Environmental actinorhodopsin expression revealed by a new in situ filtration and fixation sampler

Environmental Microbiology Reports

Volumn 4, Issue 5, 2012, Pages 491-497

  Wurzbacher, Christian ^a   Salka, Ivette ^a   Grossart, Hans Peter ^a,b  

^a LEIBNIZ INSTITUTE OF FRESHWATER ECOLOGY AND INLAND FISHERIES   (Germany)

^b UNIVERSITY OF POTSDAM   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ACTINOBACTERIA;

EID: 84867157988     PISSN: None     EISSN: 17582229     Source Type: Journal    
DOI: 10.1111/j.1758-2229.2012.00350.x     Document Type: Article

References (33)

1. Allgaier, M., and Grossart, H. (2006) Diversity and seasonal dynamics of Actinobacteria populations in four lakes in northeastern Germany. Appl Environ Microbiol 72: 3489-3497.
2. Bailly, J., Fraissinet-Tachet, L., Verner, M.-C., Debaud, J.-C., Lemaire, M., Wésolowski-Louvel, M., and Marmeisse, R. (2007) Soil eukaryotic functional diversity, a metatranscriptomic approach. ISME J 1: 632-642.
3. Beier, S., and Bertilsson, S. (2011) Uncoupling of chitinase activity and uptake of hydrolysis products in freshwater bacterioplankton. Limnol Oceanogr 56: 1179-1188.
4. Béjà, O., Suzuki, M.T., Koonin, E.V., Aravind, L., Hadd, A., Nguyen, L.P., etal. (2000) Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. Environ Microbiol 2: 516-529.
5. Burns, C.W., and Galbraith, L.M. (2007) Relating planktonic microbial food web structure in lentic freshwater ecosystems to water quality and land use. J Plankton Res 29: 127-139.
6. Cottrell, M.T., and Kirchman, D.L. (2009) Photoheterotrophic microbes in the Arctic Ocean in summer and winter. Appl Environ Microbiol 75: 4958-4966.
7. Feike, J., Jürgens, K., Hollibaugh, J.T., Krüger, S., Jost, G., and Labrenz, M. (2011) Measuring unbiased metatranscriptomics in suboxic waters of the central Baltic Sea using a new in situ fixation system. ISME J 6: 461-470.
8. Frias-Lopez, J., Shi, Y., Tyson, G.W., Coleman, M.L., Schuster, S.C., Chisholm, S.W., and Delong, E.F. (2008) Microbial community gene expression in ocean surface waters. Proc Natl Acad Sci USA 105: 3805-3810.
9. Giovannoni, S.J., Bibbs, L., Cho, J.-C., Stapels, M.D., Desiderio, R., Vergin, K.L., etal. (2005) Proteorhodopsin in the ubiquitous marine bacterium SAR11. Nature 438: 82-85.
10. Gómez-Consarnau, L., González, J.M., Coll-Lladó, M., Gourdon, P., Pascher, T., Neutze, R., etal. (2007) Light stimulates growth of proteorhodopsin-containing marine Flavobacteria. Nature 445: 210-213.
11. Hahn, M.W. (2009) Description of seven candidate species affiliated with the phylum Actinobacteria, representing planktonic freshwater bacteria. Int J Syst Evol Microbiol 59: 112-117.
12. Jezbera, J., Sharma, A.K., Brandt, U., Doolittle, W.F., and Hahn, M.W. (2009) 'Candidatus Planktophila limnetica', an actinobacterium representing one of the most numerically important taxa in freshwater bacterioplankton. Int J Syst Evol Microbiol 59: 2864-2869.
13. Lami, R., Cottrell, M.T., Campbell, B.J., and Kirchman, D.L. (2009) Light-dependent growth and proteorhodopsin expression by Flavobacteria and SAR11 in experiments with Delaware coastal waters. Environ Microbiol 11: 3201-3209.
14. Legault, B.A., Lopez-Lopez, A., Alba-Casado, J.C., Doolittle, W.F., Bolhuis, H., Rodriguez-Valera, F., and Papke, R.T. (2006) Environmental genomics of 'Haloquadratum walsbyi' in a saltern crystallizer indicates a large pool of accessory genes in an otherwise coherent species. BMC Genomics 7: 171.
15. Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., etal. (2004) ARB: a software environment for sequence data. Nucl Acid Res 32: 1363-1371.
16. Martín-Cuadrado, A.-B., López-García, P., Alba, J.-C., Moreira, D., Monticelli, L., Strittmatter, A., etal. (2007) Metagenomics of the deep Mediterranean, a warm bathypelagic habitat. PLoS ONE 2: e914.
17. Martinez-Garcia, M., Swan, B.K., Poulton, N.J., Gomez, M.L., Masland, D., Sieracki, M.E., and Stepanauskas, R. (2012) High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton. ISME J 6: 113-123.
18. Mary, I., Tarran, G.A., Warwick, P.E., Terry, M.J., Scanlan, D.J., Burkill, P.H., and Zubkov, M.V. (2008) Light enhanced amino acid uptake by dominant bacterioplankton groups in surface waters of the Atlantic Ocean. FEMS Microb Ecol 63: 36-45.
19. Philosof, A., Sabehi, G., and Béjà, O. (2009) Comparative analyses of actinobacterial genomic fragments from Lake Kinneret. Environ Microbiol 11: 3189-3200.
20. Poretsky, R.S., Bano, N., Buchan, A., LeCleir, G., Kleikemper, J., Pickering, M., etal. (2005) Analysis of microbial gene transcripts in environmental samples. Appl Environ Microbiol 71: 4121-4126.
21. Poretsky, R.S., Hewson, I., Sun, S., Allen, A.E., Zehr, J.P., and Moran, M.A. (2009) Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyre. Environ Microbiol 11: 1358-1375.
22. Price, M.N., Dehal, P.S., and Arkin, A.P. (2010) FastTree 2 - approximately maximum-likelihood trees for large alignments. PLoS ONE 5: e9490.
23. Riedel, T., Tomasch, J., Buchholz, I., Jacobs, J., Kollenberg, M., Gerdts, G., etal. (2010) Constitutive expression of the proteorhodopsin gene by a flavobacterium strain representative of the proteorhodopsin-producing microbial community in the North Sea. Appl Environ Microbiol 76: 3187-3197.
24. Sabehi, G., Loy, A., Jung, K.-H., Partha, R., Spudich, J.L., Isaacson, T., etal. (2005) New insights into metabolic properties of marine bacteria encoding proteorhodopsins. PLoS Biol 3: e273.
25. Schloss, P.D., Westcott, S.L., Ryabin, T., Hall, J.R., Hartmann, M., Hollister, E.B., etal. (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537-7541.
26. Selinger, D.W., Saxena, R.M., Cheung, K.J., Church, G.M., and Rosenow, C. (2003) Global RNA half-life analysis in Escherichia coli reveals positional patterns of transcript degradation. Genome Res 13: 216-223.
27. Sharma, A.K., Zhaxybayeva, O., Papke, R.T., and Doolittle, W.F. (2008) Actinorhodopsins: proteorhodopsin-like gene sequences found predominantly in non-marine environments. Environ Microbiol 10: 1039-1056.
28. Sharma, A.K., Sommerfeld, K., Bullerjahn, G.S., Matteson, A.R., Wilhelm, S.W., Jezbera, J., etal. (2009) Actinorhodopsin genes discovered in diverse freshwater habitats and among cultivated freshwater Actinobacteria. ISME J 3: 726-737.
29. Shi, Y., Tyson, G.W., Eppley, J.M., and DeLong, E.F. (2011) Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean. ISME J 5: 999-1013.
30. Steglich, C., Lindell, D., Futschik, M., Rector, T., Steen, R., and Chisholm, S.W. (2010) Short RNA half-lives in the slow-growing marine cyanobacterium Prochlorococcus. Genome Biol 11: R54.
31. Stepanauskas, R., and Sieracki, M.E. (2007) Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time. Proc Natl Acad Sci USA 104: 9052-9057.
32. Warnecke, F., Amann, R., and Pernthaler, J. (2004) Actinobacterial 16S rRNA genes from freshwater habitats cluster in four distinct lineages. Environ Microbiol 6: 242-253.
33. Yurkov, V.V., and van Gemerden, H. (1993) Impact of light/dark regimen on growth rate, biomass formation and bacteriochlorophyll synthesis in Erythromicrobium hydrolyticum. Arch Microbiol 159: 84-89.