Experimental insights into the importance of aquatic bacterial community composition to the degradation of dissolved organic matter

ISME Journal

Volumn 10, Issue 3, 2016, Pages 533-545

  Logue, Jürg B ^a,b   Stedmon, Colin A ^c   Kellerman, Anne M ^d   Nielsen, Nikoline J ^e   Andersson, Anders F ^f   Laudon, Hjalmar ^g   Lindström, Eva S ^d   Kritzberg, Emma S ^a  

^a LUND UNIVERSITY   (Sweden)

^b SCIENCE FOR LIFE LABORATORY   (Sweden)

^c TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^d UPPSALA UNIVERSITY   (Sweden)

^e UNIVERSITY OF COPENHAGEN   (Denmark)

^f ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

^g SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

AQUATIC ENVIRONMENT; BACTERIUM; BIODEGRADATION; CARBON CYCLE; COMMUNITY COMPOSITION; COMMUNITY STRUCTURE; DISSOLVED ORGANIC MATTER; ECOSYSTEM FUNCTION; MICROBIAL COMMUNITY; PHYLOGENETICS;

BACTERIA (MICROORGANISMS);

CARBON; FRESH WATER; ORGANIC COMPOUND;

BACTERIUM; BIOREMEDIATION; CLASSIFICATION; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY; PHYLOGENY;

BACTERIA; BIODEGRADATION, ENVIRONMENTAL; CARBON; FRESH WATER; ORGANIC CHEMICALS; PHYLOGENY;

EID: 84939818228     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2015.131     Document Type: Article

References (58)

1. Azam F, Fenchel T, Field JG, Gray JS, Meyerreil LA, Thingstad F. (1983). The ecological role of watercolumn microbes in the sea. Marine Ecol Prog Ser. 10: 257-263.
2. Battin TJ, Luyssaert S, Kaplan LA, AufDenkampe AK, Richter A, Tranvik LJ. (2009). The boundless carbon cycle. Nat Geosci. 2: 598-600.
3. Benjamini Y, Hochberg Y. (1995). Controlling the false discovery rate - A practical and powerful approach to multiple testing. J R Stat Soc B Met. 57: 289-300.
4. Berlemont R, Martiny AC. (2013). Phylogenetic distribution of potential cellulases in bacteria. Appl Environ Microbiol. 79: 1545-1554.
5. Bertilsson S, Eiler A, Nordqvist A, Jørgensen NOG. (2007). Links between bacterial production, amino-Acid utilization and community composition in productive lakes. ISME J. 1: 532-544.
6. Christian RR, Capone DG. (2002). Overview of issues in aquatic microbial ecology. In: Hurst CJ, Crawford RL, Knudsen GR, McInerney MJ, Stetzenbach LD (eds). Manual of Environmental Microbiology. 2nd edn. ASM Press: Washington, pp 323-328.
7. Cole JJ, Prairie YT, Caraco NF, McDowell WH, Tranvik LJ, Striegl RG, et al. (2007). Plumbing the global carbon cycle: Integrating inland waters into the terrestrial carbon budget. Ecosystems. 10: 171-184.
8. Comte J, Del Giorgio PA. (2009). Links between resources, C metabolism and the major components of bacterioplankton community structure across a range of freshwater ecosystems. Environ Microbiol. 11: 1704-1716.
9. Comte J, Del Giorgio PA. (2010). Linking the patterns of change in composition and function in bacterioplankton successions along environmental gradients. Ecology. 91: 1466-1476.
10. Covert JS, Moran MA. (2001). Molecular characterization of estuarine bacterial communities that use high- And low-molecular weight fractions of dissolved organic carbon. Aquat Microb Ecol. 25: 127-139.
11. Crump BC, Kling GW, Bahr M, Hobbie JE. (2003). Bacterioplankton community shifts in an arctic lake correlate with seasonal changes in organic matter source. Appl Environ Microbiol. 69: 2253-2268.
12. Curtis TP, Sloan WT. (2004). Prokaryotic diversity and its limits: microbial community structure in nature and implications for microbial ecology. Curr Opin Microbiol. 7: 221-226.
13. Curtis TP, Sloan WT. (2005). Exploring microbial diversity - A vast below. Science. 309: 1331-1333.
14. Del Giorgio PA, Bird DF, Prairie YT, Planas D. (1996). Flow cytometric Determination of bacterial abundance in lake plankton with the green nucleic acid stain SYTO 13. Limnol Oceanogr. 41: 783-789.
15. Dittmar T, Koch B, Hertkorn N, Kattner G. (2008). A simple and efficient method for the solid-phase extraction of dissolved organic matter (SPE-DOM) from seawater. Limnol Oceanogr Methods. 6: 230-235.
16. Engelbrektson A, Kunin V, Wrighton KC, Zvenigorodsky N, Chen F, Ochman H, et al. (2010). Experimental factors affecting PCR-based estimates of microbial species richness and evenness. ISME J. 4: 642-647.
17. Fuhrman JA, Hagström Å. (2008). Bacterial and archaeal community structure and its patterns. In: Kirchman DL (ed). Microbial Ecology of the Oceans. 2nd edn. John Wiley & Sons: Hoboken, pp 45-90.
18. Green NW, Perdue EM, Aiken GR, Butler KD, Chen HM, Dittmar T, et al. (2014). An intercomparison of three methods for the large-scale isolation of oceanic dissolved organic matter. Mar Chem. 161: 14-19.
19. Hedges JI, Eglinton G, Hatcher PG, Kirchman DL, Arnosti C, Derenne S, et al. (2000). The molecularlyuncharacterized component of nonliving organic matter in natural environments. Organic Geochem. 31: 945-958.
20. Herlemann DPR, Labrenz M, Jürgens K, Bertilsson S, Waniek JJ, AnDersson AF. (2011). Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea. ISME J. 5: 1571-1579.
21. Herlemann DPR, Manecki M, Meeske C, Pollehne F, Labrenz M, Schulz-Bull D, et al. (2014). Uncoupling of bacterial and terrigenous dissolved organic matter dynamics in Decomposition experiments. PLoS One. 9: e93945.
22. Hertkorn N, Frommberger M, Witt M, Koch BP, Schmitt-Kopplin P, Perdue EM. (2008). Natural organic matter and the event horizon of mass spectrometry. Anal Chem. 80: 8908-8919.
23. Jansson M, Persson L, DeRoos AM, Jones RI, Tranvik LJ. (2007). Terrestrial carbon and intraspecific sizevariation shape lake ecosystems. Trends Ecol Evol. 22: 316-322.
24. Judd KE, Crump BC, Kling GW. (2006). Variation in dissolved organic matter controls bacterial production and community composition. Ecology. 87: 2068-2079.
25. Kirchman DL, Dittel AI, Findlay SEG, Fischer D. (2004). Changes in bacterial activity and community structure in response to dissolved organic matter in the Hudson River, New York. Aquat Microb Ecol. 35: 243-257.
26. Kothawala DN, Stedmon CA, Müller RA, Weyhenmeyer GA, Köhler SJ, Tranvik LJ. (2014). Controls of dissolved organic matter quality: eviDence from a large-scale boreal lake survey. Global Change Biol. 20: 1101-1114.
27. Kritzberg ES, Cole JJ, Pace MM, Graneli W. (2006). Bacterial growth on allochthonous carbon in humic and nutrient-enriched lakes: Results from whole-lake C-13 addition experiments. Ecosystems. 9: 489-499.
28. Kujawinski EB. (2011). The impact of microbial metabolism on marine dissolved organic matter. Annu Rev Mar Sci. 3: 567-599.
29. Landa M, Cottrell MT, Kirchman DL, Kaiser K, MeDeiros PM, Tremblay L, et al. (2014). Phylogenetic and structural response of heterotrophic bacteria to dissolved organic matter of different chemical composition in a continuous culture study. Environ Microbiol. 16: 1668-1681.
30. LangenheDer S, Lindström ES, Tranvik LJ. (2005). Weak coupling between community composition and functioning of aquatic bacteria. Limnol Oceanogr. 50: 957-967.
31. LangenheDer S, Lindström ES, Tranvik LJ. (2006). Structure and function of bacterial communities emerging from different sources unDer iDentical conditions. Appl Environ Microbiol. 72: 212-220.
32. Laudon H, Taberman I, Ågren A, Futter M, Ottosson-Löfvenius M, Bishop K. (2013). The Krycklan Catchment Study-A flagship infrastructure for hydrology, biogeochemistry, and climate research in the boreal landscape. Water Resour Res. 49: 7154-7158.
33. Lindström ES, Feng XM, Graneli W, Kritzberg ES. (2010). The interplay between bacterial community composition and the environment Determining function of inland water bacteria. Limnol Oceanogr. 55: 2052-2060.
34. Logue JB, Lindström ES. (2008). Biogeography of bacterioplankton in inland waters. Freshwater Rev. 1: 99-114.
35. Mardis ER. (2008). Next-generation DNA sequencing methods. Ann Rev Genomics Hum Genet. 9: 387-402.
36. Martiny AC, TreseDer K, Pusch G. (2013). Phylogenetic conservatism of functional traits in microorganisms. ISME J. 7: 830-838.
37. Moran MA. (2009). Metatranscriptomics: eavesdropping on complex microbial communities. Microbe. 4: 329-335.
38. Murphy KR, Butler KD, Spencer RGM, Stedmon CA, Boehme JR, Aiken GR. (2010). Measurement of dissolved organic matter fluorescence in aquatic environments: an interlaboratory comparison. Environ Sci Technol. 44: 9405-9412.
39. Nelson CE, Wear EK. (2014). Microbial diversity and the lability of dissolved organic carbon. Proc Natl Acad Sci USA. 111: 7166-7167.
40. Oksanen J, Blanchet FG, Kindt R, Legendre P, Minchin PR, O'Hara RB, et al. (2008). vegan: Communiy Ecology Package. R package version 2.2-1.
41. Pedler BE, Aluwihare LI, Azam F. (2014). Single bacterial strain capable of significant contribution to carbon cycling in the surface ocean. Proc Natl Acad Sci USA. 111: 7202-7207.
42. Pomeroy LR. (1974). The oceans food web, a changing paradigm. Bioscience. 24: 499-504.
43. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. (2013). The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41: D590-D596.
44. Quince C, Lanzén A, Davenport RJ, Turnbaugh PJ. (2011). Removing noise from pyrosequenced amplicons. BMC Bioinformatics. 12: 38: 1-18.
45. R. (2015). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing: Vienna, Austria. http://www.R-project.org/.
46. Reed HE, Martiny JBH. (2007). Testing the functional significance of microbial composition in natural communities. FEMS Microbiol Ecol. 62: 161-170.
47. Rinke C, Schwientek P, Sczyrba A, Ivanova NN, AnDerson IJ, Cheng JF, et al. (2013). Insights into the phylogeny and coding potential of microbial dark matter. Nature. 499: 431-437.
48. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, et al. (2009). Introducing mothur: opensource, platform-inDepenDent, community-supported software for Describing and comparing microbial communities. Appl Environ Microbiol. 75: 7537-7541.
49. Shabarova T, Villiger J, Morenkov O, Niggemann J, Dittmar T, Pernthaler J. (2014). Bacterial community structure and dissolved organic matter in repeatedly flooDed subsurface karst water pools. FEMS Microbiol Ecol. 89: 111-126.
50. Solomon S, Qin D, Manning M, Chen Z, Marquis M, Averyt KB, et al. (2007). Climate Change 2007: The Physical Science Basis. Cambridge University Press: Cambridge
51. Stedmon CA, Bro R. (2008). Characterizing dissolved organic matter fluorescence with parallel factor analysis: a tutorial. Limnol Oceanogr Methods. 6: 572-579.
52. Teeling H, Fuchs BM, Becher D, Klockow C, GarDebrecht A, Bennke CM, et al. (2012). Substratecontrolled succession of marine bacterioplankton populations induced by a phytoplankton bloom. Science. 336: 608-611.
53. Tranvik LJ, Downing JA, Cotner JB, Loiselle SA, Striegl RG, Ballatore TJ, et al. (2009). Lakes and reservoirs as regulators of carbon cycling and climate. Limnol Oceanogr. 54: 2298-2314.
54. Wang Q, Garrity GM, Tiedje JM, Cole JR. (2007). Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 73: 5261-5267.
55. Wang Y, Naumann U, Wright ST, Warton DI. (2012). mvabund - An R package for moDel-based analysis of multivariate abundance data. Methods Ecol Evol. 3: 471-474.
56. Warton DI, Wright ST, Wang Y. (2012). Distance-based multivariate analyses confound location and dispersion effects. Methods Ecol Evol. 3: 89-101.
57. Weiss MS, Abele U, Weckesser J, Welte W, Schiltz E, Schulz GE. (1991). Molecular architecture and electrostatic properties of a bacterial porin. Science. 254: 1627-1630.
58. Zimmerman AE, Martiny AC, Allison SD. (2013). Microdiversity of extracellular enzyme genes among sequenced prokaryotic genomes. ISME J. 7: 1187-1199.