Chapter 39 : Bacterial Organic Carbon Cycling in Aquatic Environments

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This chapter introduces some of the important aspects of bacterial organic carbon cycling and to provides an update on the molecular biological approaches currently in use for examining carbon cycling by bacteria without cultivation. Such investigations by microbial ecologists are motivated by the desire to understand how the composition of microbial communities dictates the way that food webs and carbon cycling function in the oceans and other aquatic environments. The goal of one study by Cottrell and Kirchman was to determine whether the relative contributions of various types of bacteria to DOM consumption depend solely on the relative abundance of these types of bacteria in the community. This study used microautoradiography and fluorescent in situ hybridization (FISH) to test the hypothesis that low-molecular-weight compounds are used by all bacteria and high-molecular-weight compounds are used by a smaller, less diverse group of bacteria. In another study, Brennan et al. examined microbial xylanases in insect guts. Although the study did not include aquatic bacteria, the approach used in this study should be applicable to aquatic microbes with appropriate modification by using a DNA extraction method for aquatic microbial DNA. The great phylogenetic distance between the novel xylanases and the known xylanases suggests that microbes in the insect gut have evolved in isolation from other microbes that have been successfully cultivated.

Citation: Cottrell M. 2007. Bacterial Organic Carbon Cycling in Aquatic Environments, p 479-487. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch39

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Microbial Ecology
Sodium Dodecyl Sulfate
Aquatic Microbial Communities
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1. Azam, F.,, T. Fenchel,, J. G. Field,, J. S. Gray,, L. A. Meyerreil, and, F. Thingstad. 1983. The ecological role of water-column microbes in the sea. Mar. Ecol. Prog. Ser. 10:257263.
2. Beja, O.,, M. T. Suzuki,, E. V. Koonin,, L. Aravind,, A. Hadd,, L. P. Nguyen,, R. Villacorta,, M. Amjadi,, C. Garrigues,, S. B. Jovanovich,, R. A. Feldman, and, E. F. DeLong. 2000. Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. Environ. Microbiol. 2:516529.
3. Bostrom, K. H.,, K. Simu,, A. Hagstrom, and, L. Riemann. 2004. Optimization of DNA extraction for quantitative marine bacterioplankton community analysis. Limnol. Oceanogr. Methods 2:365373.
4. Brennan, Y.,, W. N. Callen,, L. Christoffersen,, P. Dupree,, F. Goubet,, S. Healey,, M. Hernandez,, M. Keller,, K. Li,, N. Palackal,, A. Sittenfeld,, G. Tamayo,, S. Wells,, G. P. Hazlewood,, E. J. Mathur,, J. M. Short,, D. E. Robertson, and, B. A. Steer. 2004. Unusual microbial xylanases from insect guts. Appl. Environ. Microbiol. 70:36093617.
5. Brisou, J.,, C. Tysset,, A. de Rautlin,, R. de la Roy,, R. Curcier, and, R. Moreau. 1964. Étude sur la chitinolyse a milieu marin. Ann. Inst. Pasteur 106:469478.
6. Brock, T. D. 1967. Bacterial growth rate in the sea—direct analysis by thymidine autoradiography. Science 155:8183.
7. Cohan, F. M. 2002. What are bacterial species? Annu. Rev. Microbiol. 56:457487.
8. Cottrell, M. T.,, and D. L. Kirchman. 2003. Contribution of major bacterial groups to bacterial biomass production (thymidine and leucine incorporation) in the Delaware estuary. Limnol. Oceanogr. 48:168178.
9. Cottrell, M. T.,, and D. L. Kirchman. 2000. Natural assemblages of marine proteobacteria and members of the Cytophaga-Flavobacter cluster consuming low- and high-molecular-weight dissolved organic matter. Appl. Environ. Microbiol. 66:16921697.
10. Cottrell, M. T.,, J. A. Moore, and, D. L. Kirchman. 1999. Chitinases from uncultured marine microorganisms. Appl. Environ. Microbiol. 65:25532557.
11. DeLong, E. F.,, L. T. Taylor,, T. L. Marsh, and, C. M. Preston. 1999. Visualization and enumeration of marine planktonic archaea and bacteria by using polyribonucleotide probes and fluorescent in situ hybridization. Appl. Environ. Microbiol. 65:55545563.
12. DeLong, E. F.,, G. S. Wickham, and, N. R. Pace. 1989. Phylogenetic stains—ribosomal RNA-based probes for the identification of single cells. Science 243:13601363.
13. Eguchi, M.,, and Y. Ishida. 1990. Oligotrophic properties of heterotrophic bacteria and in situ heterotrophic activity in pelagic seawaters. FEMS Microbiol. Ecol. 73:2330.
14. Eilers, H.,, J. Pernthaler, and, R. Amann. 2000. Succession of pelagic marine bacteria during enrichment: a close look at cultivation-induced shifts. Appl. Environ. Microbiol. 66:46344640.
15. Ferguson, R. L.,, E. N. Buckley, and, A. V. Palumbo. 1984. Response of marine bacterioplankton to differential filtration and confinement. Appl. Environ. Microbiol. 47:4955.
16. Fuhrman, J. A.,, and F. Azam. 1982. Thymidine incorporation as a measure of heterotrophic bacterioplankton production in marine surface waters—evaluation and field results. Mar. Biol. 66:109120.
17. Fuhrman, J. A.,, and C. C. Ouverney. 1998. Marine microbial diversity studied via 16S rRNA sequences: cloning results from coastal waters and counting of native archaea with fluorescent single cell probes. Aquat. Ecol. 32:315.
18. Giovannoni, S. J.,, and M. S. Rappé. 2000. Evolution, diversity and molecular ecology of marine prokaryotes, p. 47–84. In D. L. Kirchman (ed.), Microbial Ecology of the Oceans. Wiley-Liss, New York, N.Y.
19. Gonzalez, J. M.,, R. P. Kiene, and, M. A. Moran. 1999. Transformation of sulfur compounds by an abundant lineage of marine bacteria in the alpha-subclass of the class Proteobacteria. Appl. Environ. Microbiol. 65:38103819.
20. Hedges, J. I.,, and J. M. Oades. 1997. Comparative organic geochemistries of soils and marine sediments. Org. Geochem. 27:319361.
21. Hobbie, J. E.,, R. J. Daley, and, S. Jasper. 1977. Use of Nuclepore filters for counting bacteria by fluorescence microscopy. Appl. Environ. Microbiol. 33:12251228.
22. Hugenholtz, P.,, B. M. Goebel, and, N. R. Pace. 1998. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol. 180:47654774.
23. Jonkers, H. M.,, and R. M. M. Abed. 2003. Identification of aerobic heterotrophic bacteria from the photic zone of a hypersaline microbial mat. Aquat. Microb. Ecol. 30:127133.
24. Jorgensen, N. O. G.,, N. Kroer,, R. B. Coffin,, X. H. Yang, and, C. Lee. 1993. Dissolved free amino-acids, combined amino-acids, and DNA as sources of carbon and nitrogen to marine bacteria. Mar. Ecol. Prog. Ser. 98:135148.
25. Kaiser, K.,, and R. Benner. 2000. Determination of amino sugars in environmental samples with high salt content by high performance anion exchange chromatography and pulsed amperometric detection. Anal. Chem. 72:25662572.
26. Keil, R. G.,, and D. L. Kirchman. 1991. Contribution of dissolved free amino acids and ammonium to the nitrogen requirements of heterotrophic bacterioplankton. Mar. Ecol. Prog. Ser. 73:110.
27. Keil, R. G.,, and D. L. Kirchman. 1999. Utilization of dissolved protein and amino acids in the northern Sargasso Sea. Aquat. Microb. Ecol. 18:293300.
28. Kemp, P. F. 1993. Handbook of Methods in Aquatic Microbial Ecology. Lewis Publishers, Boca Raton, Fla.
29. Kiene, R. P.,, and L. J. Linn. 2000. Distribution and turnover of dissolved DMSP and its relationship with bacterial production and dimethylsulfide in the Gulf of Mexico. Limnol. Oceanogr. 45:849861.
30. Kiene, R. P.,, and L. J. Linn. 2000. The fate of dissolved dimethylsulfoniopropionate (DMSP) in seawater: tracer studies using S-35-DMSP. Geochim. Cosmochim. Acta 64:27972810.
31. Kirchman, D.,, E. Knees, and, R. Hodson. 1985. Leucine incorporation and its potential as a measure of protein synthesis by bacteria in natural aquatic systems. Appl. Environ. Microbiol. 49:599607.
32. Kirchman, D. L.,, A. I. Dittel,, R. R. Malmstrom, and, M. T. Cottrell. 2005. Biogeography of major bacterial groups in the Delaware Estuary. Limnol. Oceanogr. 50:16971706.
33. Kirchman, D. L.,, B. Meon,, H. W. Ducklow,, C. A. Carlson,, D. A. Hansell, and, G. F. Steward. 2001. Glucose fluxes and concentrations of dissolved combined neutral sugars (polysaccharides) in the Ross Sea and Polar Front Zone, Antarctica. Deep-Sea Res. Pt. II 48:41794197.
34. Kogure, K.,, U. Simidu, and, N. Taga. 1980. Distribution of viable marine bacteria in neritic seawater around Japan. Can. J. Microbiol. 26:318323.
35. Leboulanger, C.,, L. Oriol,, H. Jupin, and, C. Descolas-Gros. 1997. Diel variability of glycolate in the eastern tropical Atlantic Ocean. Deep-Sea Res. Pt. I 44:21312139.
36. Lee, N.,, P. H. Nielsen,, K. H. Andreasen,, S. Juretschko,, J. L. Nielsen,, K. H. Schleifer, and, M. Wagner. 1999. Combination of fluorescent in situ hybridization and microautoradiography—a new tool for structure-function analyses in microbial ecology. Appl. Environ. Microbiol. 65:12891297.
37. Malmstrom, R. R.,, M. T. Cottrell,, H. Elifantz, and, D. L. Kirchman. 2005. Biomass production and assimilation of dissolved organic matter by SAR11 bacteria in the Northwest Atlantic Ocean. Appl. Environ. Microbiol. 71:29792986.
38. Malmstrom, R. R.,, R. P. Kiene,, M. T. Cottrell, and, D. L. Kirchman. 2004. Contribution of SAR11 bacteria to dissolved dimethylsulfoniopropionate and amino acid uptake in the North Atlantic Ocean. Appl. Environ. Microbiol. 70:41294135.
39. Malmstrom, R. R.,, R. P. Kiene, and, D. L. Kirchman. 2004. Identification and enumeration of bacteria assimilating dimethylsulfoniopropionate (DMSP) in the North Atlantic and Gulf of Mexico. Limnol. Oceanogr. 49:597606.
40. Maniatis, T.,, E. F. Fritsch, and, J. Sambrook. 1982. Molecular Cloning : a Laboratory Manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
41. Martinez, J.,, D. C. Smith,, G. F. Steward, and, F. Azam. 1996. Variability in ectohydrolytic enzyme activities of pelagic marine bacteria and its significance for substrate processing in the sea. Aquat. Microb. Ecol. 10:223230.
42. Middelboe, M.,, N. H. Borch, and, D. L. Kirchman. 1995. Bacterial utilization of dissolved free amino acids, dissolved combined amino acids and ammonium in the Delaware Bay estuary: effects of carbon and nitrogen limitation. Mar. Ecol. Prog. Ser. 128:109120.
43. Moran, M. A.,, J. M. Gonzalez, and, R. P. Kiene. 2003. Linking a bacterial taxon to sulfur cycling in the sea: studies of the marine Roseobacter group. Geomicrobiol. J. 20:375388.
44. Morris, R. M.,, M. S. Rappé,, S. A. Connon,, K. L. Vergin,, W. A. Siebold,, C. A. Carlson, and, S. J. Giovannoni. 2002. SAR11 clade dominates ocean surface bacterioplankton communities. Nature 420:806810.
45. Murray, A. E.,, C. M. Preston,, R. Massana,, L. T. Taylor,, A. Blakis,, K. Wu, and, E. F. DeLong. 1998. Seasonal and spatial variability of bacterial and archaeal assemblages in the coastal waters near Anvers Island, Antarctica. Appl. Environ. Microbiol. 64:25852595.
46. Nagata, T. 2000. Production mechanisms of dissolved organic matter, p. 121–152. In D. L. Kirchman (ed.), Microbial Ecology of the Oceans. Wiley-Liss, New York, N.Y.
47. Noble, R. T.,, and J. A. Fuhrman. 1998. Use of SYBR Green I for rapid epifluorescence counts of marine viruses and bacteria. Aquat. Microb. Ecol. 14:113118.
48. Okutani, K. (ed.). 1975. Microorganisms Related to Mineralization of Chitin in Aquatic Environments. University of Tokyo Press, Tokyo, Japan.
49. Ouverney, C. C.,, and J. A. Fuhrman. 1999. Combined microautoradiography-16S rRNA probe technique for determination of radioisotope uptake by specific microbial cell types in situ. Appl. Environ. Microbiol. 65:17461752.
50. Ouverney, C. C.,, and J. A. Fuhrman. 2000. Marine planktonic archaea take up amino acids. Appl. Environ. Microbiol. 66:48294832.
51. Parker, M. S.,, E. V. Armbrust,, J. Piovia-Scott, and, R. G. Keil. 2004. Induction of photorespiration by light in the centric diatom Thalassiosira weissflogii (Bacillariophyceae): molecular characterization and physiological consequences. J. Phycol. 40:557567.
52. Pernthaler, J.,, F. O. Glockner,, W. Schonhuber, and, R. Amann. 2001. Fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes. Methods Microbiol. 30:207226.
53. Porter, K. G.,, and Y. S. Feig. 1980. The use of DAPI for identifying and counting aquatic microflora. Limnol. Oceanogr. 25:943948.
54. Rappé, M. S.,, S. A. Connon,, K. L. Vergin, and, S. J. Giovannoni. 2002. Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418:630633.
55. Rich, J. H.,, H. W. Ducklow, and, D. L. Kirchman. 1996. Concentrations and uptake of neutral monosaccharides along 140 degrees W in the equatorial Pacific: contribution of glucose to heterotrophic bacterial activity and the DOM flux. Limnol. Oceanogr. 41:595604.
56. Riesenfeld, C. S.,, R. M. Goodman, and, J. Handelsman. 2004. Uncultured soil bacteria are a reservoir of new antibiotic resistance genes. Environ. Microbiol. 6:981989.
57. Rondon, M. R.,, P. R. August,, A. D. Bettermann,, S. F. Brady,, T. H. Grossman,, M. R. Liles,, K. A. Loiacono,, B. A. Lynch,, I. A. MacNeil,, C. Minor,, C. L. Tiong,, M. Gilman,, M. S. Osburne,, J. Clardy,, J. Handelsman, and, R. M. Goodman. 2000. Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl. Environ. Microbiol. 66:25412547.
58. Rosenstock, B.,, and M. Simon. 2001. Sources and sinks of dissolved free amino acids and protein in a large and deep mesotrophic lake. Limnol. Oceanogr. 46:644654.
59. Seki, H. 1966. Seasonal fluctuation of heterotrophic bacteria in the sea of Aburatsubo Inlet. J. Oceanogr. Soc. Jpn. 22:1526.
60. Simon, M.,, and F. Azam. 1989. Protein content and protein synthesis rates of planktonic marine macteria. Mar. Ecol. Prog. Ser. 51:201213.
61. Skoog, A.,, B. Biddanda, and, R. Benner. 1999. Bacterial utilization of dissolved glucose in the upper water column of the Gulf of Mexico. Limnol. Oceanogr. 44:16251633.
62. Stein, J. L.,, T. L. Marsh,, K. Y. Wu,, H. Shizuya, and, E. F. DeLong. 1996. Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon. J. Bacteriol. 178:591599.
63. Suttle, C. A.,, A. M. Chan, and, J. A. Fuhrman. 1991. Dissolved free amino acids in the Sargasso Sea—uptake and respiration rates, turnover times, and concentrations. Mar. Ecol. Prog. Ser. 70:189199.
64. Svitil, A. L.,, and D. L. Kirchman. 1998. A chitin-binding domain in a marine bacterial chitinase and other microbial chitinases: implications for the ecology and evolution of 1,4-beta-glycanases. Microbiology (Reading) 144:12991308.
65. Tabor, P. S.,, and R. A. Neihof. 1982. Improved microautoradiographic method to determine individual microorganisms active in substrate uptake in natural waters. Appl. Environ. Microbiol. 44:945953.
66. Weiss, M. S.,, U. Abele,, J. Weckesser,, W. Welte,, E. Schiltz, and, G. E. Schulz. 1991. Molecular architecture and electrostatic properties of a bacterial porin. Science 254:16271630.
67. Wuchter, C.,, S. Schouten,, H. T. S. Boschker, and, J. S. S. Damste. 2003. Bicarbonate uptake by marine Crenarchaeota. FEMS Microbiol. Lett. 219:203207.

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