Changes in dimethylsulfoniopropionate demethylase gene assemblages in response to an induced phytoplankton bloom

Applied and Environmental Microbiology

Volumn 77, Issue 2, 2011, Pages 524-531

  Howard, Erinn C ^a,d   Sun, Shulei ^a,e   Reisch, Christopher R ^a   Del Valle, Daniela A ^b,f   Bürgmann, Helmut ^c   Kiene, Ronald P ^b   Moran, Mary Ann ^a  

^a UNIVERSITY OF GEORGIA   (United States)

^b UNIVERSITY OF SOUTH ALABAMA   (United States)

^c SWISS FEDERAL INSTITUTE OF AQUATIC SCIENCE AND TECHNOLOGY   (Switzerland)

^d NAVAL RESEARCH LABORATORY   (United States)

^e UNIVERSITY OF CALIFORNIA   (United States)

^f UNIVERSITY OF HAWAII   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

16S RRNA; AMPLICON SEQUENCES; BACTERIOPLANKTONS; CHLOROPHYLL-A CONCENTRATION; CLUSTERING CRITERIA; DEMETHYLASE; DEMETHYLATION; DIMETHYLSULFIDE; DIMETHYLSULFONIOPROPIONATE; FUNCTIONAL GENES; GULF OF MEXICO; HIGH-THROUGHPUT; MARINE BACTERIOPLANKTON; MICROBIAL ECOLOGY; NUCLEOTIDE SEQUENCES; PHYTOPLANKTON BLOOM; ROSEOBACTERS; SEAWATER MICROCOSM;

ALGAE CONTROL; BLOOMS (METAL); CHEMICAL REACTIONS; CHLOROPHYLL; ECOLOGY; PHYTOPLANKTON; RNA; SEAWATER; SULFUR; SURFACE WATERS;

GENES;

BACTERIAL DNA; DIMETHYLPROPIOTHETIN; RIBOSOME DNA; RNA 16S; SEA WATER; SULFONIUM DERIVATIVE; SULFUR;

ALGAL BLOOM; BACTERIOPLANKTON; CHLOROPHYLL A; CLADISTICS; GENETIC ANALYSIS; HETEROGENEITY; METABOLITE; MICROBIAL ECOLOGY; MICROCOSM; PHYTOPLANKTON; SEA SURFACE; SEAWATER;

ARTICLE; BACTERIUM; BIODIVERSITY; CHEMISTRY; CLASSIFICATION; CLUSTER ANALYSIS; DNA SEQUENCE; ENZYMOLOGY; GENETICS; METABOLISM; METAGENOME; MEXICO; MICROBIOLOGY; MOLECULAR GENETICS; PHYLOGENY; PHYTOPLANKTON;

BACTERIA; BIODIVERSITY; CLUSTER ANALYSIS; DNA, BACTERIAL; DNA, RIBOSOMAL; METAGENOME; MEXICO; MOLECULAR SEQUENCE DATA; PHYLOGENY; PHYTOPLANKTON; RNA, RIBOSOMAL, 16S; SEAWATER; SEQUENCE ANALYSIS, DNA; SULFONIUM COMPOUNDS; SULFUR;

FLAVOBACTERIACEAE; RHODOSPIRILLALES; ROSEOBACTER;

EID: 79551504171     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.01457-10     Document Type: Article

References (39)

1. Andreae, M. 1990. Ocean-atmosphere interactions in the global biogeochemical sulfur cycle. Mar. Chem. 30:1-29.
2. Andreae, M. O., and H. Raemdonck. 1983. Dimethyl sulfide in the surface ocean and the marine atmosphere: A global view. Science 221:744-747.
3. Biers, E. J., S. Sun, and E. C. Howard. 2009. Prokaryotic genomes and diversity in the surface ocean: Interrogating the Global Ocean Sampling metagenome. Appl. Environ. Microbiol. 75:2221-2229.
4. Charlson, R. J., J. E. Lovelock, M. O. Andreae, and S. G. Warren. 1987. Oceanic phytoplankton, atmospheric sulphur, cloud albedo and climate. Nature 326:655-661.
5. Cole, J. R., et al. 2007. The Ribosomal Database Project (RDP-II): Introducing myRDP space and quality controlled public data. Nucleic Acids Res. 35:D169-D172.
6. Curran, M. A. J., G. B. Jones, and H. Burton. 1998. Spatial distribution of dimethylsulfide and dimethylsulfoniopropiate in the Australasian sector of the Southern Ocean. J. Geophys. Res. 103:16667-16689.
7. Curson, A. R. J., R. Rogers, J. D. Todd, C. A. Brearley, and A. W. B. Johnston. 2008. Molecular genetic analysis of a dimethylsulfoniopropionate lyase that liberates the climate-changing gas dimethylsulfide in several marine alpha-proteobacteria and Rhodobacter sphaeroides. Environ. Microbiol. 10:757-767.
8. González, J. M., et al. 2000. Bacterial community structure associated with a dimethylsulfoniopropionate-producing North Atlantic algal bloom. Appl. Environ. Microbiol. 66:4237-4246.
9. Howard, E. C., et al. 2006. Bacterial taxa that limit sulfur flux from the ocean. Science 314:649-652.
10. Howard, E. C., S. Sun, E. J. Biers, and M. A. Moran. 2008. Abundant and diverse bacteria involved in DMSP degradation in marine surface waters. Environ. Microbiol. 10:2397-2410.
11. Huber, J. A., et al. 2007. Microbial population structure in the deep marine biosphere. Science 318:97-100.
12. Kiene, R. P. 1996. Production of methanethiol from dimethylsulfoniopropionate in marine surface waters. Mar. Chem. 54:69-83.
13. Kiene, R. P., L. P. Hoffman Williams, and J. E. Walker. 1998. Seawater microorganisms have a high affinity glycine betaine uptake system which also recognizes dimethylsulfoniopropionate. Aquat. Microb. Ecol. 15:39-51.
14. Kiene, R. P., L. J. Linn, J. M. Gonzalez, M. A. Moran, and J. A. Bruton. 1999. Dimethylsulfoniopropionate and methanethiol are important precursors of methionine and protein-sulfur in marine bacterioplankton. Appl. Environ. Microbiol. 65:4549-4558.
15. Kiene, R. P., and D. Slezak. 2006. Low dissolved DMSP concentrations in seawater revealed by small volume gravity filtration and dialysis sampling. Limnol. Oceanogr. 4:80-95.
16. Kirchman, D. L. 2002. The ecology of Cytophaga-Flavobacteria in aquatic systems. FEMS Microbiol. Ecol. 39:91-100.
17. Kirchman, D. L., E. K'nees, and R. E. Hodson. 1985. Leucine incorporation and its potential as a measure of protein synthesis by baceria in natural aquatic systems. Appl. Environ. Microbiol. 49:599-607.
18. Li, W., and A. Godzik. 2006. Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22:1658-1659.
19. Lovelock, J. E., R. J. Maggs, and R. A. Rasmussen. 1972. Atmospheric dimethyl sulphide and that natural sulphur cycle. Nature 237:452-453.
20. Malin, G., and G. O. Kirst. 1997. Algal production of dimethyl sulfide and its atmospheric role. J. Phycol. 33:889-896.
21. Margulies, M., et al. 2005. Genome sequencing in microfabricated highdensity picolitre reactors. Nature 437:376-380.
22. Oh, H.-M., et al. 2010. Complete genome sequence of "Candidatus Puniceispirillum marinum" IMCC1322, a representative of the SAR116 clade in the Alphaproteobacteria. J. Bacteriol. 192:3240-3241.
23. Parsons, T. R., Y. Maita, and C. M. Lalli. 1984. A manual for chemical and biological methods for seawater analysis. Pergamon, New York, NY.
24. Reisch, C. R., M. A. Moran, and W. B. Whitman. 2008. Dimethylsulfoniopropionate- dependent demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi. J. Bacteriol. 190:8018-8024.
25. Rusch, D. B., et al. 2007. The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific. PLoS Biol. 5:0398-0431.
26. Simó, R. 2001. Production of atmospheric sulfur by oceanic plankton: Biogeochemical, ecological, evolutionary links. Trends Ecol. Evol. 16:287-294.
27. Slezak, D., R. P. Kiene, D. A. Toole, R. Simó, and D. J. Kieber. 2007. Effects of solar radiation on the fate of dissolved DMSP and conversion to DMS in seawater. Aquat. Sci. 69:377-393.
28. Smith, D. C., and F. Azam. 1992. A simple, economical method for measuring bacterial protein synthesis rates in seawater using 3H-leucine. Mar. Microb. Food Webs 6:107-114.
29. Sogin, M. L., et al. 2006. Microbial diversity in the deep sea and the unexplored "rare biosphere." Proc. Natl. Acad. Sci. U. S. A. 103:12115-12120.
30. Sunda, W., D. J. Kieber, R. P. Kiene, and S. Huntsman. 2002. An antioxidant function for DMSP and DMS in marine alga. Nature 418:317-320.
31. Todd, J. D., A. R. J. Curson, C. L. Dupont, P. Nicholson, and A. W. B. Johnston. 2009. The dddP gene, encoding a novel enzyme that converts dimethylsulfoniopropionate into dimethyl sulfide, is widespread in ocean metagenomes and marine bacteria and also occurs in some ascomycete fungi. Environ. Microbiol. 11:1376-1385.
32. Todd, J. D., et al. 2007. Structural and regulatory genes required to make the gas dimethyl sulfide in bacteria. Science 315:666-669.
33. Turner, S. M., G. Malin, P. S. Liss, D. S. Harbour, and P. M. Holligan. 1988. The seasonal variation of dimethyl sulfide and dimethylsulfoniopropionate concentrations in nearshore waters. Limnol. Oceanogr. 33:364-375.
34. Varaljay, V. A., E. C. Howard, S. Sun, and M. A. Moran. 2010. Diversity of dimethylsulfoniopropionate demethylase genes in a marine ecosystem assessed by deep amplicon sequencing of dmdA primer sets. Appl. Environ. Microbiol. 76:609-617.
35. Vila, M., et al. 2004. Use of microautoradiography combined with fluorescence in situ hybridization to determine dimethylsulfoniopropionate incorporation by marine bacterioplankton taxa. Appl. Environ. Microbiol. 70: 4648-4657.
36. Vila-Costa, M., et al. 2010. Transcriptomic analysis of a marine bacterial community enriched with dimethylsulfoniopropionate. ISME J. doi:10.1038/ ismej.2010.62.
37. Wolfe, G. V. 1996. Accumulation of dissolved DMSP by marine bacteria and its degradation via bactivory, p. 277-291. In R. P. Kiene, P. T. Visscher, M. D. Keller, and G. O. Kirst (ed.), Biological and environmental chemistry of DMSP and related sulfonium compounds. Plenum Press, New York, NY.
38. Yutin, N., M. T. Suzuki, and O. Beja. 2005. Novel primers reveal wider diversity among marine aerobic anoxygenic phototrophs. Appl. Environ. Microbiol. 71:8958-8962.
39. Zubkov, M. V., et al. 2001. Linking the composition of bacterioplankton to rapid turnover of dissolved dimethylsulfoniopropionate in an algal bloom in the North Sea. Environ. Microbiol. 3:304-311.