Prokaryotic community structure and respiration during long-term incubations

MicrobiologyOpen

Volumn 1, Issue 2, 2012, Pages 214-224

  Baltar, Federico ^a   Lindh, Markus V ^a   Parparov, Arkadi ^b   Berman, Tom ^b   Pinhassi, Jarone ^a  

^a LINNAEUS UNIVERSITY   (Sweden)

^b ISRAEL OCEANOGRAPHIC AND LIMNOLOGICAL RESEARCH   (Israel)

Author keywords

Bacterioplankton; Biological oxygen demand; Community composition; Incubation; Respiration

Indexed keywords

DISSOLVED OXYGEN; FRESH WATER; ORGANIC CARBON; ORGANIC MATTER; SURFACE WATER;

ARTICLE; COMMUNITY STRUCTURE; DENATURING GRADIENT GEL ELECTROPHORESIS; INCUBATION TIME; METABOLIC RATE; MICROBIAL COMMUNITY; MICROBIAL RESPIRATION; NONHUMAN; NUCLEOTIDE SEQUENCE; OXYGEN CONSUMPTION; PHYLOGENY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROKARYOTE;

EID: 84884212940     PISSN: None     EISSN: 20458827     Source Type: Journal    
DOI: 10.1002/mbo3.25     Document Type: Article

References (40)

1. Allgaier, M., and H.-P. Grossart. 2006. Diversity and seasonal dynamics of Actinobacteria populations in four lakes in Northeastern Germany. Appl. Environ. Microbiol. 72:3489-3497.
2. Allgaier, M., S. Brückner, E. Jaspers, and H. P. Grossart. 2007. Intra- and inter-lake variability of free-living and particle-associated Actinobacteria communities. Environ. Microbiol. 9:2728-2741.
3. Amann, R. I., C. H. Lin, R. Key, L. Montgomery, and D. A. Stahl. 1992. Diversity among fibrobacter isolates - towards a phylogenetic classification. Syst. Appl. Microbiol. 15:23-31.
4. Berman, T., A. Parparov, and Y. Z. Yacobi. 2004. Planktonic community production and respiration and the impact of bacteria on carbon cycling in the photic zone of Lake Kinneret. Aquat. Microb. Ecol. 34:43-55.
5. Berman, T., Y. Z. Yacobi, A. Parparov, and G. Gal. 2010. Estimation of long-term bacterial respiration and growth efficiency in Lake Kinneret. Fems Microbiol. Ecol. 71:351-363.
6. Bischofberger, T., S. K. Cha, R. Schmitt, B. König, and W. Schmidt-Lorenz. 1990. The bacterial flora of non-carbonated, natural mineral water from the springs to reservoir and glass and plastic bottles. Int. J. Food Microbiol. 11:51-71.
7. Brown, M. V., and J. A. Fuhrman. 2005. Marine bacterial microdiversity as revealed by internal transcribed spacer analysis. Aquat. Microb. Ecol. 41:15-23.
8. Carlson, C. A., and H. W. Ducklow. 1996. Growth of bacterioplankton and consumption of dissolved organic carbon in the Sargasso Sea. Aquat. Microb. Ecol. 10:69-85.
9. Comte, J., and P. A. del Giorgio. 2011. Composition influences the pathway but not the outcome of the metabolic response of bacterioplankton to resource shifts. Plos One 6:e25266.
10. Del Giorgio, P. A., and J. J. Cole. 1998. Bacterial growth yield efficiency in natural aquatic systems. Annu. Rev. Ecol. Syst. 29:503-541.
11. Fallon, R. D., and T. D. Brock. 1979. Decomposition of blue-green algal (cyanobacterial) blooms in Lake Mendota, Wisconsin. Appl. Environ. Microbiol. 37:820.
12. Ferguson, R. L., E. N. Buckley, and A. V. Palumbo. 1984. Response of marine bacterioplankton to differential filtration and confinement. Appl. Environ. Microbiol. 47:49-55.
13. Ferreira, V., and E. Chauvet. 2012. Changes in dominance among species in aquatic hyphomycete assemblages do not affect litter decomposition rates. Aquat. Microb. Ecol. 66:1-11.
14. Field, K. G., D. Gordon, T. Wright, M. Rappé, E. Urbach, K. Vergin, and S. J. Giovannoni. 1997. Diversity and depth-specific distribution of SAR11 cluster rRNA genes from marine planktonic bacteria. Appl. Envrion. Microbiol. 63:63-70.
15. Garrity, G. 2001. Bergey's manual of systematic bacteriology. Springer-Verlag, New York.
16. Gattuso, J. P., S. Peduzzi, M. D. Pizay, and M. Tonolla. 2002. Changes in freshwater bacterial community composition during measurements of microbial and community respiration. J. Plankton Res. 24:1197-1206.
17. Glöckner, F. O., E. Zaichikov, N. Belkova, L. Denissova, J. Pernthaler, A. Pernthaler, and R. Amann. 2000. Comparative 16S rRRNA analysis of lake bacterioplankton reveals globally distributed phylogenetic clusters including an abundant group of Actinobacteria. Appl. Environ. Microbiol. 66:5053-5065.
18. Hahn, M. W., and M. Pöckel. 2005. Ecotypes of planktonic Actinobacteria with identical 16S rRNA genes adapted to thermal niches in temperate, subtropical, and tropical freshwater habitats. Appl. Environ. Microbiol. 71:766-773.
19. Holm-Hansen, O., C. J. Lorenzen, R. W. Holmes, and J. D. H. Strickland. 1965. Fluorometric determination of chlorophyll. J. Conseil 30:3-15.
20. Holmfeldt, K., C. Dziallas, J. Titelman, K. Pohlmann, H. P. Grossart, and L. Riemann. 2009. Diversity and abundance of freshwater Actinobacteria along environmental gradients in the brackish northern Baltic Sea. Environ. Microbiol. 11:2042-2054.
21. Jonas, R. B., and J. H. Tuttle. 1990. Bacterioplankton and organic carbon dynamics in the lower mesohaline Chesapeake Bay. Appl. Environ. Microbiol. 56:747-757.
22. Jürgens, K., J. M. Gasol, and D. Vaque. 2000. Bacteria-flagellate coupling in microcosm experiments in the Central Atlantic Ocean. J. Exp. Mar. Biol. Ecol. 245:127-147.
23. Kampfer, P., N. Lodders, and H. J. Busse. 2009. Arcicella rosea sp nov. isolated from tap water. Int. J. Syst. Evol. Microbiol. 59:341-344.
24. Kan, J., S. E. Evans, F. Chen, and M. T. Suzuki. 2008. Novel estuarine bacterioplankton in rRNA operon libraries from the Chesapeake Bay. Aquat. Microb. Ecol. 51:55-66.
25. Kirchman, D., E. K'Ness, and R. Hodson. 1985. Leucine incorporation and its potential as a measure of protein synthesis by bacteria in natural aquatic systems. Appl. Environ. Microbiol. 49:599-607.
26. Lee, S. H., and J. A. Fuhrman. 1991. Species composition shift of confined bacterioplankton studied at the level of community DNA. Mar. Ecol.-Prog. Ser. 79:195-201.
27. Marrase, C., E. L. Lim, and D. A. Caron. 1992. Seasonal and daily changes in bacterivory in a coatal plankton community. Mar. Ecol.-Prog. Ser. 82:281-289.
28. Martinez, J., D. C. Smith, G. F. Sterward, 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. 10:223-230.
29. Massana, R., C. Pedrós-Alió, E. O. Casamayor, and J. M. Gasol. 2001. Changes in marine bacterioplankton phylogenetic composition during incubations designed to measure biogeochemically significant parameters. Limnol. Oceanogr. 46:1181-1188.
30. McDonald, J. E., A. B. de Menezes, H. E. Allison, and A. J. McCarthy. 2009. Molecular biological detection and quantification of novel fibrobacter populations in freshwater lakes. Appl. Environ. Microbiol. 75:5148-5152.
31. Nikitin, D. I., C. Strompl, M. S. Oranskaya, and W. R. Abraham. 2004. Phylogeny of the ring-forming bacterium Arcicella aquatica gen. nov., sp nov (ex Nikitin et al. 1994), from a freshwater neuston biofilm. Int. J. Syst. Evol. Microbiol. 54:681-684.
32. Oksanen, J., F. Blanchet, R. Kindt, P. Legendre, P. R. Minchin R. O'Hara, G. L. Simpson, P. Solymos, M. Henry, H. Stevens, and H. Wagner. 2011. Vegan: Community Ecology Package. R package version 1.17-5. Available at: http://CRAN.R-project.org/package=vegan. R-project org/package=vegan
33. Ostapenia, A. P., A. Parparov, and T. Berman. 2009. Lability of organic carbon in lakes of different trophic status. Freshwater Biol. 54:1312-1323.
34. Pinhassi, J., and A. Hagstrom. 2000. Seasonal succession in marine bacterioplankton. Aquat. Microb. Ecol. 21:245-256.
35. Pommier, T., P. R. Neal, J. M. Gasol, M. Coll, S. G. Acinas, and C. Pedrós-Alió. 2010. Spatial patterns of bacterial richness and evenness in the MW Mediterranean Sea explored by pyrosequencing of the 16S rRNA. Aquat. Microb. Ecol. 61:221-233.
36. Schauer, M., V. Balagué, C. Pedrós-Alió, and R. Massana. 2003. Seasonal changes in the taxonomic composition of bacterioplankton in a coastal oligotrophic system. Aquat. Microb. Ecol. 31:163-174.
37. Sekar, R., A. Pernthaler, J. Pernthaler, F. Warnecke, T. Posch, and R. Amann. 2003. An improved protocol for quantification of freshwater Actinobacteria by fluorescence in situ hybridization. Appl. Environ. Microbiol. 69:2928-2935.
38. Warnecke, F., R. Amann, and J. Pernthaler. 2004. Actinobacterial 16S rRNA genes from freshwater habitats cluster in four distinct lineages. Environ. Microbiol. 6:242-253.
39. Zsolnay, A. 1975. Total labile carbon in the euphotic zone of the Baltic Sea as measured by BOD. Mar. Biol. 29:125-128.
40. Zwart, G., B. C. Crump, M. P. Kamst-van Agterveld, F. Hagen, and S. K. Han. 2002. Typical freshwater bacteria: an analysis of available 16S rRNA gene sequences from plankton of lakes and rivers. Aquat. Microb. Ecol. 28:141-155.