Ecological perspectives on microbes involved in N-cycling

Microbes and Environments

Volumn 29, Issue 1, 2014, Pages 4-16

  Isobe, Kazuo ^a   Ohte, Nobuhito ^a  

^a UNIVERSITY OF TOKYO   (Japan)

Author keywords

Ecosystem functions; Microbial community dynamics; Nitrogen cycle

Indexed keywords

NITROGEN;

BACTERIUM; BIODIVERSITY; CLASSIFICATION; ECOSYSTEM; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; NITROGEN CYCLE; REVIEW;

BACTERIA; BIODIVERSITY; ECOSYSTEM; NITROGEN; NITROGEN CYCLE;

EID: 84898715752     PISSN: 13426311     EISSN: 13474405     Source Type: Journal    
DOI: 10.1264/jsme2.ME13159     Document Type: Review

References (143)

1. Aber, J., W. McDowell, K. Nadelhoffer, A. Magill, G. Berntson, M. Kamakea, S. McNulty, W. Currie, L. Rustad, and I. Fernandez. 1998. Nitrogen saturation in temperate forest ecosystems. BioScience. 48:921-934.
2. Allison, S.D., and J.B.H. Martiny. 2008. Colloquium paper: resistance, resilience, and redundancy in microbial communities. Proc. Natl. Acad. Sci. U.S.A. 105:11512-11519.
3. Amano, T., I. Yoshinaga, K. Okada, T. Yamagishi, S. Ueda, A. Obuchi, Y. Sako, and Y. Suwa. 2007. Detection of anammox activity and diversity of anammox bacteria-related 16S rRNA genes in coastal marine sediment in Japan. Microbes Environ. 22:232-242.
4. Amano, T., I. Yoshinaga, T. Yamagishi, C. Van Thuoc, P.T. Thu, S. Ueda, K. Kato, Y. Sako, and Y. Suwa. 2011. Contribution of anammox bacteria to benthic nitrogen cycling in a mangrove forest and shrimp ponds, Haiphong, Vietnam. Microbes Environ. 26:1-6.
5. Attard, E., F. Poly, C. Commeaux, F. Laurent, A. Terada, B.F. Smets, S. Recous, and X. Le Roux. 2010. Shifts between Nitrospira- and Nitrobacter-like nitrite oxidizers underlie the response of soil potential nitrite oxidation to changes in tillage practices. Environ. Microbiol. 12:315-326.
6. Bakermans, C., and M. Skidmore. 2011. Microbial respiration in ice at subzero temperatures (-4°C to -33°C). Environ. Microbiol. Rep. 3:774-782.
7. Beman, J.M., B.N. Popp, and C.A. Francis. 2008. Molecular and biogeochemical evidence for ammonia oxidation by marine Crenarchaeota in the Gulf of California. ISME J. 2:429-441.
8. Berman-Frank, I., P. Lundgren, Y.B. Chen, H. Küpper, Z. Kolber, B. Bergman, and P. Falkowski. 2001. Segregation of nitrogen fxation and oxygenic photosynthesis in the marine cyanobacterium Trichodesmium. Science. 294:1534-1537.
9. Bever, J.D., T.G. Platt, and E.R. Morton. 2012. Microbial population and community dynamics on plant roots and their feedbacks on plant communities. Annu. Rev. Microbiol. 66:265-283.
10. Bronda, E. 1977. Two kinds of lithotrophs missing in nature. Z. Allg. Mikrobiol. 17:491-493.
11. Burgin, A.J., and S.K. Hamilton. 2007. Have we overemphasized the role of denitrifcation in aquatic ecosystems? A review of nitrate removal pathways. Front. Ecol. Environ. 5:89-96.
12. Canfeld, D.E., A.N. Glazer, and P.G. Falkowski. 2010. The evolution and future of earth's nitrogen cycle. Science 330:192-196.
13. Capone, D.G. 1997. Trichodesmium, a globally signifcant marine cyanobacterium. Science 276:1221-1229.
14. Church, M., B. Jenkins, D. Karl, and J. Zehr. 2005. Vertical distributions of nitrogen-fxing phylotypes at Stn Aloha in the oligotrophic North Pacifc Ocean. Aqua. Microbial. Ecol. 38:3-14.
15. Church, M.J., C.M. Short, B.D. Jenkins, D.M. Karl, and J.P. Zehr. 2005. Temporal patterns of nitrogenase gene (nifH) expression in the oligotrophic North Pacifc Ocean. Appl. Environ. Microbiol. 71:5362-5370.
16. Clark, D.R., A.P. Rees, and I. Joint. 2008. Ammonium regeneration and nitrifcation rates in the oligotrophic Atlantic Ocean: implications for new production estimates. Limnol. Oceanogr. 53:52-62.
17. Dalsgaard, T., B. Thamdrup, L. Farías, and N. Peter Revsbech. 2012. Anammox and denitrifcation in the oxygen minimum zone of the eastern South Pacifc. Limnol. Oceanogr. 57:1331-1346.
18. De Boer, W., and G.A. Kowalchuk. 2001. Nitrifcation in acid soils: micro-organisms and mechanisms. Soil Biol. Biochem. 33:853-866.
19. Devol, A.H. 2003. Nitrogen cycle: solution to a marine mystery. Nature 422:575-576.
20. Dewi Puspita, I., Y. Kamagata, M. Tanaka, K. Asano, and C.H. Nakatsu. 2012. Are uncultivated bacteria really uncultivable? Microbes Environ. 27:356-366.
21. Di, H.J., K.C. Cameron, J.P. Shen, C.S. Winefeld, M. O'Callaghan, S. Bowatte, and J.Z. He. 2009. Nitrifcation driven by bacteria and not archaea in nitrogen-rich grassland soils. Nat. Geosci. 2:621-624.
22. Ettwig, K.F., T. van Alen, K.T. van de Pas-Schoonen, M.S.M. Jetten, and M. Strous. 2009. Enrichment and molecular detection of denitrifying methanotrophic bacteria of the NC10 phylum. Appl. Environ. Microbiol. 75:3656-3662.
23. Ettwig, K.F., M.K. Butler, D. Le Paslier, et al. 2010. Nitrite-driven anaerobic methane oxidation by oxygenic bacteria. Nature 464:543-548.
24. Falkowski, P.G., T. Fenchel, and E.F. Delong. 2008. The microbial engines that drive earth's biogeochemical cycles. Science 320:1034-1039.
25. Farnelid, H., A.F. Andersson, S. Bertilsson, W.A. Al-Soud, L.H. Hansen, S. Sørensen, G.F. Steward, Å. Hagström, and L. Riemann. 2011. Nitrogenase gene amplicons from global marine surface waters are dominated by genes of non-cyanobacteria. PLoS One 6:e19223.
26. Fierer, N., M.A. Bradford, and R.B. Jackson. 2007. Toward an ecological classifcation of soil bacteria. Ecology 88:1354-1364.
27. Finzi-Hart, J.A., J. Pett-Ridge, P.K. Weber, R. Popa, S.J. Fallon, T. Gunderson, I.D. Hutcheon, K.H. Nealson, and D.G. Capone. 2009. Fixation and fate of C and N in the cyanobacterium Trichodesmium using nanometer-scale secondary ion mass spectrometry. Proc. Natl. Acad. Sci. U.S.A. 106:6345-6350.
28. Fujimura, R., Y. Sato, T. Nishizawa, K. Nanba, K. Oshima, M. Hattori, T. Kamijo, and H. Ohta. 2012. Analysis of early bacterial communities on volcanic deposits on the Island of Miyake (Miyake-jima), Japan: a 6-year study at a fxed site. Microbes Environ. 27:19-29.
29. Fujitani, H., Y. Aoi, and S. Tsuneda. 2013. Selective enrichment of two different types of Nitrospira-like nitrite-oxidizing bacteria from a wastewater treatment plant. Microbes Environ. 28:236-243.
30. Geisseler, D., W.R. Horwath, R.G. Joergensen, and B. Ludwig. 2010. Pathways of nitrogen utilization by soil microorganisms-a review. Soil Biol. Biochem. 42:2058-2067.
31. Girvan, M.S., C.D. Campbell, K. Killham, J.I. Prosser, and L.A. Glover. 2005. Bacterial diversity promotes community stability and functional resilience after perturbation. Environ. Microbiol. 7:301-313.
32. Graham, D.W., C.W. Knapp, E.S. Van Vleck, K. Bloor, T.B. Lane, and C.E. Graham. 2007. Experimental demonstration of chaotic instability in biological nitrifcation. ISME J. 1:385-393.
33. Griffn, B.M., J. Schott, and B. Schink. 2007. Nitrite, an electron donor for anoxygenic photosynthesis. Science 316:1870.
34. Gubry-Rangin, C., B. Hai, C. Quince, M. Engel, B.C. Thomson, P. James, M. Schloter, R.I. Griffths, J.I. Prosser, and G.W. Nicol. 2011. Niche specialization of terrestrial archaeal ammonia oxidizers. Proc. Natl. Acad. Sci. U.S.A. 108:21206-21211.
35. Haroon, M.F., S. Hu, Y. Shi, M. Imelfort, J. Keller, P. Hugenholtz, Z. Yuan, and G.W. Tyson. 2013. Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage. Nature 500:567-570.
36. Hawkes, C.V., I.F. Wren, D.J. Herman, and M.K. Firestone. 2005. Plant invasion alters nitrogen cycling by modifying the soil nitrifying community. Ecol. Lett. 8:976-985.
37. Hayakawa, A., M. Hatakeyama, R. Asano, Y. Ishikawa, and S. Hidaka. 2013. Nitrate reduction coupled with pyrite oxidation in the surface sediments of a sulfde-rich ecosystem. J. Geophys. Research: Biogeosci. 118:639-649.
38. Henderson, S.L., C.E. Dandie, C.L. Patten, B.J. Zebarth, D.L. Burton, J.T. Trevors, and C. Goyer. 2010. Changes in denitrifer abundance, denitrifcation gene mRNA levels, nitrous oxide emissions, and denitrifcation in anoxic soil microcosms amended with glucose and plant residues. Appl. Environ. Microbiol. 76:2155-2164.
39. Hong, Y., W. Youshao, and F. Chen. 2013. Archaea dominate ammonia oxidizers in the Permian water ecosystem of midland basin. Microbes Environ. 28:396-399.
40. Hu, S., R.J. Zeng, L.C. Burow, P. Lant, J. Keller, and Z. Yuan. 2009. Enrichment of denitrifying anaerobic methane oxidizing microorganisms. Environ. Microbiol. Rep. 1:377-384.
41. Inaba, S., F. Ikenishi, M. Itakura, M. Kikuchi, S. Eda, N. Chiba, C. Katsuyama, Y. Suwa, H. Mitsui, and K. Minamisawa. 2012. N2O emission from degraded soybean nodules depends on denitrifcation by Bradyrhizobium japonicum and other microbes in the rhizosphere. Microbes Environ. 27:470-476.
42. Ishii, S., S. Ikeda, K. Minamisawa, and K. Senoo. 2011. Nitrogen cycling in rice paddy environments: past achievements and future challenges. Microbes Environ. 26:282-292.
43. Ishii, S., H. Ohno, M. Tsuboi, S. Otsuka, and K. Senoo. 2011. Identifcation and isolation of active N2O reducers in rice paddy soil. ISME J. 5:1936-1945.
44. Isobe, K., K. Koba, S. Otsuka, and K. Senoo. 2011. Nitrifcation and nitrifying microbial communities in forest soils. J. Fore. Res. 16:351-362.
45. Isobe, K., Y. Suwa, J. Ikutani, et al. 2011. Analytical techniques for quantifying 15N/14N of nitrate, nitrite, total dissolved nitrogen and ammonium in environmental samples using a gas chromatograph equipped with a quadrupole mass spectrometer. Microbes Environ. 26:46-53.
46. Isobe, K., K. Koba, Y. Suwa, J. Ikutani, Y. Fang, M. Yoh, J. Mo, S. Otsuka, and K. Senoo. 2012. High abundance of ammonia-oxidizing archaea in acidifed subtropical forest soils in southern China after long-term N deposition. FEMS Microbiol. Ecol. 80:193-203.
47. Isobe, K., K. Koba, Y. Suwa, et al. 2012. Nitrite transformations in an N-saturated forest soil. Soil Biol. Biochem. 52:61-63.
48. Itoh, H., S. Ishii, Y. Shiratori, K. Oshima, S. Otsuka, M. Hattori, and K. Senoo. 2013. Seasonal transition of active bacterial and archaeal communities in relation to water management in paddy soils. Microbes Environ. 28:370-380.
49. Janssen, P.H. 2006. Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl. Environ. Microbiol. 72:1719-1728.
50. Jayakumar, A., M.M.D. Al-Rshaidat, B.B. Ward, and M.R. Mulholland. 2012. Diversity, distribution, and expression of diazotroph nifH genes in oxygen-defcient waters of the Arabian Sea. FEMS Microbiol. Ecol. 82:597-606.
51. Jones, C.M., D.R.H. Graf, D. Bru, L. Philippot, and S. Hallin. 2013. The unaccounted yet abundant nitrous oxide-reducing microbial community: a potential nitrous oxide sink. ISME J. 7:417-726.
52. Jones, R.T., M.S. Robeson, C.L. Lauber, M. Hamady, R. Knight, and N. Fierer. 2009. A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses. ISME J. 3:442-453.
53. Jumadi, O., Y. Hala, A. Muis, A. Ali, M. Palennari, K. Yagi, and K. Inubushi. 2008. Infuences of chemical fertilizers and a nitrifcation inhibitor on greenhouse gas fuxes in a corn (Zea mays L.) feld in Indonesia. Microbes Environ. 23:29-34.
54. Kaiser, K., and R. Benner. 2008. Major bacterial contribution to the ocean reservoir of detrital organic carbon and nitrogen. Limnol. Oceanogr. 53:99-112.
55. Kalvelage, T., M.M. Jensen, S. Contreras, N.P. Revsbeth, P. Lam, M. Günter, J. LaRoche, G. Lavik, and M.M.M. Kuypers. 2011. Oxygen sensitivity of anammox and coupled N-cycle processes in oxygen minimum zones. PLoS One 6: e29299.
56. Kartal, B., W.J. Maalcke, N.M. de Almeida, et al. 2011. Molecular mechanism of anaerobic ammonium oxidation. Nature 479:127-130.
57. Kato, S., K. Hashimoto, and K. Watanabe. 2012. Microbial inter-species electron transfer via electric currents through conductive minerals. Proc. Natl. Acad. Sci. U.S.A. 109:10042-10046.
58. Katsuyama, C., N. Kondo, Y. Suwa, T. Yamagishi, M. Itoh, N. Ohte, H. Kimura, K. Nagaosa, and K. Kato. 2008. Denitrifcation activity and relevant bacteria revealed by nitrite reductase gene fragments in soil of temperate mixed forest. Microbes Environ. 23:337-345.
59. Kaur, K., S. Goyal, and K.K. Kapoor. 2008. Impact of organic fertilizers with and without chemical fertilizers on soil chemical properties and the establishment of nitrogen-fxing bacteria in the rhizosphere. Microbes Environ. 23:313-316.
60. Kindaichi, T., T. Awata, Y. Suzuki, K. Tanabe, M. Hatamoto, N. Ozaki, and A. Ohashi. 2011. Enrichment using an up-fow column reactor and community structure of marine anammox bacteria from coastal sediment. Microbes Environ. 26:67-73.
61. Kirchman, D.L. 1994. The uptake of inorganic nutrients by hetero-trophic bacteria. Microbial Ecol. 28:255-271.
62. Koch, A.L. 2001. Oligotrophs versus copiotrophs. BioEssays. 23:657-661.
63. Kojima, H., M. Tsutsumi, K. Ishikawa, T. Iwata, M. Mußmann, and M. Fukui. 2012. Distribution of putative denitrifying methane oxidizing bacteria in sediment of a freshwater lake, Lake Biwa. Syst. Appl. Microbiol. 35:233-238.
64. Kondo, K., K. Yoshimatsu, and T. Fujiwara. 2012. Expression, and molecular and enzymatic characterization of Cu-containing nitrite reductase from a marine ammonia-oxidizing gammaproteo-bacterium, Nitrosococcus oceani. Microbes Environ. 27:407-412.
65. Könneke, M., A.E. Bernhard, J.R. de La Torre, C.B. Walker, J.B. Waterbury, and D.A. Stahl. 2005. Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437:543-546.
66. Kowalchuk, G.A., and J.R. Stephen. 2001. Ammonia-oxidizing bacteria: a model for molecular microbial ecology. Annu. Rev. Microbiol. 55:485-529.
67. Lam, P., G. Lavik, M.M. Jensen, J. van de Vossenberg, M. Schmid, D. Woebken, D. Gutierrez, R. Amann, M.S.M. Jetten, and M.M.M. Kuypers. 2009. Revising the nitrogen cycle in the Peruvian oxygen minimum zone. Proc. Natl. Acad. Sci. U.S.A. 106:4752-4757.
68. Lehtovirta-Morley, L.E., K. Stoecker, A. Vilcinskas, J.I. Prosser, and G.W. Nicol. 2011. Cultivation of an obligate acidophilic ammonia oxidizer from a nitrifying acid soil. Proc. Natl. Acad. Sci. U.S.A. 108:15892-15897.
69. Li, M., H. Cao, Y.G. Hong, and J.D. Gu. 2011. Seasonal dynamics of anammox bacteria in estuarial sediment of the Mai Po Nature Reserve revealed by analyzing the 16S rRNA and hydrazine oxidore-ductase (hzo) genes. Microbes Environ. 26:15-22.
70. Lin, L., Z. Li, C. Hu, X. Zhang, S. Chang, L. Yang, Y. Li, and Q. An. 2012. Plant growth-promoting nitrogen-fxing enterobacteria are in association with sugarcane plants growing in Guangxi, China. Microbes Environ. 27:391-398.
71. Lipson, D.A., and S.K. Schmidt. 2004. Seasonal changes in an alpine soil bacterial community in the Colorado rocky mountains. Appl. Environ. Microbiol. 70:2867-2879.
72. Lipson, D.A., C.W. Schadt, and S.K. Schmidt. 2002. Changes in soil microbial community structure and function in an alpine dry meadow following spring snow melt. Microbial Ecol. 43:307-314.
73. Lücker, S., B. Nowka, T. Rattei, E. Spieck, and H. Daims. 2013. The genome of Nitrospina gracilis illuminates the metabolism and evolution of the major marine nitrite oxidizer. Front. Microbiol. 4:27.
74. Luesken, F.A., M.L. Wu, H.J.M. Op den Camp, J.T. Keltjens, H. Stunnenberg, K.J. Francoijs, M. Strous, and M.S. Jetten. 2012. Effect of oxygen on the anaerobic methanotroph 'Candidatus Methylomirabilis oxyfera': kinetic and transcriptional analysis. Environ. Microbiol. 14:1024-1034.
75. Martens-Habbena, W., P.M. Berube, H. Urakawa, J.R. de La Torre, and D.A. Stahl. 2009. Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria. Nature 461:976-979.
76. Martin, A.P., and P. Pondaven. 2006. New primary production and nitrifcation in the western subtropical North Atlantic: a modeling study. Global Biogeochem. Cycles 20:GB4014.
77. Martiny, A.C., K. Treseder, and G. Pusch. 2013. Phylogenetic conservatism of functional traits in microorganisms. ISME J. 7:830-838.
78. Matsumoto, S., D. Ishikawa, G. Saeki, Y. Aoi, and S. Tsuneda. 2010. Microbial population dynamics and community structure during the formation of nitrifying granules to treat ammonia-rich inorganic wastewater. Microbes Environ. 25:164-170.
79. Matsutani, N., T. Nakagawa, K. Nakamura, R. Takahashi, K. Yoshihara, and T. Tokuyama. 2011. Enrichment of a novel marine ammonia-oxidizing archaeon obtained from sand of an Eelgrass Zone. Microbes Environ. 26:23-29.
80. McCarthy, M.D. 1998. Major bacterial contribution to marine dissolved organic nitrogen. Science 281:231-234.
81. Mitchell, M.J., D.J. Raynal, and C.T. Driscoll. 1996. Biogeochemistry of a forested watershed in the central Adirondack Mountains: temporal changes and mass balances. Water, Air, Soil Pollu. 88:355-369.
82. Moisander, P.H., R.A. Beinart, I. Hewson, A.E. White, K.S. Johnson, C.A. Carlson, J.P. Montoya, and J.P. Zehr. 2010. Unicellular cyano-bacterial distributions broaden the oceanic N2 fxation domain. Science 327:1512-1514.
83. Montoya, J.P., C.M. Holl, J.P. Zehr, A. Hansen, T.A. Villareal, and D.G. Capone. 2004. High rates of N2 fxation by unicellular diazotrophs in the oligotrophic Pacifc Ocean. Nature 430:1027-1032.
84. Moore, R.M., S. Punshon, C. Mahaffey, and D. Karl. 2009. The relationship between dissolved hydrogen and nitrogen fxation in ocean waters. Deep Sea Res. Part I: Oceanogr. Res. Pap. 56:1449-1458.
85. Morimoto, S., M. Hayatsu, Y. Takada Hoshino, K. Nagaoka, M. Yamazaki, T. Karasawa, M. Takenaka, and H. Akiyama. 2011. Quantitative analyses of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in felds with different soil types. Microbes Environ. 26:248-253.
86. Mulder, A., A.A. Graaf, L.A. Robertson, and J.G. Kuenen. 1995. Anaerobic ammonium oxidation discovered in a denitrifying fuidized bed reactor. FEMS Microbiol Ecol. 16:177-184.
87. Mykytczuk, N.C.S., S.J. Foote, C.R. Omelon, G. Southam, C.W. Greer, and L.G. Whyte. 2013. Bacterial growth at -15°C; molecular insights from the permafrost bacterium Planococcus halocryophilus Or1. ISME J. 7:1211-1126.
88. Narihiro, T., and Y. Kamagata. 2013. Cultivating yet-to-be cultivated microbes: the challenge continues. Microbes Environ. 28:163-165.
89. Ohte, N., M. Mitchell, H. Shibata, N. Tokuchi, H. Toda, and G. Iwatsubo. 2001. Comparative evaluation on nitrogen saturation of forest catchments in Japan and Northeastern United States. Springer Netherlands. Water, Air, Soil Pollu. 130:649-654.
90. Okabe, S., Y. Nakamura, and H. Satoh. 2012. Community structure and in situ activity of nitrifying bacteria in Phragmites root-associated bioflms. Microbes Environ. 27:242-249.
91. Okubo, T., T. Tsukui, H. Maita, et al. 2012. Complete genome sequence of Bradyrhizobium sp. S23321: insights into symbiosis evolution in soil oligotrophs. Microbes Environ. 27:306-315.
92. Pett-Ridge, J., W.L. Silver, and M.K. Firestone. 2006. Redox fuctu-ations frame microbial community impacts on N-cycling rates in a humid tropical forest soil. Biogeochem. 8:95-110.
93. Philippot, L., J. Cuhel, N.P.A. Saby, D. Chèneby, A. Chronáková, D. Bru, D. Arrouays, F. Martin-Laurent, and M. Simek. 2009. Mapping feld-scale spatial patterns of size and activity of the denitrifer community. Environ Microbiol. 11:1518-1526.
94. Philippot, L., J. Andert, C.M. Jones, D. Bru, and S. Hallin. 2010. Importance of denitrifers lacking the genes encoding the nitrous oxide reductase for N2O emissions from soil. Glob. Change Biol. 17:1497-1504.
95. Raes, J., and P. Bork. 2008. Molecular eco-systems biology: towards an understanding of community function. Nature Rev. Microbiol. 6:693-699.
96. Raghoebarsing, A.A., A. Pol, K.T. van de Pas-Schoonen, et al. 2006. A microbial consortium couples anaerobic methane oxidation to denitrifcation. Nature 440:918-921.
97. Ravishankara, A.R., J.S. Daniel, and R.W. Portmann. 2009. Nitrous oxide (N2O): the dominant ozone-depleting substance emitted in the 21st century. Science 326:123-125.
98. Reguera, G., K.D. McCarthy, T. Mehta, J.S. Nicoll, M.T. Tuominen, and D.R. Lovley. 2005. Extracellular electron transfer via microbial nanowires. Nature 435:1098-1101.
99. Richards, F. 1965. Anoxic basins and fjords, p. 611-645. In J. Riley and G. Skirrow (ed.), Chemical Oceanography. Academic Press, London.
100. Saito, T., S. Ishii, S. Otsuka, M. Nishiyama, and K. Senoo. 2008. Identifcation of novel Betaproteobacteria in a succinate-assimilating population in denitrifying rice paddy soil by using stable isotope probing. Microbes Environ. 23:192-200.
101. Sakami, T. 2012. Distribution of ammonia-oxidizing archaea and bacteria in the surface sediments of Matsushima Bay in relation to environmental variables. Microbes Environ. 27:61-66.
102. Sanford, R.A., D.D. Wagner, Q. Wu, et al. 2012. Unexpected nondenitrifer nitrous oxide reductase gene diversity and abundance in soils. Proc. Natl. Acad. Sci. U.S.A. 109:19709-19714.
103. Sato, Y., H. Ohta, T. Yamagishi, et al. 2012. Detection of anammox activity and 16S rRNA genes in ravine paddy feld soil. Microbes Environ. 27:316-319.
104. Schadt, C.W., A.P. Martin, D.A. Lipson, and S.K. Schmidt. 2003. Seasonal dynamics of previously unknown fungal lineages in tundra soils. Science 301:1359-1361.
105. Schimel, J.P., and J. Bennett. 2004. Nitrogen mineralization: challenges of a changing paradigm. Ecology 85:591-602.
106. Schimel J.P., J Bennet, and N. Fierer. 2005. Microbial community composition and soil nitrogen cycling: is there really a connection? p. 171-188. In R.D. Bardgett, M.B. Usher, and D.W. Hopkins (ed.) Biological Diversity and Function in Soil. Cambridge University Press, USA.
107. Schloss, P.D., and J. Handelsman. 2004. Status of the microbial census. Microbiol. Mol. Biol. Rev. 68:686-691.
108. Schott, J., B.M. Griffn, and B. Schink. 2010. Anaerobic phototrophic nitrite oxidation by Thiocapsa sp. strain KS1 and Rhodopseudomonas sp. strain LQ17. Microbiol. 156:2428-2437.
109. Shibata, H., Y. Hasegawa, T. Watanabe, and K. Fukuzawa. 2013. Impact of snowpack decrease on net nitrogen mineralization and nitrifcation in forest soil of northern Japan. Biogeochemistry 116:69-82.
110. Shimomura, Y., S. Morimoto, Y. Takada Hoshino, Y. Uchida, H. Akiyama, and M. Hayatsu. 2012. Comparison among amoA primers suited for quantifcation and diversity analyses of ammonia-oxidizing bacteria in soil. Microbes Environ. 27:94-98.
111. Sorokin, D.Y., S. Lücker, D. Vejmelkova, et al. 2012. Nitrifcation expanded: discovery, physiology and genomics of a nitrite-oxidizing bacterium from the phylum Chlorofexi. ISME J. 6:2245-2256.
112. Strous, M., E. Pelletier, S. Mangenot, et al. 2006. Deciphering the evolution and metabolism of an anammox bacterium from a community genome. Nature 440:790-794.
113. Strous, M., J.A. Fuerst, E.H. Kramer, S. Logemann, G. Muyzer, K.T. van de Pas-Schoonen, R. Webb, J. G. Kuenen, and M.S. Jetten. 1999. Missing lithotroph identifed as new planctomycete. Nature 400:446-449.
114. Tago, K., S. Ishii, T. Nishizawa, S. Otsuka, and K. Senoo. 2011. Phylogenetic and functional diversity of denitrifying bacteria isolated from various rice paddy and rice-soybean rotation felds. Microbes Environ. 26:30-35.
115. Takada Hoshino, Y., S. Morimoto, M. Hayatsu, K. Nagaoka, C. Suzuki, T. Karasawa, M. Takenaka, and H. Akiyama. 2011. Effect of soil type and fertilizer management on archaeal community in upland feld soils. Microbes Environ. 26:307-316.
116. Takahashi, M., T. Yamada, M. Tanno, H. Tsuji, and A. Hiraishi. 2011. Nitrate removal effciency and bacterial community dynamics in denitrifcation processes using poly (L-lactic acid) as the solid substrate. Microbes Environ. 26:212-219.
117. Teske, A., E. Alm, J.M. Regan, S. Toze, B.E. Rittmann, and D.A. Stahl. 1994. Evolutionary relationships among ammonia- and nitrite-oxidizing bacteria. J. Bacteriol. 176:6623-6630.
118. Thamdrup, B. 2012. New pathways and processes in the global nitrogen cycle. Annu. Rev. Ecol. Evol. Syst. 43:407-428.
119. Thompson, A.W., R.A. Foster, A. Krupke, B.J. Carter, N. Musat, D. Vaulot, M.M.M. Kuypers, and J.P. Zehr. 2012. Unicellular cyano-bacterium symbiotic with a single-celled eukaryotic alga. Science 337:1546-1550.
120. Tripp, H.J., S.R. Bench, K.A. Turk, R.A. Foster, B.A. Desany, F. Niazi, J.P. Affourtit, and J.P. Zehr. 2010. Metabolic streamlining in an open-ocean nitrogen-fxing cyanobacterium. Nature 464:90-94.
121. Ushiki, N., H. Fujitani, Y. Aoi, and S. Tsuneda. 2013. Isolation of Nitrospira belonging to sublineage II from a wastewater treatment plant. Microbes Environ. 28:346-353.
122. Vitousek, P., and R. Howarth. 1991. Nitrogen limitation on land and in the sea: how can it occur? Biogeochem. 13:87-115.
123. Voss, M., and J.P. Montoya. 2009. Nitrogen cycle: oceans apart. Nature 461:49-50.
124. Wada, E., and A. Hattori. 1991. Nitrogen in the Sea: Forms, Abundances, and Rate Processes. CRC Press Llc, USA.
125. Wang, Y., G. Zhu, H.R. Harhangi, B. Zhu, M.S.M. Jetten, C. Yin, and H.J.M. Op den Camp. 2012. Co-occurrence and distribution of nitrite-dependent anaerobic ammonium and methane-oxidizing bacteria in a paddy soil. FEMS microbial. Lett. 336:79-88.
126. Ward, B.B., A.H. Devol, J.J. Rich, B.X. Chang, S.E. Bulow, H. Naik, A. Pratihary, and A. Jayakumar. 2009. Denitrifcation as the dominant nitrogen loss process in the Arabian Sea. Nature 461:78-81.
127. Wieder, W.R., C.C. Cleveland, P.G. Taylor, D.R. Nemergut, E.L. Hinckley, L. Philippot, D. Bru, S.R. Weintraub, M. Martin, and A.R. Townsend. 2012. Experimental removal and addition of leaf litter inputs reduces nitrate production and loss in a lowland tropical forest. Biogeochem. 113:629-642.
128. Wilson, J.B., E. Spijkerman, and J. Huisman. 2007. Is there really insuffcient support for Tilman's R* concept? A comment on Miller et al. American Nat. 169:700-706.
129. Wood, D.W., J.C. Setubal, R. Kaul, et al. 2001. The genome of the natural genetic engineer Agrobacterium tumefaciens C58. Science 294:2317-2323.
130. Yamamoto, N., R. Oishi, Y. Suyama, C. Tada, and Y. Nakai. 2012. Ammonia-oxidizing bacteria rather than ammonia-oxidizing archaea were widely distributed in animal manure composts from feld-scale facilities. Microbes Environ. 27:519-524.
131. Yang, W.H., K.A. Weber, and W.L. Silver. 2012. Nitrogen loss from soil through anaerobic ammonium oxidation coupled to iron reduction. Nature Geosci. 5:538-541.
132. Yasuda, T., M. Waki, I. Yoshinaga, T. Amano, K. Suzuki, Y. Tanaka, T. Yamagishi, and Y. Suwa. 2011. Evidence of exponential growth of an anammox population in an anaerobic batch culture. Microbes Environ. 26:266-269.
133. Yool, A., A.P. Martin, C. Fernández, and D.R. Clark. 2007. The signifcance of nitrifcation for oceanic new production. Nature 447:999-1002.
134. Yoshida, M., S. Ishii, S. Otsuka, and K. Senoo. 2010. nirK-harboring denitrifers are more responsive to denitrifcation-inducing conditions in rice paddy soil than nirS-harboring bacteria. Microbes Environ. 25:45-48.
135. Yoshida, M., S. Ishii, D. Fujii, S. Otsuka, and K. Senoo. 2012. Identifcation of active denitrifers in rice paddy soil by DNA- and RNA-based analyses. Microbes Environ. 27:456-461.
136. Yoshinaga, I., T. Amano, T. Yamagishi, K. Okada, S. Ueda, Y. Sako, and Y. Suwa. 2011. Distribution and diversity of anaerobic ammonium oxidation (anammox) bacteria in the sediment of a eutrophic freshwater lake, Lake Kitaura, Japan. Microbes Environ. 26:189-197.
137. Zehr, J.P. 2011. Nitrogen fxation by marine cyanobacteria. Trends Microbiol. 19:162-173.
138. Zehr, J.P., S.R. Bench, B.J. Carter, I. Hewson, F. Niazi, T. Shi, H.J. Tripp, and J.P. Affourtit. 2008. Globally distributed uncultivated oceanic N2-fxing cyanobacteria lack oxygenic photosystem II. Science 322:1110-1112.
139. Zehr, J.P., J.P. Montoya, I. Hewson, et al. 2007. Nitrogenase gene expression and N2 fxation in the North Pacifc Subtropical Gyre. Limnol. Oceanogr. 52:169-183.
140. Zehr, J.P., J.B. Waterbury, P.J. Turner, J.P. Montoya, E. Omoregie, G.F. Steward, A. Hansen, and D.M. Karl. 2001. Unicellular cyano-bacteria fx N2 in the subtropical North Pacifc Ocean. Nature 412:635-638.
141. Zhang, L.M., P.R. Offre, J.Z. He, D.T. Verhamme, G.W. Nicol, and J.I. Prosser. 2010. Autotrophic ammonia oxidation by soil thaumar-chaea. Proc. Natl. Acad. Sci. U.S.A. 17240-17245.
142. Zhu, G., S. Wang, Y. Wang, C. Wang, N. Risgaard-Petersen, M.S. Jetten, and C. Yin. 2011. Anaerobic ammonia oxidation in a fertilized paddy soil. ISME J. 5:1905-1912.
143. Zimmerman, A.E., A.C. Martiny, and S.D. Allison. 2013. Microdiversity of extracellular enzyme genes among sequenced prokaryotic genomes. ISME J. 7:1187-1199.