全部 标题 作者
关键词 摘要

OALib Journal期刊
ISSN: 2333-9721
费用:99美元

查看量下载量

相关文章

更多...

Patterns of Microbially Driven Carbon Cycling in the Ocean: Links between Extracellular Enzymes and Microbial Communities

DOI: 10.1155/2014/706082

Full-Text   Cite this paper   Add to My Lib

Abstract:

Heterotrophic microbial communities play a central role in the marine carbon cycle. They are active in nearly all known environments, from the surface to the deep ocean, in the sediments, and from the equator to the Poles. In order to process complex organic matter, these communities produce extracellular enzymes of the correct structural specificity to hydrolyze substrates to sizes sufficiently small for uptake. Extracellular enzymatic hydrolysis thus initiates heterotrophic carbon cycling. Our knowledge of the enzymatic capabilities of microbial communities in the ocean is still underdeveloped. Recent studies, however, suggest that there may be large-scale patterns of enzymatic function in the ocean, patterns of community function that may be connected to emerging patterns of microbial community composition. Here I review some of these large-scale contrasts in microbial enzyme activities, between high-latitude and temperate surface ocean waters, contrasts between inshore and offshore waters, changes with depth gradients in the ocean, and contrasts between the water column and underlying sediments. These contrasting patterns are set in the context of recent studies of microbial communities and patterns of microbial biogeography. Focusing on microbial community function as well as composition and potential should yield clearer understanding of the factors driving carbon cycling in the ocean. 1. Introduction Organic matter remineralization by heterotrophic microbial communities is a central component of the marine carbon cycle. These communities process approximately half of all CO2 initially fixed into organic carbon by phytoplankton [1], transforming, repackaging, and respiring dissolved and particulate organic carbon (DOC and POC) and simultaneously regenerating nutrients. In benthic environments, heterotrophic microbes act as the final filter through which organic matter passes before burial, a process that removes CO2 from the atmosphere on geologic timescales [2]. The activities of heterotrophic microbial communities therefore affect marine environments on spatial scales from local to global and on timescales from minutes to millennia. Despite the importance of microbially driven carbon cycling, the specific factors that determine the extent, rate, and location of organic matter remineralization in the ocean are poorly understood. For example, DOC, one of the largest actively cycling organic carbon reservoirs on earth [3], is operationally defined as being labile, semilabile, semirefractory, or refractory [4], based on timescales of removal in

References

[1]  F. Azam and F. Malfatti, “Microbial structuring of marine ecosystems,” Nature Reviews Microbiology, vol. 5, no. 10, pp. 782–791, 2007.
[2]  J. I. Hedges, “Global biogeochemical cycles: progress and problems,” Marine Chemistry, vol. 39, no. 1–3, pp. 67–93, 1992.
[3]  J. I. Hedges, “Why dissolved organics matter,” in Biogeochemistry of Marine Dissolved Organic Matter, D. A. Hansell and C. A. Carlson, Eds., pp. 1–33, Academic Press, San Diego, Calif, USA, 2002.
[4]  D. A. Hansell, C. A. Carlson, and R. Schlitzer, “Net removal of major marine dissolved organic carbon fractions in the subsurface ocean,” Global Biogeochemical Cycles, vol. 26, no. 1, Article ID GB1016, 2012.
[5]  C. A. Carlson, “Production and removal processes,” in Biogeochemistry of Dissolved Organic Matter, D. A. Hansell and C. A. Carlson, Eds., pp. 91–139, Academic Press, San Diego, Calif, USA, 2002.
[6]  D. A. Hansell, “Recalcitrant dissolved organic carbon fractions,” Annual Review of Marine Science, vol. 5, pp. 421–445, 2013.
[7]  G. L. Cowie, J. I. Hedges, F. G. Prahl, and G. J. de Lance, “Elemental and major biochemical changes across an oxidation front in a relict turbidite: an oxygen effect,” Geochimica et Cosmochimica Acta, vol. 59, no. 1, pp. 33–46, 1995.
[8]  C. Arnosti and M. Holmer, “Carbon cycling in a continental margin sediment: contrasts between organic matter characteristics and remineralization rates and pathways,” Estuarine, Coastal and Shelf Science, vol. 58, no. 1, pp. 197–208, 2003.
[9]  S. G. Wakeham, C. Lee, J. I. Hedges, P. J. Hernes, and M. L. Peterson, “Molecular indicators of diagenetic status in marine organic matter,” Geochimica et Cosmochimica Acta, vol. 61, no. 24, pp. 5363–5369, 1997.
[10]  C. Lee, S. Wakeham, and C. Arnosti, “Particulate organic matter in the sea: the composition conundrum,” Ambio, vol. 33, no. 8, pp. 565–575, 2004.
[11]  J. A. Fuhrman, J. A. Steele, I. Hewson et al., “A latitudinal diversity gradient in planktonic marine bacteria,” Proceedings of the National Academy of Sciences of the United States of America, vol. 105, no. 22, pp. 7774–7778, 2008.
[12]  T. Pommier, B. Canb?ck, L. Riemann et al., “Global patterns of diversity and community structure in marine bacterioplankton,” Molecular Ecology, vol. 16, no. 4, pp. 867–880, 2007.
[13]  C. Arnosti, A. D. Steen, K. Ziervogel, S. Ghobrial, and W. H. Jeffrey, “Latitudinal gradients in degradation of marine dissolved organic carbon,” PLoS ONE, vol. 6, no. 12, Article ID e28900, 2011.
[14]  A. Teske, A. Durbin, K. Ziervogel, C. Cox, and C. Arnosti, “Microbial community composition and function in permanently cold seawater and sediments from an Arctic fjord of Svalbard,” Applied and Environmental Microbiology, vol. 77, no. 6, pp. 2008–2018, 2011.
[15]  M. S. Weiss, U. Abele, J. Weckesser, W. Welte, E. Schiltz, and G. E. Schulz, “Molecular architecture and electrostatic properties of a bacterial porin,” Science, vol. 254, no. 5038, pp. 1627–1630, 1991.
[16]  R. I. Amann, W. Ludwig, and K.-. Schleifer, “Phylogenetic identification and in situ detection of individual microbial cells without cultivation,” Microbiological Reviews, vol. 59, no. 1, pp. 143–169, 1995.
[17]  J. B. H. Martiny, B. J. M. Bohannan, J. H. Brown et al., “Microbial biogeography: putting microorganisms on the map,” Nature Reviews Microbiology, vol. 4, no. 2, pp. 102–112, 2006.
[18]  H. Agogué, D. Lamy, P. R. Neal, M. L. Sogin, and G. J. Herndl, “Water mass-specificity of bacterial communities in the North Atlantic revealed by massively parallel sequencing,” Molecular Ecology, vol. 20, no. 2, pp. 258–274, 2011.
[19]  F. M. Lauro, D. McDougald, T. Thomas et al., “The genomic basis of trophic strategy in marine bacteria,” Proceedings of the National Academy of Sciences of the United States of America, vol. 106, no. 37, pp. 15527–15533, 2009.
[20]  M. Martinez-Garcia, D. M. Brazel, B. K. Swan et al., “Capturing single cell genomes of active polysaccharide degraders: an unexpected contribution of verrucomicrobia,” PLoS ONE, vol. 7, no. 4, Article ID e35314, 2012.
[21]  R. Stepanauskas and M. E. Sieracki, “Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time,” Proceedings of the National Academy of Sciences of the United States of America, vol. 104, no. 21, pp. 9052–9057, 2007.
[22]  R. S. Poretsky, S. Sun, X. Mou, and M. A. Moran, “Transporter genes expressed by coastal bacterioplankton in response to dissolved organic carbon,” Environmental Microbiology, vol. 12, no. 3, pp. 616–627, 2010.
[23]  Y. Shi, J. McCarren, and E. F. Delong, “Transcriptional responses of surface water marine microbial assemblages to deep-sea water amendment,” Environmental Microbiology, vol. 14, no. 1, pp. 191–206, 2012.
[24]  E. Rebuffet, A. Groisillier, A. Thompson et al., “Discovery and structural characterization of a novel glycosidase family of marine origin,” Environmental Microbiology, vol. 13, no. 5, pp. 1253–1270, 2011.
[25]  F. L. Poole II, B. A. Gerwe, R. C. Hopkins et al., “Defining genes in the genome of the hyperthermophilic archaeon Pyrococcus furiosus: implications for all microbial genomes,” Journal of Bacteriology, vol. 187, no. 21, pp. 7325–7332, 2005.
[26]  S. Beier, C. M. Jones, V. Mohit, S. Hallin, and S. Bertilsson, “Global phylogeography of chitinase genes in aquatic metagenomes,” Applied and Environmental Microbiology, vol. 77, no. 3, pp. 1101–1106, 2011.
[27]  H. Elifantz, L. A. Waidner, V. K. Michelou, M. T. Cottrell, and D. L. Kirchman, “Diversity and abundance of glycosyl hydrolase family 5 in the North Atlantic Ocean,” FEMS Microbiology Ecology, vol. 63, no. 3, pp. 316–327, 2008.
[28]  M. T. Cottrell and D. L. Kirchman, “Natural assemblages of marine proteobacteria and members of the Cytophaga-flavobacter cluster consuming low- and high-molecular-weight dissolved organic matter,” Applied and Environmental Microbiology, vol. 66, no. 4, pp. 1692–1697, 2000.
[29]  H.-G. Hoppe, “Significance of exoenzymatic activities in the ecology of brackish water: measurements by means of methylumbelliferyl-substrates,” Marine Ecology Progress Series, vol. 11, pp. 299–308, 1983.
[30]  M. Somville and G. Billen, “A method for determining exoproteolytic activity in natural waters,” Limnology & Oceanography, vol. 28, no. 1, pp. 190–193, 1983.
[31]  M. Somville, “Measurement and study of substrate specificity of exoglucosidase activity in eutrophic water,” Applied and Environmental Microbiology, vol. 48, no. 6, pp. 1181–1185, 1984.
[32]  J. R. Christian and D. M. Karl, “Bacterial ectoenzymes in marine waters: Activity ratios and temperature responses in three oceanographic provinces,” Limnology and Oceanography, vol. 40, no. 6, pp. 1042–1049, 1995.
[33]  R. Fukuda, Y. Sohrin, N. Saotome, H. Fukuda, T. Nagata, and I. Koike, “East-west gradient in ectoenzyme activities in the subarctic Pacific: possible regulation by zinc,” Limnology and Oceanography, vol. 45, no. 4, pp. 930–939, 2000.
[34]  R. Zaccone, A. Boldrin, G. Caruso et al., “Enzymatic activities and prokaryotic abundance in relation to organic matter along a West-East Mediterranean Transect (TRANSMED Cruise),” Microbial Ecology, vol. 64, no. 1, pp. 54–66, 2012.
[35]  M. J. McBride, G. Xie, E. C. Martens et al., “Novel features of the polysaccharide-digesting gliding bacterium Flavobacterium johnsoniae as revealed by genome sequence analysis,” Applied and Environmental Microbiology, vol. 75, no. 21, pp. 6864–6875, 2009.
[36]  R. M. Weiner, L. E. Taylor II, B. Henrissat et al., “Complete genome sequence of the complex carbohydrate-degrading marine bacterium, Saccharophagus degradans strain 2–40 T,” PLoS Genetics, vol. 4, no. 5, Article ID e1000087, 2008.
[37]  R. A. J. Warren, “Microbial hydrolysis of polysaccharides,” Annual Review of Microbiology, vol. 50, pp. 183–212, 1996.
[38]  C. Arnosti, “Measurement of depth- and site-related differences in polysaccharide hydrolysis rates in marine sediments,” Geochimica et Cosmochimica Acta, vol. 59, no. 20, pp. 4247–4257, 1995.
[39]  S. Pantoja, C. Lee, and J. F. Marecek, “Hydrolysis of peptides in seawater and sediment,” Marine Chemistry, vol. 57, no. 1-2, pp. 25–40, 1997.
[40]  C. Arnosti, “Microbial extracellular enzymes and the marine carbon cycle,” Annual Review of Marine Science, vol. 3, pp. 401–425, 2011.
[41]  C. Arnosti and D. J. Repeta, “Oligosaccharide degradation by anaerobic marine bacteria: characterization of an experimental system to study polymer degradation in sediments,” Limnology and Oceanography, vol. 39, no. 8, pp. 1865–1877, 1994.
[42]  C. Arnosti, D. J. Repeta, and N. V. Blough, “Rapid bacterial degradation of polysaccharides in anoxic marine systems,” Geochimica et Cosmochimica Acta, vol. 58, no. 12, pp. 2639–2652, 1994.
[43]  S. Pantoja and C. Lee, “Peptide decomposition by extracellular hydrolysis in coastal seawater and salt marsh sediment,” Marine Chemistry, vol. 63, no. 3-4, pp. 273–291, 1999.
[44]  C. Arnosti, “Substrate specificity in polysaccharide hydrolysis: contrasts between bottom water and sediments,” Limnology and Oceanography, vol. 45, no. 5, pp. 1112–1119, 2000.
[45]  C. Arnosti, S. Durkin, and W. H. Jeffrey, “Patterns of extracellular enzyme activities among pelagic marine microbial communities: implications for cycling of dissolved organic carbon,” Aquatic Microbial Ecology, vol. 38, no. 2, pp. 135–145, 2005.
[46]  Y. Obayashi and S. Suzuki, “Proteolytic enzymes in coastal surface seawater: significant activity of endopeptidases and exopeptidases,” Limnology and Oceanography, vol. 50, no. 2, pp. 722–726, 2005.
[47]  Y. Obayashi and S. Suzuki, “Occurrence of exo- and endopeptidases in dissolved and particulate fractions of coastal seawater,” Aquatic Microbial Ecology, vol. 50, no. 3, pp. 231–237, 2008.
[48]  Z. Liu, M. E. Kobiela, G. A. McKee et al., “The effect of chemical structure on the hydrolysis of tetrapeptides along a river-to-ocean transect: AVFA and SWGA,” Marine Chemistry, vol. 119, no. 1–4, pp. 108–120, 2010.
[49]  G. L. Cowie and J. I. Hedges, “Biochemical indicators of diagenetic alteration in natural organic matter mixtures,” Nature, vol. 369, no. 6478, pp. 304–307, 1994.
[50]  B. Dauwe, J. J. Middelburg, P. M. J. Herman, and C. H. R. Heip, “Linking diagenetic alteration of amino acids and bulk organic matter reactivity,” Limnology and Oceanography, vol. 44, no. 7, pp. 1809–1814, 1999.
[51]  C. Arnosti, “Functional differences between Arctic seawater and sedimentary microbial communities: contrasts in microbial hydrolysis of complex substrates,” FEMS Microbiology Ecology, vol. 66, no. 2, pp. 343–351, 2008.
[52]  A. D. Steen and C. Arnosti, “Extracellular peptidase and carbohydrate hydrolase activities in an Arctic fjord (Smeerenburgfjord, Svalbard),” Aquatic Microbial Ecology, vol. 69, no. 2, pp. 93–99, 2013.
[53]  Y. Obayashi, N. Ueoka, and S. Suzuki, “Degradation and utilization of protein derived from Pseudomonas aeruginosa by marine microbial community,” Journal of Oceanography, vol. 66, no. 4, pp. 513–521, 2010.
[54]  A. E. Kriss, I. E. Mishustina, and E. V. Zemtsova, “Biochemical activity of micro-organisms isolated from various regions of the World Ocean,” Journal of General Microbiology, vol. 29, pp. 221–232, 1962.
[55]  A. D. Steen, L. Hamdan, and C. Arnosti, “Dynamics of high molecular weight dissolved organic carbon in the Chesapeake Bay: insights from enzyme activities, carbohydrate concentrations, and microbial metabolism,” Limnology and Oceanography, vol. 53, pp. 936–947, 2008.
[56]  K. Ziervogel and C. Arnosti, “Enzyme activities in the Delaware Estuary affected by elevated suspended sediment load,” Estuarine, Coastal and Shelf Science, vol. 84, no. 2, pp. 253–258, 2009.
[57]  L. D'Ambrosio, K. Ziervogel, B. MacGregor, A. Teske, and C. Arnosti, “Composition and enzymatic function of particle-associated and free-living bacteria: a coastal/offshore comparison,” The ISME Journal, 2014.
[58]  F. O. Gl?ckner, M. Kube, M. Bauer et al., “Complete genome sequence of the marine planctomycete Pirellula sp. strain 1,” Proceedings of the National Academy of Sciences of the United States of America, vol. 100, no. 14, pp. 8298–8303, 2003.
[59]  A.-C. Alderkamp, M. Van Rijssel, and H. Bolhuis, “Characterization of marine bacteria and the activity of their enzyme systems involved in degradation of the algal storage glucan laminarin,” FEMS Microbiology Ecology, vol. 59, no. 1, pp. 108–117, 2007.
[60]  J. A. Dodsworth, P. C. Blainey, S. K. Murugapiran et al., “Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage,” Nature Communications, vol. 4, article 1854, 2013.
[61]  D. P. R. Herlemann, D. Lundin, M. Labrenz et al., “Metagenomic de novo assembly of an aquatic representative of the verrucomicrobial class Spartobacteria,” Applied and Environmental Microbiology, vol. 4, no. 3, Article ID e00569-12, 9 pages, 2013.
[62]  C. Wegner, T. Richter-Heitmann, A. Klindworth et al., “Expression of sulfatases in Rhodopirellula baltica and the diversity of sulfatases in the genus Rhodopirellula,” Marine Genomics, vol. 9, pp. 51–61, 2013.
[63]  A. D. Steen, K. Ziervogel, S. Ghobrial, and C. Arnosti, “Functional variation among polysaccharide-hydrolyzing microbial communities in the Gulf of Mexico,” Marine Chemistry, vol. 138-139, pp. 13–20, 2012.
[64]  T. Nagata, C. Tamburini, J. Arístegui et al., “Emerging concepts on microbial processes in the bathypelagic ocean—ecology, biogeochemistry, and genomics,” Deep-Sea Research II: Topical Studies in Oceanography, vol. 57, no. 16, pp. 1519–1536, 2010.
[65]  F. Baltar, J. Arístegui, E. Sintes, H. M. van Aken, J. M. Gasol, and G. J. Herndl, “Prokaryotic extracellular enzymatic activity in relation to biomass production and respiration in the meso- and bathypelagic waters of the (sub)tropical Atlantic,” Environmental Microbiology, vol. 11, no. 8, pp. 1998–2014, 2009.
[66]  F. Baltar, J. Arístegui, J. M. Gasol, E. Sintes, H. M. van Aken, and G. J. Herndl, “High dissolved extracellular enzymatic activity in the deep central Atlantic ocean,” Aquatic Microbial Ecology, vol. 58, no. 3, pp. 287–302, 2010.
[67]  F. Baltar, J. Arístegui, J. M. Gasol, T. Yokokawa, and G. J. Herndl, “Bacterial versus Archaeal origin of extracellular enzymatic activity in the Northeast Atlantic deep waters,” Microbial Ecology, vol. 65, no. 2, pp. 277–288, 2013.
[68]  M. B. Karner, E. F. Delong, and D. M. Karl, “Archaeal dominance in the mesopelagic zone of the Pacific Ocean,” Nature, vol. 409, no. 6819, pp. 507–510, 2001.
[69]  E. F. DeLong, C. M. Preston, T. Mincer et al., “Community genomics among stratified microbial assemblages in the ocean's interior,” Science, vol. 311, no. 5760, pp. 496–503, 2006.
[70]  A. Vezzi, S. Campanaro, M. D'Angelo et al., “Life at depth: photobacterium profundum genome sequence and expression analysis,” Science, vol. 307, no. 5714, pp. 1459–1461, 2005.
[71]  R. L. Hansman, S. Griffin, J. T. Watson et al., “The radiocarbon signature of microorganisms in the mesopelagic ocean,” Proceedings of the National Academy of Sciences of the United States of America, vol. 106, no. 16, pp. 6513–6518, 2009.
[72]  B. K. Swan, M. Martinez-Garcia, C. M. Preston et al., “Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean,” Science, vol. 333, no. 6047, pp. 1296–1300, 2011.
[73]  M. Boutrif, M. Garel, M. T. Cottrell, and C. Tamburini, “Assimilation of marine extracellular polymeric substances by deep-sea prokaryotes in the NW Mediterranean Sea,” Environmental Microbiology Reports, vol. 3, no. 6, pp. 705–709, 2011.
[74]  C. A. Carlson, D. A. Hansell, N. B. Nelson et al., “Dissolved organic carbon export and subsequent remineralization in the mesopelagic and bathypelagic realms of the North Atlantic basin,” Deep-Sea Research Part II: Topical Studies in Oceanography, vol. 57, no. 16, pp. 1433–1445, 2010.
[75]  Z. Cardman, C. Arnosti, A. Durbin, et al., “Verrucomicrobia: candidates for polysaccharide-degrading bacterioplankton in an Arctic fjord of Svalbard,” Applied and Environmental Microbiology, vol. 80, pp. 3749–3756, 2014.
[76]  A. E. Zimmerman, A. C. Martiny, and S. D. Allison, “Microdiversity of extracellular enzyme genes among sequenced prokaryotic genomes,” The ISME Journal, vol. 7, no. 6, pp. 1187–1199, 2013.
[77]  J. D. Pakulski and R. Benner, “An improved method for the hydrolysis and MBTH analysis of dissolved and particulate carbohydrates in seawater,” Marine Chemistry, vol. 40, no. 3-4, pp. 143–160, 1992.
[78]  C. Panagiotopoulos and R. Sempéré, “Analytical methods for the determination of sugars in marine samples: a historical perspective and future directions,” Limnology and Oceanography: Methods, vol. 3, pp. 419–454, 2005.
[79]  J. I. Hedges, J. A. Baldock, Y. Gélinas, C. Lee, M. Peterson, and S. G. Wakeham, “Evidence for non-selective preservation of organic matter in sinking marine particles,” Nature, vol. 409, no. 6822, pp. 801–804, 2001.
[80]  C. Arnosti and D. J. Repeta, “Extracellular enzyme activity in anaerobic bacterial cultures: evidence of pullulanase activity among mesophilic marine bacteria,” Applied and Environmental Microbiology, vol. 60, no. 3, pp. 840–846, 1994.
[81]  J. A. Gilbert, D. Field, P. Swift et al., “The seasonal structure of microbial communities in the Western English Channel,” Environmental Microbiology, vol. 11, no. 12, pp. 3132–3139, 2009.
[82]  J. A. Gilbert, J. A. Steele, J. G. Caporaso et al., “Defining seasonal marine microbial community dynamics,” The ISME Journal, vol. 6, no. 2, pp. 298–308, 2012.
[83]  M. Schattenhofer, B. M. Fuchs, R. Amann, M. V. Zubkov, G. A. Tarran, and J. Pernthaler, “Latitudinal distribution of prokaryotic picoplankton populations in the Atlantic Ocean,” Environmental Microbiology, vol. 11, no. 8, pp. 2078–2093, 2009.
[84]  P. R. Gómez-Pereira, B. M. Fuchs, C. Alonso, M. J. Oliver, J. E. Van Beusekom, and R. Amann, “Distinct flavobacterial communities in contrasting water masses of the North Atlantic Ocean,” ISME Journal, vol. 4, no. 4, pp. 472–487, 2010.
[85]  K. L. Vergin, B. Done, C. A. Carlson, and S. J. Giovannoni, “Spatiotemporal distributions of rare bacterioplankton populations indicate adaptive strategies in the oligotrophic ocean,” Aquatic Microbial Ecology, vol. 71, no. 1, pp. 1–13, 2013.
[86]  J. A. Gilbert, D. Field, P. Swift et al., “The taxonomic and functional diversity of microbes at a temperate coastal site: a “multi-omic” study of seasonal and diel temporal variation,” PLoS ONE, vol. 5, no. 11, Article ID e15545, 2010.
[87]  P. R. Gómez-Pereira, M. Schüler, B. M. Fuchs et al., “Genomic content of uncultured Bacteroidetes from contrasting oceanic provinces in the North Atlantic Ocean,” Environmental Microbiology, vol. 14, no. 1, pp. 52–66, 2012.
[88]  T. J. Williams, D. Wilkins, E. Long et al., “The role of planktonic Flavobacteria in processing algal organic matter in coastal East Antarctica revealed using metagenomics and metaproteomics,” Environmental Microbiology, vol. 15, no. 5, pp. 1302–1317, 2013.
[89]  C. E. Nelson and C. A. Carlson, “Tracking differential incorporation of dissolved organic carbon types among diverse lineages of Sargasso Sea bacterioplankton,” Environmental Microbiology, vol. 14, no. 6, pp. 1500–1516, 2012.
[90]  H. Sarmento and J. M. Gasol, “Use of phytoplankton-derived dissolved organic carbon by different types of bacterioplankton,” Environmental Microbiology, vol. 14, no. 9, pp. 2348–2360, 2012.
[91]  H. Elifantz, R. R. Malmstrom, M. T. Cottrell, and D. L. Kirchman, “Assimilation of polysaccharides and glucose by major bacterial groups in the Delaware Estuary,” Applied and Environmental Microbiology, vol. 71, no. 12, pp. 7799–7805, 2005.
[92]  H. Elifantz, A. I. Dittel, M. T. Cottrell, and D. L. Kirchman, “Dissolved organic matter assimilation by heterotrophic bacterial groups in the western Arctic Ocean,” Aquatic Microbial Ecology, vol. 50, no. 1, pp. 39–49, 2007.
[93]  D. L. Kirchman, H. Elifantz, A. I. Dittel, R. R. Malmstrom, and M. T. Cottrell, “Standing stocks and activity of Archaea and Bacteria in the western Arctic Ocean,” Limnology and Oceanography, vol. 52, no. 2, pp. 495–507, 2007.
[94]  J. Ghiglione, P. E. Galand, T. Pommier et al., “Pole-to-pole biogeography of surface and deep marine bacterial communities,” Proceedings of the National Academy of Sciences of the United States of America, vol. 109, no. 43, pp. 17633–17638, 2012.
[95]  A. J. Baldwin, J. A. Moss, J. D. Pakulski, P. Catala, F. Joux, and W. H. Jeffrey, “Microbial diversity in a Pacific Ocean transect from the Arctic to Antarctic circles,” Aquatic Microbial Ecology, vol. 41, no. 1, pp. 91–102, 2005.
[96]  F. Baltar, J. Arístegui, J. M. Gasol, S. Hernández-León, and G. J. Herndl, “Strong coast-ocean and surface-depth gradients in prokaryotic assemblage structure and activity in a coastal transition zone region,” Aquatic Microbial Ecology, vol. 50, no. 1, pp. 63–74, 2007.
[97]  T. Yokokawa, D. de Corte, E. Sintes, and G. J. Herndl, “Spatial patterns of bacterial abundance, activity and community composition in relation to water masses in the eastern Mediterranean Sea,” Aquatic Microbial Ecology, vol. 59, no. 2, pp. 185–195, 2010.
[98]  L. J. Hamdan, R. B. Coffin, M. Sikaroodi, J. Greinert, T. Treude, and P. M. Gillevet, “Ocean currents shape the microbiome of Arctic marine sediments,” The ISME Journal, vol. 7, no. 4, pp. 685–696, 2013.
[99]  L. Zinger, L. A. Amaral-Zettler, J. A. Fuhrman et al., “Global patterns of bacterial beta-diversity in seafloor and seawater ecosystems,” PLoS ONE, vol. 6, no. 9, Article ID e24570, 2011.
[100]  C. Arnosti, B. M. Fuchs, R. Amann, and U. Passow, “Contrasting extracellular enzyme activities of particle-associated bacteria from distinct provinces of the North Atlantic Ocean,” Frontiers in Microbiology, vol. 3, article 425, 2012.
[101]  M. Schattenhofer, J. Wulf, I. Kostadinov, F. O. Gl?ckner, M. V. Zubkov, and B. M. Fuchs, “Phylogenetic chraacterisation of picoplanktonic populatinos with high and low nucleic acid concent in the North Atlanti Ocean,” Systematic and Applied Microbiology, vol. 34, pp. 470–475, 2011.
[102]  J. Comte, L. Fauteux, and P. A. del Giorgio, “Links between metabolic plasticity and functional redundancy in freshwater bacterioplankton communities,” Frontiers in Microbiology, vol. 4, p. 112, 2013.
[103]  C. Burke, P. Steinberg, D. Rusch, S. Kjelleberg, and T. Thomas, “Bacterial community assembly based on functional genes rather than species,” Proceedings of the National Academy of Sciences of the United States of America, vol. 108, no. 34, pp. 14288–14293, 2011.
[104]  S. M. Hatosy, J. B. Martiny, R. Sachdeva, J. Steele, J. A. Fuhrman, and A. C. Martiny, “Beta diversity of marine bacteria depends on temporal scale,” Ecology, vol. 94, pp. 1898–1904, 2013.
[105]  A. E. Murray, C. Arnosti, C. L. De La Rocha, H. Grossart, and U. Passow, “Microbial dynamics in autotrophic and heterotrophic seawater mesocosms. II. Bacterioplankton community structure and hydrolytic enzyme activities,” Aquatic Microbial Ecology, vol. 49, no. 2, pp. 123–141, 2007.
[106]  C. Arnosti, H. P. Grossart, M. Mühling, I. Joint, and U. Passow, “Dynamics of extracellular enzyme activities in seawater under changed atmospheric pCO2: a mesocosm investigation,” Aquatic Microbial Ecology, vol. 64, no. 3, pp. 285–298, 2011.
[107]  H. Teeling, B. M. Fuchs, D. Becher et al., “Substrate-controlled succession of marine bacterioplankton populations induced by a phytoplankton bloom,” Science, vol. 336, no. 6081, pp. 608–611, 2012.
[108]  H. P. Grossart, M. Allgaier, U. Passow, and U. Riebesell, “Testing the effect of CO2 concentration on the dynamics of marine heterotrophic bacterioplankton,” Limnology and Oceanography, vol. 51, no. 1 I, pp. 1–11, 2006.
[109]  N. Yamada and M. Suzumura, “Effects of seawater acidification on hydrolytic enzyme activities,” Journal of Oceanography, vol. 66, no. 2, pp. 233–241, 2010.
[110]  E. W. Maas, C. S. Law, J. A. Hall et al., “Effect of ocean acidification on bacterial abundance, activity and diversity in the Ross Sea, Antarctica,” Aquatic Microbial Ecology, vol. 70, no. 1, pp. 1–15, 2013.
[111]  M. Simon, H. Grossart, B. Schweitzer, and H. Ploug, “Microbial ecology of organic aggregates in aquatic ecosystems,” Aquatic Microbial Ecology, vol. 28, no. 2, pp. 175–211, 2002.
[112]  H. Ploug and B. B. J?rgensen, “A net-jet flow system for mass transfer and microsensor studies of sinking aggregates,” Marine Ecology Progress Series, vol. 176, pp. 279–290, 1999.
[113]  E. F. DeLong, D. G. Franks, and A. L. Alldredge, “Phylogenetic diversity of aggregate-attached vs. free-living marine bacterial assemblages,” Limnology & Oceanography, vol. 38, no. 5, pp. 924–934, 1993.
[114]  M. M. Moeseneder, C. Winter, and G. J. Herndl, “Horizontal and vertical complexity of attached and free-living bacteria of the eastern Mediterranean Sea, determined by 16S rDNA and 16S rRNA fingerprints,” Limnology and Oceanography, vol. 46, no. 1, pp. 95–107, 2001.
[115]  M. Karner and G. J. Herndl, “Extracellular enzymatic activity and secondary production in free-living and marine-snow-associated bacteria,” Marine Biology, vol. 113, no. 2, pp. 341–347, 1992.
[116]  D. C. Smith, M. Simon, A. L. Alldredge, and F. Azam, “Intense hydrolytic enzyme activity on marine aggregates and implications for rapid particle dissolution,” Nature, vol. 359, no. 6391, pp. 139–142, 1992.
[117]  J. Rath and G. J. Herndi, “Characteristics and diversity of β-D-glucosidase (EC 3.2.1.21) activity in marine snow,” Applied and Environmental Microbiology, vol. 60, no. 3, pp. 807–813, 1994.
[118]  H.-P. Grossart and H. Ploug, “Microbial degradation of organic carbon and nitrogen on diatom aggregates,” Limnology and Oceanography, vol. 46, no. 2, pp. 267–277, 2001.
[119]  A. Zoppini, A. Puddu, S. Fazi, M. Rosati, and P. Sist, “Extracellular enzyme activity and dynamics of bacterial community in mucilaginous aggregates of the northern Adriatic Sea,” Science of the Total Environment, vol. 353, no. 1-3, pp. 270–286, 2005.
[120]  J. T. Hollibaugh, P. S. Wong, and M. C. Murrell, “Similarity of particle-associated and free-living bacterial communities in northern San Francisco Bay, California,” Aquatic Microbial Ecology, vol. 21, no. 2, pp. 103–114, 2000.
[121]  M. Agis, M. Unanue, J. Iriberri, and G. J. Herndl, “Bacterial colonization and ectoenzymatic activity in phytoplankton-derived model particles—part II: cleavage and uptake of carbohydrates,” Microbial Ecology, vol. 36, no. 1, pp. 66–74, 1998.
[122]  M. Unanue, I. Azúa, J. M. Arrieta, A. Labirua-Iturburu, L. Egea, and J. Iriberri, “Bacterial colonization and ectoenzymatic activity in phytoplankton-derived model particles: cleavage of peptides and uptake of amino acids,” Microbial Ecology, vol. 35, no. 2, pp. 136–146, 1998.
[123]  K. Ziervogel and C. Arnosti, “Polysaccharide hydrolysis in aggregates and free enzyme activity in aggregate-free seawater from the north-eastern Gulf of Mexico,” Environmental Microbiology, vol. 10, no. 2, pp. 289–299, 2008.
[124]  K. Ziervogel, A. D. Steen, and C. Arnosti, “Changes in the spectrum and rates of extracellular enzyme activities in seawater following aggregate formation,” Biogeosciences, vol. 7, no. 3, pp. 1007–1017, 2010.
[125]  K. Ziervogel, L. McKay, B. Rhodes et al., “Microbial activities and dissolved organic matter dynamics in oil-contaminated surface seawater from the deepwater horizon oil spill site,” PLoS ONE, vol. 7, no. 4, Article ID e34816, 2012.
[126]  C. Arnosti, K. Ziervogel, T. Yang, and A. Teske, “Oil-derived marine aggregates—hot spots of polysaccharide degradation by specialized bacterial communities,” In Press.
[127]  S. C. Keith and C. Arnosti, “Extracellular enzyme activity in a river-bay-shelf transect: variations in polysaccharide hydrolysis rates with substrate and size class,” Aquatic Microbial Ecology, vol. 24, no. 3, pp. 243–253, 2001.
[128]  S. D. Allison, “Cheaters, diffusion and nutrients constrain decomposition by microbial enzymes in spatially structured environments,” Ecology Letters, vol. 8, no. 6, pp. 626–635, 2005.
[129]  Y. A. Vetter, J. W. Deming, P. A. Jumars, and B. B. Krieger-Brockett, “A predictive model of bacterial foraging by means of freely released extracellular enzymes,” Microbial Ecology, vol. 36, no. 1, pp. 75–92, 1998.
[130]  H. J. Folse III and S. D. Allison, “Cooperation, competition, and coalitions in enzyme-producing microbes: Social evolution and nutrient depolymerization rates,” Frontiers in Microbiology, vol. 3, p. 338, 2012.
[131]  C. Arnosti, C. Bell, D. L. Moorhead et al., “Extracellular enzymes in terrestrial, freshwater, and marine environments: perspectives on system variability and common research needs,” Biogeochemistry, vol. 117, no. 1, pp. 5–21, 2014.
[132]  R. G. Burns, J. L. DeForest, J. Marxsen et al., “Soil enzymes in a changing environment: current knowledge and future directions,” Soil Biology & Biochemistry, vol. 58, pp. 216–234, 2013.
[133]  M. T. Cottrell, L. Yu, and D. L. Kirchman, “Sequence and expression analyses of Cytophaga-like hydrolases in a western arctic metagenomic library and the Sargasso Sea,” Applied and Environmental Microbiology, vol. 71, no. 12, pp. 8506–8513, 2005.
[134]  K. Drescher, C. D. Nadell, H. A. Stone, N. S. Wingreen, and B. L. Bassler, “Solutions to the public goods dilemma in bacterial biofilms,” Current Biology, vol. 24, no. 1, pp. 50–55, 2014.
[135]  A. D. Steen and C. Arnosti, “Long lifetimes of β-glucosidase, leucine aminopeptidase, and phosphatase in Arctic seawater,” Marine Chemistry, vol. 123, no. 1–4, pp. 127–132, 2011.
[136]  L. S. Chernin, M. K. Winson, J. M. Thompson et al., “Chitinolytic activity in Chromobacterium violaceum: substrate analysis and regulation by quorum sensing,” Journal of Bacteriology, vol. 180, no. 17, pp. 4435–4441, 1998.
[137]  L. Gram, H. Grossart, A. Schlingloff, and T. Ki?rboe, “Possible quorum sensing in marine snow bacteria: production of acylated homoserine lactones by Roseobacter strains isolated from marine snow,” Applied and Environmental Microbiology, vol. 68, no. 8, pp. 4111–4116, 2002.

Full-Text

comments powered by Disqus

Contact Us

service@oalib.com

QQ:3279437679

WhatsApp +8615387084133

WeChat 1538708413