The functional and taxonomic richness of wastewater treatment plant microbial communities are associated with each other and with ambient nitrogen and carbon availability

Environmental Microbiology

Volumn 17, Issue 12, 2015, Pages 4851-4860

  Johnson, David R ^a,b   Lee, Tae Kwon ^b   Park, Joonhong ^b   Fenner, Kathrin ^a,c   Helbling, Damian E ^b,d  

^a ETH ZURICH   (Switzerland)

^b Department of Environmental Microbiology ^*  (Switzerland)

^c Yonsei University   (South Korea)

^d Cornell University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CARBON; NITROGEN; RNA 16S; WASTE WATER;

BACTERIUM; BIODIVERSITY; CLASSIFICATION; ECOLOGY; GENETICS; METABOLISM; MICROBIAL CONSORTIUM; MICROBIOLOGY; PHYSIOLOGY; WASTE WATER; WATER MANAGEMENT;

BACTERIA; BIODIVERSITY; CARBON; ECOLOGY; MICROBIAL CONSORTIA; NITROGEN; RNA, RIBOSOMAL, 16S; WASTE WATER; WATER PURIFICATION;

EID: 84955746315     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/1462-2920.12429     Document Type: Article

References (44)

1. Beazley, M.J., Martinez, R.J., Rajan, S., Powell, J., Piceno, Y.M., Tom, L.M., etal. (2012) Microbial community analysis of a coastal salt marsh affected by the Deepwater Horizon oil spill. PLoS ONE 7: e41305.
2. Bell, T., Newman, J.A., Silverman, B.W., Turner, S.L., and Lilley, A.K. (2005) The contribution of species richness and composition to bacterial services. Nature 436: 1157-1160.
3. Benjamini, Y., and Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B Methodol 57: 289-300.
4. Briones, A., and Raskin, L. (2003) Diversity and dynamics of microbial communities in engineered environments and their implications for process stability. Curr Opin Microbiol 14: 270-276.
5. Bryant, J.A., Stewart, F.J., Eppley, J.M., and DeLong, E.F. (2012) Microbial community phylogenetic and trait diversity declines with depth in a marine oxygen minimum zone. Ecology 93: 1659-1673.
6. Cadotte, M.W., Carscadden, K., and Mirotchnick, N. (2011) Beyond species: functional diversity and the maintenance of ecological processes and services. J Appl Ecol 48: 1079-1087.
7. Cardinale, B.J. (2011) Biodiversity improves water quality through niche partitioning. Nature 472: 86-89.
8. Chao, A. (1987) Estimating the population size for capture-recapture data with unequal catchability. Biometrics 43: 783-791.
9. Chapin, F.S., Walker, B.H., Hobbs, R.J., Hooper, D.U., Lawton, J.H., Sala, O.E., and Tilman, D. (1997) Biotic control over the functioning of ecosystems. Science 277: 500-504.
10. Clara, M., Kreuzinger, N., Strenn, B., Gans, O., and Kroiss, H. (2005) The solids retention time - a suitable design parameter to evaluate the capacity of wastewater treatment plants to remove micropollutants. Water Res 39: 97-106.
11. Cook, K.L., Garland, J.L., Layton, A.C., Dionisi, H.M., Levine, L.S., and Sayler, G.S. (2006) Effect of microbial species richness on community stability and community function in a model plant-based wastewater processing system. Microb Ecol 52: 725-737.
12. Edgar, R.C., Haas, B.J., Clemente, J.C., Quince, C., and Knight, R. (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27: 2194-2200.
13. Egli, T. (1995) The ecological and physiological significance of the growth of heterotrophic microorganisms with mixtures of substrates. Adv Microb Ecol 14: 305-386.
14. Fernandez, A.S., Hashsham, S.A., Dollhopf, S.L., Raskin, L., Glagoleva, O., Dazzo, F.B., etal. (2000) Flexible community structure correlates with stable community function in methanogenic bioreactor communities perturbed by glucose. Appl Environ Microbiol 66: 4058-4067.
15. Fierer, N., Leff, J.W., Adams, B.J., Nielsen, U.N., Bates, S.T., Lauber, C.L., etal. (2012) Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proc Natl Acad Sci USA 109: 21390-21395.
16. Gentile, M.E., Jessup, C.M., Nyman, J.L., and Criddle, C.S. (2007) Correlation of functional instability and community dynamics in denitrifying dispersed-growth reactors. Appl Environ Microbiol 73: 680-690.
17. Gilbert, J.A., Field, D., Swift, P., Thomas, S., Cummings, D., Temperton, B., etal. (2010) The taxonomic and functional diversity of microbes at a temperate coastal site: a 'multi-omic' study of seasonal and diel temporal variation. PLoS ONE 5: e15545.
18. Hashsham, S.A., Fernandez, A.S., Dollhopf, S.L., Dazzo, F.B., Hickey, R.F., Tiedje, J.M., and Criddle, C.S. (2000) Parallel processing of substrate correlates with greater functional stability in methanogenic bioreactor communities perturbed by glucose. Appl Environ Microbiol 66: 4050-4057.
19. He, S., Wurtzel, O., Singh, K., Froula, J.L., Yilmaz, S., Tringe, S.G., etal. (2010) Validation of two ribosomal RNA removal methods for microbial metatranscriptomics. Nat Methods 7: 807-812.
20. Helbling, D.E., Johnson, D.R., Honti, M., and Fenner, K. (2012a) Micropollutant biotransformation kinetics associate with WWTP process performance parameters and microbial community characteristics. Environ Sci Technol 46: 10579-10588.
21. Helbling, D.E., Ackermann, M., Fenner, K., Kohler, H.P., and Johnson, D.R. (2012b) The activity level of a microbial community function can be predicted from its metatranscriptome. ISME J 6: 902-904.
22. Hernandez-Raquet, G., Durand, E., Braun, F., Cravo-Laureau, C., and Godon, J.J. (2013) Impact of microbial diversity depletion on xenobiotic degradation by sewage-activated sludge. Environ Microbiol Rep 5: 588-594.
23. Johnson, D.R., Lee, P.K.H., Holmes, V.F., and Alvarez-Cohen, L. (2005) An internal reference technique for accurately quantifying specific mRNAs by Real-time PCR with application to the tceA reductive dehalogenase gene. Appl Environ Microbiol 71: 3866-3871.
24. Kovárová-Kovar, K., and Egli, T. (1998) Growth kinetics of suspended microbial cells: from single-substrate-controlled growth to mixed-substrate kinetics. Microbiol Mol Biol Rev 62: 646-666.
25. Krakat, N., Schmidt, S., and Scherer, P. (2010) Mesophilic fermentation of renewable biomass: does hydraulic retention time regulate methanogen diversity? Appl Environ Microbiol 76: 6322-6326.
26. Meyer, F., Paarmann, D., D'Souza, M., Olson, R., Glass, E.M., Kubal, M., etal. (2008) The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9: 386.
27. Minchin, P.R. (1987) An evaluation of relative robustness of techniques for ecological ordinations. Vegetatio 69: 89-107.
28. Naeem, S., and Wright, J.P. (2003) Disentangling biodiversity effects on ecosystem functioning: deriving solutions to a seemingly insurmountable problem. Ecol Lett 6: 567-579.
29. Oksanen, J., Blanchet, F.G., Kindt, R., Legendre, P., Minchin, P.R., O'Hara, R.B., etal. (2013) Vegan: Community Ecology Package, 2.0-7 edn. [WWW document]. URL http://cran.r-project.org/web/packages/vegan/index.html
30. Overbeek, R., Begley, T., Butler, R.M., Choudhuri, J.V., Chuang, H.Y., Cohoon, M., etal. (2005) The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res 33: 5691-5702.
31. Parnell, J.J., Rompato, G., Latta, L.C., Pfrender, M.E., Van Nostrand, J.D., He, Z., etal. (2010) Functional biogeography as evidence of gene transfer in hypersaline microbial communities. PLoS ONE 5: e12919.
32. Pruesse, E., Quast, C., Knittel, K., Fuchs, B.M., Ludwig, W., Peplies, J., etal. (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35: 7188-7196.
33. Quince, C., Lanzen, A., Davenport, R.J., and Turnbaugh, P.J. (2011) Removing noise from pyrosequenced amplicons. BMC Bioinformatics 12: 38.
34. Quince, C., Lanzén, A., Curtis, T.P., Davenport, R.J., Hall, N., Head, I.M., etal. (2009) Accurate determination of microbial diversity from 454 pyrosequencing data. Nat Methods 6: 639-641.
35. R Development Core Team. (2013) R: A Language and Environment for Statistical Computing, 3.0.1 edn. Vienna, Austria: R Foundation for Statistical Computing.
36. Rittmann, B.E., and McCarty, P.L. (2001) Environmental Biotechnology: Principles and Applications. New York, NY, USA: McGraw-Hill.
37. Saikaly, P.E., and Oerther, D.B. (2004) Bacterial competition in activated sludge: theoretical analysis of varying solids retention times on diversity. Microb Ecol 48: 274-284.
38. Saikaly, P.E., Stroot, P.G., and Oerther, D.B. (2005) Use of 16S rRNA gene terminal restriction fragment analysis to assess the impact of solids retention time on the bacterial diversity of activated sludge. Appl Environ Microbiol 71: 5814-5822.
39. 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.
40. Schwarzenbach, R.P., Escher, B.I., Fenner, K., Hofstetter, T.B., Johnson, C.A., von Gunten, U., and Wehrli, B. (2006) The challenge of micropollutants in aquatic systems. Science 313: 1072-1077.
41. Werner, J.J., Knights, D., Garcia, M.L., Scalfone, N.B., Smith, S., Yarasheski, K., etal. (2011) Bacterial community structures are unique and resilient in full-scale bioenergy systems. Proc Natl Acad Sci USA 108: 4158-4163.
42. Wittebolle, L., Vervaeren, H., Verstraete, W., and Boon, N. (2008) Quantifying community dynamics of nitrifiers in functionally stable reactors. Appl Environ Microbiol 74: 286-293.
43. Yang, C., Zhang, W., Liu, R., Li, Q., Li, B., Wang, S., etal. (2011) Phylogenetic diversity and metabolic potential of activated sludge microbial communities in full-scale wastewater treatment plants. Environ Sci Technol 45: 7408-7415.
44. Yergeau, E., Bokhorst, S., Kang, S., Zhou, J., Greer, C.W., Aerts, R., and Kowalchuk, G.A. (2012) Shifts in soil microorganisms in response to warming are consistent across a range of Antarctic environments. ISME J 6: 692-702.