology of deep-sea hydrothermal vents. Science 229:717–725
Jetten MS, Logemann S, Muyzer G, Robertson LA, de Vries S, van
Loosdrecht MC, Kuenen JG (1997) Novel principles in the microbial conversion of nitrogen compounds. Antonie Van Leeuwenhoek
71:75–93
Jickells T et al (2005) Global iron connections between desert
dust, ocean oiogeochemistry, and climate knowledge. Science
303:67–71
Jørgensen BB (1977) The sulfur cycle of a coastal marine sediment.
Limnol Oceanogr 22:817–832
Jørgensen BB (1983) The microbial sulphur cycle. In: Krumbein WE
(ed) Microbial geochemistry. Blackwell Scientific Publication,
Oxford, pp 91–124
Jørgensen BB (1990) A thiosulfate shunt in the sulfur cycle of marine
sediments. Science 249:152–154
Jørgensen BB (2000) Bacteria and marine biogeochemistry. In: Schulz
HD, Zabel M (eds) Marine geochemistry. Springer, Berlin/
Heidelberg/New York, pp 173–207
Jørgensen BB, Fenchel T (1974) The sulfur cycle of a marine sediment
model system. Mar Biol 24:189–201
Karl DM (2002) Microbiological oceanography – hidden in a sea of
microbes. Nature 415:590–591
Karl DM (2007) The marine phosphorus cycle. In: Hurst CJ et al (eds)
Manual of environmental microbiology, 3rd edn. American Society
of Microbiology, Washington, DC, pp 523–539
Karl DM, Tilbrook BD (1994) Production and transport of methane in
oceanic particulate organic matter. Nature 368:732–734
Knittel K, Boetius A (2009) Anaerobic oxidation of methane: progress
with an unknown process. Annu Rev Microbiol 63:311–334
Knittel K, Lo ¨sekann T, Boetius A, Kort R, Amann R (2005) Diversity
and distribution of methanotrophic Archaea at cold seeps. Appl
Environ Microbiol 71:467–479
Koide K, Osono T, Takeda H (2005) Fungal succession and decomposition of Camellia japonica leaf litter. Ecol Res 20:599–609
Ku ¨sel K, Dorsch T, Acker G, Stackebrandt E (1999) Microbial reduction of Fe(III) in acidic sediments: isolation of Acidiphilium
cryptum JF-5 capable of coupling the re ´duction of Fe(III) to the
oxidation of glucose. Appl Environ Microbiol 65:3633–3640
614
J.-C. Bertrand et al.
reduction in sediments: evaluation of single step chromium reduction method. Biogeochemistry 8:205–222
Francis CA, Co EM, Tebo BM (2001) Enzymaticmanganese(II) oxidation by a marine alpha-proteobacterium. Appl Environ Microbiol
67:4024–4029
Frontier S, et Pichot-Viale D (1998) Ecosyste `mes: Structure,
fonctionnement, e ´volution, 2e e ´dition. Dunod, Paris
Fung I, John J, Lerner J, Matthews E, Prather M, Steele LP, Fraser PJ
(1991) Three-dimensional model synthesis of the global methane
cycle. J Phys Res 96(D7):13033–13065
Galloway JN, Aber JD, Erisman JW, Seitzinger SP, Howarth RW,
Cowling EB, Cosby BJ (2003) The nitrogen cascade. Bioscience
53:341–356
Gans J, Wolinsky M, Dunbar J (2005) Computational improvements
reveal great bacterial diversity and high metal toxicity in soil.
Science 309:1387–1390
Garcia J-L, Patel BKC, Ollivier B (2000) Taxonomic, phylogenetic,
and ecological diversity of methanogenic Archaea. Anaerobe
6:205–226
Gilbert F, Bonin P, Stora G (1995) Effect of bioturbation on denitrification in a marine sediment from the West Mediterranean littoral.
Hydrobiologia 304:49–58
Goevert D, Conrad R (2009) Effect of substrate concentration on
carbon isotope fractionation during acetoclastic methanogenesis
by Methanosarcina barkeri and M. acetivorans and in rice field
soil. Appl Environ Microbiol 75:2605–2612
Graham JW, Cooper SC (1959) Biological origin of manganese-rich
deposits of the sea floor. Nature 183:1050–1051
Grossi V, Cuny P, Caradec S, Nerini D, Pancost R, Gilbert F (2006)
Impact of feeding by Arenicola marina (L.) and ageing of faecal
material on fatty acid distribution and bacterial community structure in marine sediments: an expe ´rimental approach. J Exp Mar Biol
Ecol 336:54–64
Hanson RS, Hanson TE (1996) Methanotrophic bacteria. Microbiol
Rev 60:439–471
Haroon MF et al (2013) Anaerobic oxidation of methane coupled
to nitrate reduction in a novel archaeal lineage. Nature
500:567–570
Hauck RD, Bouldin DR (1961) Distribution of isotopic nitrogen gas
during denitrification. Nature 191:871–872
Hegler F, Popsth NR, Jiang J, Kappler A (2008) Physiology
of phototrophic iron (II)-oxidizing bacteria: implications for
modern and ancient environments. FEMS Microbiol Ecol
66:250–260
Herbert RA (1999) Nitrogen cycling in coastal marine ecosystems.
FEMS Microbiol Rev 23:563–590
Hernesmaa A, Bjorklof K, Kiikkila O, Fritze H, Haahtela K,
Romantschuk M (2005) Structure and function of microbial
communities in the rhizosphere of Scots pine after tree-felling.
Soil Biol Biochem 37:777–785
Hinrichs K-U, Hayes JM, Sylva SP, Brewer PG, De Long EF (1999)
Methane-consuming archaebacteria in marine sediments. Nature
398:802–805
Hinrichs K-U, Summons RE, Orphan V, Sylva SP, Jayes JM (2000)
Molecular and isotopic analysis of anaerobic methane-oxidizing
communities in marine sediments. Org Geochem 31:1685–1701
Hoeler TM, Alperin MJ, Albert DB, Martens CS (1994) Field and
laboratory studies of methane oxidation in an anoxic marine sediment: evidence for a methanogen-sulfate reducer consortium. Glob
Biogeochem Cycle 8:451–463
Houghton JT, Ding Y, Griggs DJ, Noguer M, van der Linden PJ, Dai X,
Maskell K, Johnson CA (2004) Climate change 2001: the scientific
basis. Contribution of working group I to the third assessment report
of the Intergovernmental Panel on Climate Change. Cambridge
University Press, Cambridge
Hu S, Zeng RJ, Burow LC, Lant P, Keller J, Yuan Z (2009) Enrichment
of denitrifying anaerobic methane oxidizing microorganisms. Environ Microbiol Rep 1:377–384
Hutsch BW, Augustin J, Merbach W (2002) Plant rhizodeposition – an
important source for carbon turnover in soils. J Plant Nut Soil Sci
165:397–407
IPCC (1995) Greenhouse gas inventory reference manual. IPCC
Guidelines for National Greenhouse Gas Inventories. United
Nations Environment Programme (UNEP), the Organisation for
Economic Co-operation and Development (OECD), the International Energy Agency (IEA) and the Intergovernmental Panel on
Climate Change (IPCC), Bracknell
IPCC (2007) Climate change 2007: the physical science basis. Contribution of working group I to the fourth assessment report IPCC. In:
Solomon S, Qin D, Manning M, Chen Z, Marquis M, Averyt KB,
Tignor M, Mille HL (eds). Cambridge University Press, Cambridge/
New York
Jahn MK, Haderlein SB, Meckenstock RU (2005) Anaerobic degradation of benzene, toluene, ethylbenzene, and o-xylene in sedimentfree iron-reducing enrichment cultures. Appl Environ Microbiol
71:3355–3358
Jannasch HW, Mottl MJ (1985) Geomicrobiology of deep-sea hydrothermal vents. Science 229:717–725
Jetten MS, Logemann S, Muyzer G, Robertson LA, de Vries S, van
Loosdrecht MC, Kuenen JG (1997) Novel principles in the microbial conversion of nitrogen compounds. Antonie Van Leeuwenhoek
71:75–93
Jickells T et al (2005) Global iron connections between desert
dust, ocean oiogeochemistry, and climate knowledge. Science
303:67–71
Jørgensen BB (1977) The sulfur cycle of a coastal marine sediment.
Limnol Oceanogr 22:817–832
Jørgensen BB (1983) The microbial sulphur cycle. In: Krumbein WE
(ed) Microbial geochemistry. Blackwell Scientific Publication,
Oxford, pp 91–124
Jørgensen BB (1990) A thiosulfate shunt in the sulfur cycle of marine
sediments. Science 249:152–154
Jørgensen BB (2000) Bacteria and marine biogeochemistry. In: Schulz
HD, Zabel M (eds) Marine geochemistry. Springer, Berlin/
Heidelberg/New York, pp 173–207
Jørgensen BB, Fenchel T (1974) The sulfur cycle of a marine sediment
model system. Mar Biol 24:189–201
Karl DM (2002) Microbiological oceanography – hidden in a sea of
microbes. Nature 415:590–591
Karl DM (2007) The marine phosphorus cycle. In: Hurst CJ et al (eds)
Manual of environmental microbiology, 3rd edn. American Society
of Microbiology, Washington, DC, pp 523–539
Karl DM, Tilbrook BD (1994) Production and transport of methane in
oceanic particulate organic matter. Nature 368:732–734
Knittel K, Boetius A (2009) Anaerobic oxidation of methane: progress
with an unknown process. Annu Rev Microbiol 63:311–334
Knittel K, Lo ¨sekann T, Boetius A, Kort R, Amann R (2005) Diversity
and distribution of methanotrophic Archaea at cold seeps. Appl
Environ Microbiol 71:467–479
Koide K, Osono T, Takeda H (2005) Fungal succession and decomposition of Camellia japonica leaf litter. Ecol Res 20:599–609
Ku ¨sel K, Dorsch T, Acker G, Stackebrandt E (1999) Microbial reduction of Fe(III) in acidic sediments: isolation of Acidiphilium
cryptum JF-5 capable of coupling the re ´duction of Fe(III) to the
oxidation of glucose. Appl Environ Microbiol 65:3633–3640
614
J.-C. Bertrand et al.