Information de reference pour ce titreAccession Number: | 00125945-200705000-00006.
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Author: | Mincer, Tracy J. 1; Church, Matthew J. 2; Taylor, Lance Trent 3; Preston, Christina 3; Karl, David M. 2; DeLong, Edward F. 1,*
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Institution: | (1)Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, MA 02139, USA. (2)School of Ocean and Earth Science and Technology, Department of Oceanography, University of Hawaii, Honolulu, HI 96822, USA. (3)Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA.
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Title: | |
Source: | Environmental Microbiology. 9(5):1162-1175, May 2007.
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Abstract: | Summary: The recent isolation of the ammonia-oxidizing crenarchaeon Nitrosopumilus maritimus has expanded the known phylogenetic distribution of nitrifying phenotypes beyond the domain Bacteria. To further characterize nitrification in the marine environment and explore the potential crenarchaeal contribution to this process, we quantified putative nitrifying genes and phylotypes in picoplankton genomic libraries and environmental DNA samples from coastal and open ocean habitats. Betaproteobacteria ammonia monooxygenase subunit A (amoA) gene copy numbers were low or undetectable, in stark contrast to crenarchaeal amoA-like genes that were broadly distributed and reached up to 6 x 104 copies ml-1. Unexpectedly, in the North Pacific Subtropical Gyre, a deeply branching crenarchaeal group related to a hot spring clade (pSL12) was at times abundant below the euphotic zone. Quantitative data suggested that the pSL12 relatives also contain archaeal amoA-like genes. In both coastal and open ocean habitats, close relatives of known nitrite-oxidizing Nitrospina species were well represented in genomic DNA libraries and quantitative PCR profiles. Planktonic Nitrospina depth distributions correlated with those of Crenarchaea. Overall, the data suggest that amoA-containing Crenarchaea are more phylogenetically diverse than previously reported. Additionally, distributional patterns of planktonic Crenarchaea and Nitrospina species suggest potential metabolic interactions between these groups in the ocean's water column.
Copyright (C) 2007 Blackwell Publishing Ltd.
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References: | Arp, D.J., and Stein, L.Y. (2003) Metabolism of inorganic N compounds by ammonia-oxidizing bacteria. Crit Rev Biochem Mol Biol 38: 471-495.
Barns, S.M., Delwiche, C.F., Palmer, J.D., and Pace, N.R. (1996) Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. Proc Natl Acad Sci USA 93: 9188-9193.
Beja, O., Suzuki, M.T., Koonin, E.V., Aravind, L., Hadd, A., Nguyen, L.P., et al. (2000) Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. Environ Microbiol 2: 516-529.
Beja, O., Koonin, E.V., Aravind, L., Taylor, L.T., Seitz, H., Stein, J.L., et al. (2002) Comparative genomic analysis of archaeal genotypic variants in a single population and in two different oceanic provinces. Appl Environ Microbiol 68: 335-345.
Brown, M.V., Schwalbach, M.S., Hewson, I., and Fuhrman, J.A. (2005) Coupling 16S-ITS rDNA clone libraries and automated ribosomal intergenic spacer analysis to show marine microbial diversity: development and application to a time series. Environ Microbiol 7: 1466-1479.
Church, M.J., DeLong, E.F., Ducklow, H.W., Karner, M.B., Preston, C.M., and Karl, D.M. (2003) Abundance and distribution of planktonic Archaea and Bacteria in the waters west of the Antarctic Peninsula. Limnol Oceanogr 48: 1893-1902.
Codispoti, L.A., Brandes, J.A., Christensen, J.P., Devol, A.H., Naqvi, S.W.A., Paerl, H.W., and Yoshinari, T. (2001) The oceanic fixed nitrogen and nitrous oxide budgets: moving targets as we enter the anthropocene? Sci Mar 65: 85-105.
Dalsgaard, T., Canfield, D.E., Petersen, J., Thamdrup, B., and Acuna-Gonzalez, J. (2003) N2 production by the anammox reaction in the anoxic water column of Golfo Dulce, Costa Rica. Nature 422: 606-608.
DeLong, E.F., Franks, D.G., and Alldredge, A.L. (1993) Phylogenetic diversity of aggregate-attached vs free-living marine bacterial assemblages. Limnol Oceanogr 38: 924-934.
DeLong, E.F., Taylor, L.T., Marsh, T.L., and Preston, C.M. (1999) Visualization and enumeration of marine planktonic archaea and bacteria by using polyribonucleotide probes and fluorescent in situ hybridization. Appl Environ Microbiol 65: 5554-5563.
DeLong, E.F., Preston, C.M., Mincer, T., Rich, V., Hallam, S.J., Frigaard, N.U., et al. (2006) Community genomics among stratified microbial assemblages in the ocean's interior. Science 311: 496-503.
Dore, J.E., and Karl, D.M. (1996) Nitrification in the euphotic zone as a source for nitrite, nitrate, and nitrous oxide at Station ALOHA. Limnol Oceanogr 41: 1619-1628.
Francis, C.A., Roberts, K.J., Beman, J.M., Santoro, A.E., and Oakley, B.B. (2005) Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. Proc Natl Acad Sci USA 102: 14683-14688.
Frigaard, N.U., Martinez, A., Mincer, T.J., and DeLong, E.F. (2006) Proteorhodopsin lateral gene transfer between marine planktonic Bacteria and Archaea. Nature 439: 847-850.
Fuchs, B.M., Woebken, D., Zubkov, M.V., Burkill, P., and Amann, R. (2005) Molecular identification of picoplankton populations in contrasting waters of the Arabian Sea. Aquat Microb Ecol 39: 145-157.
Goreau, T.J., Kaplan, W.A., Wofsy, S.C., McElroy, M.B., Valois, F.W., and Watson, S.W. (1980) Production of NO(2) and N(2)O by nitrifying bacteria at reduced concentrations of oxygen. Appl Environ Microbiol 40: 526-532.
Guerrero, M.A., and Jones, R.D. (1996) Photoinhibition of marine nitrifying bacteria. 1. Wavelength-dependent response. Mar Ecol Prog Ser 141: 183-192.
Hallam, S., Konstantinidis, K., Brochier, C., Putnam, N., Schleper, C., Watanabe, Y., et al. (2006a) Genomic analysis of the uncultivated marine crenarchaeon Cenarchaeum symbiosum. Proc Natl Acad Sci USA 103: 18296-18301.
Hallam, S.J., Mincer, T.J., Schleper, C., Preston, C.M., Roberts, K., Richardson, P.M., and DeLong, E.F. (2006b) Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota. PLoS Biol 4: e95.
Herndl, G.J., Reinthaler, T., Teira, E., van Aken, H., Veth, C., Pernthaler, A., and Pernthaler, J. (2005) Contribution of Archaea to total prokaryotic production in the deep Atlantic Ocean. Appl Environ Microbiol 71: 2303-2309.
Horrigan, S.G., Carlucci, A.F., and Williams, P.M. (1981) Light inhibition of nitrification in sea surface films. J Mar Res 39: 557-565.
Horz, H.P., Barbrook, A., Field, C.B., and Bohannan, B.J.M. (2004) Ammonia-oxidizing bacteria respond to multifactorial global change. Proc Natl Acad Sci USA 101: 15136-15141.
Ingalls, A.E., Shah, S.R., Hansman, R.L., Aluwihare, L.I., Santos, G.M., Druffel, E.R., and Pearson, A. (2006) Quantifying archaeal community autotrophy in the mesopelagic ocean using natural radiocarbon. Proc Natl Acad Sci USA 103: 6442-6447.
Jetten, M.S.M., Cirpus, I., Kartal, B., van Niftrik, L., van de Pas-Schoonen, K.T., Sliekers, O., et al. (2005) 1994-2004: 10 years of research on the anaerobic oxidation of ammonium. Biochem Soc Trans 33: 119-123.
Karl, D.M. (2002) Nutrient dynamics in the deep blue sea. Trends Microbiol 10: 410-418.
Karner, M.B., DeLong, E.F., and Karl, D.M. (2001) Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature 409: 507-510.
Konneke, M., Bernhard, A.E., de la Torre, J.R., Walker, C.B., Waterbury, J.B., and Stahl, D.A. (2005) Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437: 543-546.
Konstantinidis, K.T., and Tiedje, J.M. (2005) Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA 102: 2567-2572.
Koops, H.P., and Pommerening-Roser, A. (2001) Distribution and ecophysiology of the nitrifying bacteria emphasizing cultured species. FEMS Microbiol Ecol 37: 1-9.
Kowalchuk, G.A., and Stephen, J.R. (2001) Ammonia-oxidizing bacteria: a model for molecular microbial ecology. Annu Rev Microbiol 55: 485-529.
Kuypers, M.M., Sliekers, A.O., Lavik, G., Schmid, M., Jorgensen, B.B., Kuenen, J.G., et al. (2003) Anaerobic ammonium oxidation by anammox bacteria in the Black Sea. Nature 422: 608-611.
Leininger, S., Urich, T., Schloter, M., Schwark, L., Qi, J., Nicol, G.W., et al. (2006) Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442: 806-809.
Massana, R., Murray, A.E., Preston, C.M., and DeLong, E.F. (1997) Vertical distribution and phylogenetic characterization of marine planktonic Archaea in the Santa Barbara Channel. Appl Environ Microbiol 63: 50-56.
Moreira, D., Rodriguez-Valera, F., and Lopez-Garcia, P. (2006) Metagenomic analysis of mesopelagic Antarctic plankton reveals a novel deltaproteobacterial group. Microbiology 152: 505-517.
Morris, R.M., Rappe, M.S., Urbach, E., Connon, S.A., and Giovannoni, S.J. (2004) Prevalence of the Chloroflexi-related SAR202 bacterioplankton cluster throughout the mesopelagic zone and deep ocean. Appl Environ Microbiol 70: 2836-2842.
Murray, A.E., Preston, C.M., Massana, R., Taylor, L.T., Blakis, A., Wu, K., and DeLong, E.F. (1998) Seasonal and spatial variability of bacterial and archaeal assemblages in the coastal waters near Anvers Island, Antarctica. Appl Environ Microbiol 64: 2585-2595.
Nold, S.C., Zhou, J., Devol, A.H., and Tiedje, J.M. (2000) Pacific Northwest marine sediments contain ammonia-oxidizing bacteria in the beta subdivision of the Proteobacteria. Appl Environ Microbiol 66: 4532-4535.
O'Mullan, G.D., and Ward, B.B. (2005) Relationship of temporal and spatial variabilities of ammonia-oxidizing bacteria to nitrification rates in Monterey Bay, California. Appl Environ Microbiol 71: 697-705.
Olson, R.J. (1981) Differential photoinhibition of marine nitrifying bacteria: a possible mechanism for the formation of the primary nitrite maximum. J Mar Res 39: 227-238.
Park, H.D., Wells, G.F., Bae, H., Criddle, C.S., and Francis, C.A. (2006) Occurrence of ammonia-oxidizing archaea in wastewater treatment plant bioreactors. Appl Environ Microbiol 72: 5643-5647.
Pearson, A., McNichol, A.P., Benitez-Nelson, B.C., Hayes, J.M., and Eglinton, T.I. (2001) Origins of lipid biomarkers in Santa Monica Basin surface sediment: a case study using compound-specific Delta C-14 analysis. Geochim Cosmochim Acta 65: 3123-3137.
Preston, C.M., Wu, K.Y., Molinski, T.F., and DeLong, E.F. (1996) A psychrophilic crenarchaeon inhabits a marine sponge: Cenarchaeum symbiosum gen. nov., sp. nov. Proc Natl Acad Sci USA 93: 6241-6246.
Rotthauwe, J.H., Witzel, K.P., and Liesack, W. (1997) The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations. Appl Environ Microbiol 63: 4704-4712.
Rutherford, K., Parkhill, J., Crook, J., Horsnell, T., Rice, P., Rajandream, M.A., and Barrell, B. (2000) Artemis: sequence visualization and annotation. Bioinformatics 16: 944-945.
Suzuki, M.T., Taylor, L.T., and DeLong, E.F. (2000) Quantitative analysis of small-subunit rRNA genes in mixed microbial populations via 5'-nuclease assays. Appl Environ Microbiol 66: 4605-4614.
Suzuki, M.T., Preston, C.M., Beja, O., de la Torre, J.R., Steward, G.F., and DeLong, E.F. (2004) Phylogenetic screening of ribosomal RNA gene-containing clones in Bacterial Artificial Chromosome (BAC) libraries from different depths in Monterey Bay. Microb Ecol 48: 473-488.
Swofford, D. (2000) Phylogenetic Analysis Using Parsimony (and Other Methods), Version 4.0b10. Sunderland, MA, USA: Sinauer Associates.
Treusch, A.H., Leininger, S., Kletzin, A., Schuster, S.C., Klenk, H.P., and Schleper, C. (2005) Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling. Environ Microbiol 7: 1985-1995.
Venter, J.C., Remington, K., Heidelberg, J.F., Halpern, A.L., Rusch, D., Eisen, J.A., et al. (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66-74.
Vetriani, C., Jannasch, H.W., MacGregor, B.J., Stahl, D.A., and Reysenbach, A.L. (1999) Population structure and phylogenetic characterization of marine benthic Archaea in deep-sea sediments. Appl Environ Microbiol 65: 4375-4384.
Ward, B.B., and Carlucci, A.F. (1985) Marine ammonia- and nitrite-oxidizing bacteria: serological diversity determined by immunofluorescence in culture and in the environment. Appl Environ Microbiol 50: 194-201.
Ward, B.B., Olson, R.J., and Perry, M.J. (1982) Microbial nitrification rates in the primary nitrite maximum off Southern California. Deep-Sea Res 29: 247-255.
Watson, S.W., and Waterbury, J.B. (1971) Characteristics of two marine nitrite oxidizing bacteria, Nitrospina gracilis nov. gen. nov. sp. and Nitrococcus mobilis nov. gen. nov. sp. Arch Mikrobiol 77: 203-230.
van der Wielen, P.W., Bolhuis, H., Borin, S., Daffonchio, D., Corselli, C., Giuliano, L., et al. (2005) The enigma of prokaryotic life in deep hypersaline anoxic basins. Science 307: 121-123.
Wright, T.D., Vergin, K.L., Boyd, P.W., and Giovannoni, S.J. (1997) A novel delta-subdivision proteobacterial lineage from the lower ocean surface layer. Appl Environ Microbiol 63: 1441-1448.
Wuchter, C., Schouten, S., Boschker, H.T., and Sinninghe Damste, J.S. (2003) Bicarbonate uptake by marine Crenarchaeota. FEMS Microbiol Lett 219: 203-207.
Wuchter, C., Abbas, B., Coolen, M.J.L., Herfort, L., van Bleijswijk, J., Timmers, P., et al. (2006) Archaeal nitrification in the ocean. Proc Natl Acad Sci USA 103: 12317-12322.
Yayanos, A.A. (1995) Microbiology to 10,500 meters in the deep sea. Annu Rev Microbiol 49: 777-805.
Zaballos, M., Lopez-Lopez, A., Ovreas, L., Bartual, S.G., D'Auria, G., Alba, J.C., et al. (2006) Comparison of prokaryotic diversity at offshore oceanic locations reveals a different microbiota in the Mediterranean Sea. FEMS Microbiol Ecol 56: 389-405.
Zehr, J.P., and Ward, B.B. (2002) Nitrogen cycling in the ocean: new perspectives on processes and paradigms. Appl Environ Microbiol 68: 1015-1024.
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Language: | English.
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Document Type: | Research article.
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Journal Subset: | Life Sciences.
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ISSN: | 1462-2912
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NLM Journal Code: | dxc, 100883692
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