The quality of organic matter shapes the functional biogeography of bacterioplankton across boreal freshwater ecosystems

Global Ecology and Biogeography

Volumn 24, Issue 12, 2015, Pages 1487-1498

  Ruiz González, Clara ^a   Niño García, Juan Pablo ^a   Lapierre, Jean François ^a,b   del Giorgio, Paul A ^a  

^a UNIVERSITÉ DU QUÉBEC À MONTRÉAL   (Canada)

^b MICHIGAN STATE UNIVERSITY   (United States)

Author keywords

Aquatic bacterial communities; Biodiversity function; Boreal ecosystems; DOM composition; Functional biogeography; Large scale spatial patterns; Trait based approaches

Indexed keywords

BACTERIOPLANKTON; BIODIVERSITY; BIOGEOGRAPHY; COMMUNITY COMPOSITION; DISSOLVED ORGANIC MATTER; FRESHWATER ECOSYSTEM; MICROBIAL COMMUNITY; SPATIAL VARIATION;

CANADA; QUEBEC [CANADA];

BACTERIA (MICROORGANISMS);

EID: 84946481595     PISSN: 1466822X     EISSN: 14668238     Source Type: Journal    
DOI: 10.1111/geb.12356     Document Type: Article

References (52)

1. Allison, S.D. & Martiny, J.B.H. (2008) Resistance, resilience, and redundancy in microbial communities. Proceedings of the National Academy of Sciences USA, 105, 11512-11519.
2. Barberán, A., Fernandez-Guerra, A., Bohannan, B.J.M. & Casamayor, E.O. (2012) Exploration of community traits as ecological markers in microbial metagenomes. Molecular Ecology, 21, 1909-1917.
3. Barberán, A., Ramirez, K.S., Left, J.W., Bradford, M.A., Wall, D.H. & Fierer, N. (2014) Why are some microbes more ubiquitous than others? Predicting the habitat breadth of soil bacteria. Ecology Letters, 7, 794-802.
4. Battin, T.J., Kaplan, L.A., Findlay, S., Hopkinson, C.S., Marti, E., Packman, A.I., Newbold, J.D. & Sabater, F. (2008) Biophysical controls of organic carbon fluxes in fluvial networks. Nature Geoscience, 1, 95-100.
5. Besemer, K., Singer, G., Quince, C., Bertuzzo, E., Sloan, W. & Battin, T.J. (2013) Headwaters are critical reservoirs of microbial diversity for fluvial networks. Proceedings of the Royal Society B: Biological Sciences, 280, 20131760.
6. Burke, C., Steinberg, P., Rusche, D., Kjelleberga, S. & Thomasa, T. (2011) Bacterial community assembly based on functional genes rather than species. Proceedings of the National Academy of Sciences USA, 108, 14288-14293.
7. Caporaso, J.G., Kuczynski, J., Stombaugh, J. etal. (2010) QIIME allows analysis of high-throughput community sequencing data. Nature Methods, 7, 335-336.
8. Caporaso, J.G., Lauber, C.L., Walters, W.A., Berg-Lyons, D., Huntley, J., Fierer, N., Owens, S.M., Betley, J., Fraser, J., Bauer, M., Gormley, N., Gilbert, J.A., Smith, G. & Knight, R. (2012) Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME Journal, 6, 1621-1624.
9. 13C addition to contrasting lakes. Ecology, 86, 2737-2750.
10. Clarke, K.R. (1993) Non-parametric multivariate analysis of changes in community structure. Australian Journal of Ecology, 18, 117-143.
11. Comte, J. & del Giorgio, P.A. (2009) Links between resources, C metabolism and the major components of bacterioplankton community structure across a range of freshwater ecosystems. Environmental Microbiology, 11, 1704-1716.
12. Crump, B.C., Adams, H.E., Hobbie, J.E. & Kling, G.W. (2007) Biogeography of bacterioplankton in lakes and streams of an Arctic tundra catchment. Ecology, 88, 1365-1378.
13. Crump, B.C., Amaral-Zettler, L.A. & Kling, G.W. (2012) Microbial diversity in arctic freshwaters is structured by inoculation of microbes from soils. ISME Journal, 6, 1629-1639.
14. Edgar, R.C. (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 26, 2460-2461.
15. Fellman, J.B., Spencer, R.G.M., Raymond, P.A., Pettit, N.E., Skrzypek, G., Hernes, P.J. & Grierson, P.F. (2014) Dissolved organic carbon biolability decreases along with its modernization in fluvial networks in an ancient landscape. Ecology, 95, 2622-2632.
16. Fierer, N., Barberán, A. & Laughlin, D.C. (2014) Seeing the forest for the genes: using metagenomics to infer the aggregated traits of microbial communities. Frontiers in Microbiology, 5, 614.
17. Fujii, M., Kojima, H., Iwata, T., Urabe, J. & Fukui, M. (2012) Dissolved organic carbon as major environmental factor affecting bacterioplankton communities in mountain lakes of eastern Japan. Environmental Microbiology, 63, 496-508.
18. Garland, J.L., Mills, A.L. & Young, J.S. (2001) Relative effectiveness of kinetic analysis vs single point readings for classifying environmental samples based on community-level physiological profiles (CLPP). Soil Biology and Biochemistry, 33, 1059-1066.
19. Geobase (2009) Land Cover, Circa 2000-Vector.
20. Green, J.L., Bohannan, B.J.M. & Whitaker, R.J. (2008) Microbial biogeography: from taxonomy to traits. Science, 320, 1039-1042.
21. Guillemette, F.S., McCallister, L. & del Giorgio, P.A. (2013) Differentiating the degradation dynamics of algal and terrestrial carbon within complex natural dissolved organic carbon in temperate lakes. Journal of Geophysical Research: Biogeosciences, 118, 963-973.
22. Hartigan, J.A. & Wong, M.A. (1979) Algorithm AS 136: a k-means clustering algorithm. Applied Statistics, 28, 100-108.
23. Hijmans, R.J., Cameron, S.E., Parra, J.L., Jones, P.G. & Jarvis, A. (2005) Very high resolution interpolated climate surfaces for global land areas. International Journal of Climatology, 25, 1965-1978.
24. Jiang, X., Langille, M.G.I., Neches, R.Y., Elliot, M., Levin, S.A., Eisen, J.A., Weitz, J.S. & Dushoff, J. (2012) Functional biogeography of ocean microbes revealed through non-negative matrix factorization. PLoS ONE, 7, e43866.
25. Jones, S.E. & Lennon, J.T. (2010) Dormancy contributes to the maintenance of microbial diversity. Proceedings of the National Academy of Sciences USA, 107, 5881-5886.
26. Kothawala, D.N., Stedmon, C.A., Müller, R.A., Weyhenmeyer, G.A., Köhler, S.J. & Tranvik, L. (2014) Controls of dissolved organic matter quality: evidence from a large-scale boreal lake survey. Global Change Biology, 20, 1101-1114.
27. Krause, S., Le Roux, X., Niklaus, P.A., Van Bodegom, P.M., Lennon, J.T., Bertilsson, S., Grossart, H.P., Philippot, L. & Bodelier, P.L.E. (2014) Trait-based approaches for understanding microbial biodiversity and ecosystem functioning. Frontiers in Microbiology, 5, 251.
28. Lambert, T., Pierson-Wickmann, A.C., Gruau, G., Jaffrezic, A., Peritjean, P., Thibault, J.N. & Jeanneau, L. (2013) Hydrologically driven seasonal changes in the sources and production mechanisms of dissolved organic carbon in a small lowlands catchment. Water Resouces Research, 49, 5792-5803.
29. Langenheder, S., Lindstrom, E.S. & Tranvik, L. (2005) Weak coupling between community composition and functioning of aquatic bacteria. Limnology and Oceanography, 50, 957-967.
30. Lapierre, J.F. & del Giorgio, P.A. (2014) Partial coupling and differential regulation of biologically and photochemically labile dissolved organic carbon across boreal aquatic networks. Biogeosciences, 11, 5969-5985.
31. 2 emissions in boreal aquatic ecosystems. Nature Communications, 4, 2972.
32. Lear, G., Bellamy, J., Case, B.S., Lee, J.E. & Buckley, H.B. (2014) Fine-scale spatial patterns in bacterial community composition and function within freshwater ponds. ISME Journal, 8, 1715-1726.
33. Lindström, E.S., Kamst-Van Agterveld, M.P. & Zwart, G. (2005) Distribution of typical freshwater bacterial groups is associated with pH, temperature, and lake water retention time. Applied and Environmental Microbiology, 71, 8201-8206.
34. 2 fluxes. Limnology and Oceanography, 53, 1204-1216.
35. Magoc, T. & Salzberg, S. (2011) FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics, 27, 2957-2963.
36. Martiny, A.C., Treseder, K. & Pusch, G. (2013) Phylogenetic conservatism of functional traits in microorganisms. ISME Journal, 7, 830-838.
37. Martiny, J.B.H., Eisen, J.A., Penn, K., Allison, S.D. & Horner-Devine, M.C. (2011) Drivers of bacterial beta-diversity depend on spatial scale. Proceedings of the National Academy of Sciences USA, 108, 7850-7854.
38. Nemergut, D.R., Shade, A. & Violle, C. (2014) When, where and how does microbial community composition matter? Frontiers in Microbiology, 5, doi:10.3389/fmicb.2014.00497.
39. Ochman, H., Lawrence, J.G. & Groisman, E.A. (2000) Lateral gene transfer and the nature of bacterial innovation. Nature, 405, 299-304.
40. Preston-Mafham, J., Boddy, L. & Randerson, P.F. (2002) Analysis of microbial community functional diversity using sole-carbon-source utilisation profiles: a critique. FEMS Microbiology Ecology, 42, 1-14.
41. Raes, J., Letunic, I., Yamada, T., Jensen, L.J. & Bork, P. (2011) Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data. Molecular Systems Biology, 7, 1-9.
42. 4 fluxes across boreal lakes, and contribution to diffusive C emissions. Global Change Biology, 21, 1124-1139.
43. Severin, I., Lindström, E.S. & Östman, O. (2014) Relationships between bacterial community composition, functional trait composition and functioning are context dependent - but what is the context? PLoS ONE, 11, e112409.
44. Stubbins, A., Lapierre, J.F., Berggren, M., Prairie, Y.T., Dittmar, T. & del Giorgio, P.A. (2014) What's in an EEM? Molecular signatures associated with dissolved organic fluorescence in boreal Canada. Environmental Science and Technology, 48, 10598-10606.
45. Swenson, N.G. & Enquist, B.J. (2007) Ecological and evolutionary determinants of a key plant functional trait: wood density and its community-wide variation across latitude and elevation. Americal Journal of Botany, 94, 451-459.
46. Tamames, J., Abellán, J., Pignatelli, M., Camacho, A. & Moya, A. (2010) Environmental distribution of prokaryotic taxa. BMC Microbiology, 10, 85.
47. Torsvik, V., Øvreås, L. & Thingstad, T.F. (2002) Prokaryotic diversity: magnitude, dynamics, and controlling factors. Science, 296, 1064-1066.
48. Violle, C., Navas, M.L., Vile, D., Kazakou, E., Fortunel, C., Hummel, I., Hummel, I. & Garnier, E. (2007) Let the concept of trait be functional! Oikos, 116, 882-892.
49. Violle, C., Reich, P.B., Pacalae, S.W., Enquist, B.J. & Kattge, J. (2014) The emergence and promise of functional biogeography. Proceedings of the National Academy of Sciences USA, 111, 13690-13696.
50. Vogt, R.J., Peres-Neto, P.R. & Beisner, B.E. (2013) Using functional traits to investigate the determinants of crustacean zooplankton community structure. Oikos, 122, 1700-1709.
51. Wallenstein, M.D. & Hall, E.K. (2012) A trait-based framework for predicting when and where microbial adaptation to climate change will affect ecosystem functioning. Biogeochemistry, 109, 35-47.
52. Wang, Q., Garrity, G.M., Tiedje, J.M. & Cole, J.R. (2007) Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology, 73, 5261-5267.