Chapter 31 : An Overview of Methodologies in Aquatic Microbial Ecology

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This chapter reflects the integrative nature of aquatic microbial ecology. It has been structured around areas that influence the role of the microbial community in ecosystem function such as diversity and community structure of primary and secondary producers, growth and grazing of primary and secondary producers, the role of bacteria in geochemical cycling, and specialized environments. The field of aquatic microbial ecology is being revolutionized by genetic and genomic approaches. Pioneering work in the late 1980s, which started with community analysis based on the PCR amplification of the 16S rRNA gene from many different types of bacteria, has expanded to encompass the analysis of multiple genomes from many individuals in many populations in the community (metagenome). Tringe et al. used environmental gene tags (EGTs), or short sequences that contain fragments of functional genes from whole genome shotgun libraries, to compare the microbial communities from three different ecosystems. In general, there are two approaches to measuring bacterial community activity in aquatic systems: (i) the direct tracer approach, which measures the conversion of a labeled substrate to a product of interest, and (ii) isotope dilution methods, in which the product pool is labeled and the dilution of the labeled product pool by new unlabeled product formation gives an estimate of the rate of production. Direct tracer methods have been employed for organic carbon, inorganic carbon, sulfur, nitrogen, phosphorus, and metal cycling. The future challenge is going to be to integrate activity and community structure measurements with ecosystem measurements of physicochemical fluxes.

Citation: Hullar M. 2007. An Overview of Methodologies in Aquatic Microbial Ecology, p 393-398. 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.ch31
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1. Adamczyk, J.,, M. Hesselsoe,, N. Iversen,, M. Horn,, A. Lehner,, P. H. Nielsen,, M. Schloter,, P. Roslev, and, M. Wagner. 2003. The isotope array, a new tool that employs substrate-mediated labeling of rRNA for determination of microbial community structure and function. Appl. Environ. Microbiol. 69: 68756887.
2. 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.
3. Beja, O.,, E. N. Spudich,, J. L. Spudich,, M. Leclerc, and, E. F. DeLong. 2001. Proteorhodopsin phototrophy in the ocean. Nature 411: 786789.
4. Bernhard, A. E.,, T. Donn,, A. E. Giblin, and, D. A. Stahl. 2005. Loss of diversity of ammonia-oxidizing bacteria correlates with increasing salinity in an estuary system. Environ. Microbiol. 7: 12891297.
5. Boschker, H. T.,, W. de Graaf,, M. Koster,, L. Meyer-Reil, and, T. E. Cappenberg. 2001. Bacterial populations and processes involved in acetate and propionate consumption in anoxic brackish sediment. FEMS Microbiol. Ecol. 35: 97103.
6. Castiglioni, B.,, E. Rizzi,, A. Frosini,, K. Sivonen,, P. Rajaniemi,, A. Rantala,, M. A. Mugnai,, S. Ventura,, A. Wilmotte,, C. Boutte,, S. Grubisic,, P. Balthasart,, C. Consolandi,, R. Bordoni,, A. Mezzelani,, C. Battaglia, and, G. De Bellis. 2004. Development of a universal microarray based on the ligation detection reaction and 16S rRNA gene polymorphism to target diversity of cyanobacteria. Appl. Environ. Microbiol. 70: 71617172.
7. Chen, K.,, and L. Pachter. 2005. Bioinformatics for whole-genome shotgun sequencing of microbial communities. PLoS Comput. Biol. 1: 106112.
8. Christian, R. R.,, and D. G. Capone. 2002. Overview of issues in aquatic microbial ecology, p. 323–328. In C. J. Hurst,, R. L. Crawford,, G. R. Knudsen,, M. J. McInerney, and, L. D. Stetzenbach (ed.), Manual of Environmental Microbiology, 2nd ed. ASM Press, Washington, D.C.
9. Coffin, R. B.,, B. Fry,, B. J. Peterson, and, R. T. Wright. 1989. Carbon isotopic compositions of estuarine bacteria. Limnol. Oceanogr. 34: 13051310.
10. Coffin, R. B.,, D. J. Velinsky,, R. Devereux,, W. A. Price, and, L. A. Cifuentes. 1990. Stable carbon isotope analysis of nucleic acids to trace sources of dissolved substrates used by estuarine bacteria. Appl. Environ. Microbiol. 56: 20122020.
11. Crump, B. C.,, G. W. Kling,, M. Bahr, and, J. E. Hobbie. 2003. Bacterioplankton community shifts in an arctic lake correlate with seasonal changes in organic matter source. Appl. Environ. Microbiol. 69: 22532268.
12. Dehnert, M.,, R. Plaumann,, W. E. Helm, and, M. T. Hutt. 2005. Genome phylogeny based on short-range correlations in DNA sequences. J. Comput. Biol. 12: 545553.
13. de la Torre, J. R.,, L. M. Christianson,, O. Beja,, M. T. Suzuki,, D. M. Karl,, J. Heidelberg, and, E. F. DeLong. 2003. Proteorhodopsin genes are distributed among divergent marine bacterial taxa. Proc. Natl. Acad. Sci. USA 100: 1283012835.
14. Delcher, A. L.,, D. Harmon,, S. Kasif,, O. White, and, S. L. Salzberg. 1999. Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 27: 46364641.
15. Delcher, A. L.,, S. Kasif,, R. D. Fleischmann,, J. Peterson,, O. White, and, S. L. Salzberg. 1999. Alignment of whole genomes. Nucleic Acids Res. 27: 23692376.
16. Delcher, A. L.,, A. Phillippy,, J. Carlton, and, S. L. Salzberg. 2002. Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res. 30: 24782483.
17. DeLong, E. F.,, C. M. Preston,, T. Mincer,, V. Rich,, S. J. Hallam,, N. U. Frigaard,, A. Martinez,, M. B. Sullivan,, R. Edwards,, B. R. Brito,, S. W. Chisholm, and, D. M. Karl. 2006. Community genomics among stratified microbial assemblages in the ocean’s interior. Science 311: 496503.
18. Donachie, S. P.,, S. Hou,, K. S. Lee,, C. W. Riley,, A. Pikina,, C. Belisle,, S. Kempe,, T. S. Gregory,, A. Bossuyt,, J. Boerema,, J. Liu,, T. A. Freitas,, A. Malahoff, and, M. Alam. 2004. The Hawaiian Archipelago: a microbial diversity hotspot. Microb. Ecol. 48: 509520.
19. Dorigo, U.,, L. Volatier, and, J. F. Humbert. 2005. Molecular approaches to the assessment of biodiversity in aquatic microbial communities. Water Res. 39: 22072218.
20. 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.
21. Giovannoni, S. J.,, T. B. Britschgi,, C. L. Moyer, and, K. G. Field. 1990. Genetic diversity in Sargasso Sea bacterioplankton. Nature 345: 6063.
22. Hiorns, W. D.,, B. A. Methe,, S. A. Nierzwicki-Bauer, and, J. P. Zehr. 1997. Bacterial diversity in Adirondack mountain lakes as revealed by 16S rRNA gene sequences. Appl. Environ. Microbiol. 63: 29572960.
23. Hugenholtz, P. 2002. Exploring prokaryotic diversity in the genomic era. Genome Biol. 3: REVIEWS0003.
24. Hullar, M. A.,, L. A. Kaplan, and, D. A. Stahl. 2006. Recurring seasonal dynamics of microbial communities in stream habitats. Appl. Environ. Microbiol. 72: 713722.
25. Jenkins, B. D.,, G. F. Steward,, S. M. Short,, B. B. Ward, and, J. P. Zehr. 2004. Fingerprinting diazotroph communities in the Chesapeake Bay by using a DNA macroarray. Appl. Environ. Microbiol. 70: 17671776.
26. Kan, J.,, T. E. Hanson,, J. M. Ginter,, K. Wang, and, F. Chen. 2005. Metaproteomic analysis of Chesapeake Bay microbial communities. Saline Syst. 1: 7.
27. Kirchman, D. L.,, E. K’nees, and, R. E. Hodson. 1985. Leucine incorporation and its potential as a measure of protein synthesis by bacteria in natural aquatic systems. Appl. Environ. Microbiol. 49: 599607.
28. Konneke, 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: 543546.
29. Lander, E. S.,, and M. S. Waterman. 1988. Genomic mapping by fingerprinting random clones: a mathematical analysis. Genomics 2: 231239.
30. 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.
31. Loy, A.,, and L. Bodrossy. 2006. Highly parallel microbial diagnostics using oligonucleotide microarrays. Clin. Chim. Acta 363: 106119.
32. MacGregor, B. J.,, V. Bruchert,, S. Fleischer, and, R. Amann. 2002. Isolation of small-subunit rRNA for stable isotopic characterization. Environ. Microbiol. 4: 451464.
33. 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.
34. 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.
35. McCallister, S. L.,, J. E. Bauer,, J. E. Cherrier, and, H. W. Ducklow. 2004. Assessing sources and ages of organic matter supporting river and estuarine bacterial production: a multiple-isotope (delta C-14, delta C-13, and delta N-15) approach. Limnol. Oceanogr. 49: 16871702.
36. Odum, H. T. 1988. Self-organization, transformity, and information. Science 242: 11321139.
37. Olsen, G. J.,, D. J. Lane,, S. J. Giovannoni,, N. R. Pace, and, D. A. Stahl. 1986. Microbial ecology and evolution: a ribosomal RNA approach. Annu. Rev. Microbiol. 40: 337365.
38. Orphan, V. J.,, C. H. House,, K. U. Hinrichs,, K. D. McKeegan, and, E. F. DeLong. 2001. Methane-consuming archaea revealed by directly coupled isotopic and phylogenetic analysis. Science 293: 484487.
39. 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.
40. Pace, N.,, D. Stahl,, D. Lane, and, G. Olsen. 1986. The analysis of natural microbial populations by rRNA sequences. Adv. Microb. Ecol. 9: 155.
41. Pearson, A.,, A. L. Sessions,, K. J. Edwards, and, J. M. Hayes. 2004. Phylogenetically specific separation of rRNA from prokaryotes for isotopic analysis. Mar. Chem. 92: 295306.
42. Pomeroy, L. R. 1974. Oceans food web, a changing paradigm. Bioscience 24: 499504.
43. Radajewski, S.,, P. Ineson,, N. R. Parekh, and, J. C. Murrell. 2000. Stable-isotope probing as a tool in microbial ecology. Nature 403: 646649.
44. Ram, R. J.,, N. C. Verberkmoes,, M. P. Thelen,, G. W. Tyson,, B. J. Baker,, R. C. Blake II,, M. Shah,, R. L. Hettich, and, J. F. Banfield. 2005. Community proteomics of a natural microbial biofilm. Science 308: 19151920.
45. Rappe, M. S.,, S. A. Connon,, K. L. Vergin, and, S. J. Giovannoni. 2002. Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418: 630633.
46. Rappe, M. S.,, and S. J. Giovannoni. 2003. The uncultured microbial majority. Annu. Rev. Microbiol. 57: 369394.
47. Riesenfeld, C. S.,, P. D. Schloss, and, J. Handelsman. 2004. Metagenomics: genomic analysis of microbial communities. Annu. Rev. Genet. 38: 525552.
48. Rocap, G.,, F. W. Larimer,, J. Lamerdin,, S. Malfatti,, P. Chain,, N. A. Ahlgren,, A. Arellano,, M. Coleman,, L. Hauser,, W. R. Hess,, Z. I. Johnson,, M. Land,, D. Lindell,, A. F. Post,, W. Regala,, M. Shah,, S. L. Shaw,, C. Steglich,, M. B. Sullivan,, C. S. Ting,, A. Tolonen,, E. A. Webb,, E. R. Zinser, and, S. W. Chisholm. 2003. Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 424: 10421047.
49. Salzberg, S. L.,, A. L. Delcher,, S. Kasif, and, O. White. 1998. Microbial gene identification using interpolated Markov models. Nucleic Acids Res. 26: 544548.
50. Salzberg, S. L.,, M. Pertea,, A. L. Delcher,, M. J. Gardner, and, H. Tettelin. 1999. Interpolated Markov models for eukaryotic gene finding. Genomics 59: 2431.
51. Sandberg, R.,, C. I. Branden,, I. Ernberg, and, J. Coster. 2003. Quantifying the species-specificity in genomic signatures, synonymous codon choice, amino acid usage and G+C content. Gene 311: 3542.
52. Schulze, W. X.,, G. Gleixner,, K. Kaiser,, G. Guggenberger,, M. Mann, and, E. D. Schulze. 2005. A proteomic fingerprint of dissolved organic carbon and of soil particles. Oecologia 142: 335343.
53. Taroncher-Oldenburg, G.,, E. M. Griner,, C. A. Francis, and, B. B. Ward. 2003. Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment. Appl. Environ. Microbiol. 69: 11591171.
54. Tringe, S. G.,, C. von Mering,, A. Kobayashi,, A. A. Salamov,, K. Chen,, H. W. Chang,, M. Podar,, J. M. Short,, E. J. Mathur,, J. C. Detter,, P. Bork,, P. Hugenholtz, and, E. M. Rubin. 2005. Comparative metagenomics of microbial communities. Science 308: 554557.
55. van Mooy, B. A.,, A. H. Devol, and, R. G. Keil. 2004. Quantifying 3H-thymidine incorporation rates by a phylogenetically defined group of marine planktonic bacteria (Bacteriodetes phylum). Environ. Microbiol. 6: 10611069.
56. Venter, J. C.,, K. Remington,, J. F. Heidelberg,, A. L. Halpern,, D. Rusch,, J. A. Eisen,, D. Wu,, I. Paulsen,, K. E. Nelson,, W. Nelson,, D. E. Fouts,, S. Levy,, A. H. Knap,, M. W. Lomas,, K. Nealson,, O. White,, J. Peterson,, J. Hoffman,, R. Parsons,, H. Baden-Tillson,, C. Pfannkoch,, Y. H. Rogers, and, H. O. Smith. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 6674.
57. Verducci, J. S.,, V. F. Melfi,, S. Lin,, Z. Wang,, S. Roy, and, C. K. Sen. 2006. Microarray analysis of gene expression: considerations in data mining and statistical treatment. Physiol. Genomics 25: 355363.
58. Wagner, M.,, P. H. Nielsen,, A. Loy,, J. L. Nielsen, and, H. Daims. 2006. Linking microbial community structure with function: fluorescence in situ hybridization-microautoradiography and isotope arrays. Curr. Opin. Biotechnol. 17: 8391.
59. Wendl, M. C.,, and R. H. Waterston. 2002. Generalized gap model for bacterial artificial chromosome clone fingerprint mapping and shotgun sequencing. Genome Res. 12: 19431949.
60. Wilmes, P.,, and P. L. Bond. 2004. The application of two-dimensional polyacrylamide gel electrophoresis and downstream analyses to a mixed community of prokaryotic microorganisms. Environ. Microbiol. 6: 911920.
61. Wilmes, P.,, and P. L. Bond. 2006. Metaproteomics: studying functional gene expression in microbial ecosystems. Trends Microbiol. 14: 9297.
62. Wuchter, C.,, S. Schouten,, H. T. Boschker, and, J. S. Sinninghe Damste. 2003. Bicarbonate uptake by marine Crenarchaeota. FEMS Microbiol. Lett. 219: 203207.

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