Disturbance and temporal partitioning of the activated sludge metacommunity

ISME Journal

Volumn 9, Issue 2, 2015, Pages 425-435

  Vuono, David C ^a   Benecke, Jan ^a   Henkel, Jochen ^a   Navidi, William C ^a   Cath, Tzahi Y ^a   Munakata Marr, Junko ^a   Spear, John R ^a   Drewes, Jörg E ^a,b  

^a Department of Geology and Geological Engineering   (United States)

^b TECHNICAL UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS);

PHOSPHORUS; SEWAGE;

BACTERIUM; BIODIVERSITY; BIOREACTOR; CLASSIFICATION; DENITRIFICATION; ECOSYSTEM; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; NITRIFICATION; SEWAGE;

BACTERIA; BIODIVERSITY; BIOREACTORS; DENITRIFICATION; ECOSYSTEM; NITRIFICATION; PHOSPHORUS; SEWAGE;

EID: 84921598845     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2014.139     Document Type: Article

References (62)

1. Allison SD, Martiny JBH. (2008). Resistance, resilience, and redundancy in microbial communities. Proc Natl Acad Sci 105: 11512-11519.
2. Armitage DW, Gallagher KL, Youngblut ND, Buckley DH, Zinder SH. (2012). Millimeter-scale patterns of phylogenetic and trait diversity in a salt marsh microbial mat. Front Microbiol 3: 293.
3. Capo raso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK et al. (2010). QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7: 335-336.
4. Caporaso JG, Lauber CL, Costello EK, Berg-Lyons D, Gonzalez A, Stombaugh J et al. (2011). Moving pictures of the human microbiome. Genome Biol 12: R50.
5. Carpenter SR. (1996). Microcosm experiments have limited relevance for community and ecosystem ecology. Ecology 77: 677-680.
6. Chao A, Chiu C-H, Jost L. (2010). Phylogenetic diversity measures based on Hill numbers. Philos Trans R Soc Lond B Biol Sci 365: 3599-3609.
7. H.M.P. Consortium (2012). Structure, function and diversity of the healthy human microbiome. Nature 486: 207-214.
8. Costello EK, Gordon JI, Secor SM, Knight R. (2010). Postprandial remodeling of the gut microbiota in Burmese pythons. ISME J 4: 1375-1385.
9. Daigger GT. (2009). Evolving urban water and residuals management paradigms: water reclamation and reuse, decentralization, and resource recovery. Water Environ Res 81: 809-823.
10. Daims H, Taylor MW, Wagner M. (2006). Wastewater treatment: a model system for microbial ecology. Trends Biotechnol 24: 483-489.
11. Dethlefsen L, Relman D. (2010). Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci 108: 4554-4561.
12. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. (2011). UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27: 2194-2200.
13. Faith DP. (1992). Conservation evaluation and phylogenetic diversity. Biol Conserv 61: 1-10.
14. Fierer N, Bradford MA, Jackson RB. (2007). Toward an ecological classification of soil bacteria. Ecology 88: 1354-1364.
15. Fierer N, H amady M, Lauber CL, Knight R. (2008). The influence of sex, handedness, and washing on the diversity of hand surface bacteria. Proc Natl Acad Sci USA 105: 17994-17999.
16. Haegeman B, Hamelin J, Moriarty J, Neal P, Dushoff J, Weitz JS. (2013). Robust estimation of microbial diversity in theory and in practice. ISME J 7: 1092-1101.
17. He S,McMahon KD 2011). ' Candidatus Accumulibacter' gene expression in response to dynamic EBPR conditions ISME J 5, 329-340
18. Helbling DE, Johnson DR, Honti M, Fenner K. (2012). Micropollutant biotransformation kinetics as sociate with WWTP process parameters and microbial community characteristics. Environ Sci Technol 46: 10579-10588.
19. Hill MO. (1973). Diversity and Evenness: A Unifying Notation and Its Consequences. Ecology 54: 427-432.
20. Horn HS. (1974). The ecology of secondary succession. Annu Rev Ecol Syst 5: 25-37.
21. Johnson DR, Goldschmidt F, Lilja EE, Ackermann M. (2012). Metabolic specialization and the assembly of microbial communities. ISME J 6: 1985-1991.
22. Jones SE, Lennon JT. (2010). Dormancy contributes to the maintenance of microbial diversity. Proc Natl Acad Sci 107: 5881-5886.
23. Jost L. (2006). Entropy and diversity. Oikos 113: 363-375.
24. Jost L. (2007). Paritioning diversity into independent alpha and beta components. Ecology 88: 2427-2439.
25. Klappenbach J a, Saxman PR, Cole JR, Schmidt TM. (2001). rrndb: the Ribosomal RNA Operon Copy Number Database. Nucleic Acids Res 29: 181-184.
26. Lee ZM-P, Bussema C, Schmidt TM. (2009). rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea. Nucleic Acids Res. 37: D489-D493.
27. Leibold MA, Holyoak M, Mouquet N, Amarasekare P, Chase JM, Hoopes MF et al. (2004). The metacommunity concept: a framework for multi-scale community ecology. Ecology Letters 7: 601-613.
28. Leinster T, Cobbold C a. (2012). Measuring diversity: the importance of species similarity. Ecology 93: 477-489.
29. Lücker S, Wagner M, Maixner F, Pelletier E, Koch H, Vacherie B et al. (2010). A Nitrospira metagenomeilluminates the physiology and evolution of globally important nitrite-oxidizing bacteria. Proc Natl Acad Sci 107: 13479-13484.
30. Maixner F, Noguera DR, Anneser B, Stoecker, Wegl G, Wagner M et al. (2006). Nitrite concentration influences the population structure of Nitrospira-like bacteria. Environ Microbiol 8: 1487-1495.
31. Maixner F,WagnerM, Lücker S, Pelletier E, Schmitz-Esser S, Hace K et al. (2008). Environmental genomics reveals a functional chlorite dismutase in the nitrite-oxidizing bacterium ''Candidatus Nitrospira defluvii''. E nviron Microbiol 10: 3043-3056.
32. McMahon KD, Martin HG, Hugenholtz P. (2007). Integrating ecology into biotechnology. Curr Opin Biotechnol 18: 287-292.
33. Ofiteru ID, Lunn M, Curtis TP, Wells GF, Criddle CS, Francis C et al. (2010). Combined niche and neutral effects in a microbial wastewater treatment community. Proc Natl Acad Sci USA 107: 15345-15350.
34. Pholchan MK, Bap tista JDC, Davenport RJ, Curtis TP. (2010). Systematic study of the effect of operating variables on reactor performance and microbial diversity in laboratory-scale activated sludge reactors. Water Res 44: 1341-1352.
35. Pianka E. (1970). On r-And K-selection.AmNat 102: 592-597.
36. Reeder J, Knight R. (2010). Rapid denoising of pyrosequencing amplicon data: exploiting the rank-Abundance distribution. Nat Methods 7: 668-669.
37. Reznick D, Bryant M, Bashey F. (2002). r-And K-Selection Revisited: the role of population regulation in life-history evolution. Ecology 83: 1509-1520.
38. Saikaly PE,Stroot PG,Oerther DB. 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. Saunders AM, Larsen P, Nielsen PH. (2013). Comparison of nutrient-removing microbial communities in activated sludge from full-scale MBRs and conventional plants. Water Sci Technol 68: 366-371.
40. Schloss PD. (2 010). The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies. PLoS Comput Biol 6: e1000844.
41. Schloss PD, Gevers D, Westcott S L. (2011). Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS One 6: e27310.
42. Schloss PD, Westcott SL. (2011). Assessing and improving methods used in operational taxonomic unit-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol 77: 3219-3226.
43. 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.
44. Seviour R, Nielsen PH. (2010). Microbial Ecology of Activated Sludge, 1st edn. IWA Publishing: London, UK.
45. Shade A, Mcmanus PS, Handelsman J. (2013). Unexpected diversity during community succession in the apple flower microbiome. MBio 4: 1-12.
46. Shade A, Read JS, Youngblut ND, Fierer N, Knight R, Kratz TK et al. (2012). Lake microbial communities are resilient after a whole-ecosystem disturbance. ISME J 6: 2153-2167.
47. Sloan WT, Woodcock S, Lunn M, Head IM, Curtis TP. (2007). Modeling taxa-Abundance distributions in microbial communities using environmental sequence data. Microb Ecol 53: 443-455.
48. Sorokin DY, Lücker S, Vejmelkova D, Kostrikina N a, Kleerebezem R, Rijpstra WIC et al. (2012). Nitrification expanded: discovery, physiology and genomics of a nitrite-oxidizing bacterium from the phylum C hloroflexi. ISME J 6: 2245-2256.
49. Strous M, Pelletier E, Mangenot S, Rattei T, Lehner A, Taylor MW et al. (2006). Deciphering the evolution and metabolism of an anammox bacterium from a community genome. Nature 440: 790-794.
50. Sun Y, Yunpeng C, Huse SM, Knight R, Farmerie WG, Wang X et al. (2011). A large-scale benchmark study of existing algorithms for taxonomy-independent microbial commu nity analysis. Brief Bioinform 13: 107-121.
51. Tan TW, Ng HY, Ong SL. (2008). Effect of mean cell residence time on the performance and microbial diversity of pre-denitrification submerged membrane bioreactors.Chemosphere 70: 387-396.
52. Tchobanoglous G, Burton F, Stensel D. (2003). Wastewater Engineering; Treatment and Reuse, 4th edn. McGraw-Hill Inc.: New York.
53. Vuono D, Henkel J, Benecke J, Cath TY, Reid T, Johnson L et al. (2013). Flexible hybrid membrane treatment systems for tailored nutrient management: a new paradigm in urban wastewater treatment. J Memb Sci 446: 34-41.
54. W agner M. (2002). Bacterial community composition and function in sewage treatment systems. Curr Opin Biotechnol 13: 218-227.
55. Wells GF, Park H-D, Eggleston B, Francis CA, Criddle CS. (2011). Fin e-scale bacterial community dynamics and the taxa-time relationship within a full-scale activated sludge bioreactor. Water Res 45: 5476-5488.
56. Wells GF, Park H-D, Yeung C-H, Eggleston B, Francis CA, Cridd le CS. (2009). Ammonia-oxidizing communities in a highly aerated full-scale activated sludge bioreactor: betaproteobacterial dynamics and low relative abundance of Crenarchaea. Environ Microbiol 11: 2310-2328.
57. Wern er JJ, Knights D, Garcia ML, Scalfone NB, Smith S, Yarasheski K et al. (2011). Bacterial community structures are unique and resilient in full-scale bioenergy systems. Proc Natl Acad Sci 108: 4158-4163.
58. Xia Y, Kong Y, Thomsen TR, Halkjaer Nielsen P. (2008). Identification and ecophysiological characterization of epiphytic protein-hydrolyzing saprospiraceae ('' Candidatus Epiflobacter'' spp.) in activated sludge. Appl Environ Microbiol 74: 2229-2238.
59. Yang C, Zhang W, Liu R, Li Q, Li B, Wang S et al. (2011). Phylogenetic diversity and metabolic potential of activated sludge microbial communities in full-scale wastewate r treatment plants. Environ Sci Technol 45: 7408-7415.
60. Ye L,Shao M-F,Zhang T,Tong AHY,Lok S. 2011 Analysis of the bacterial community in a laboratoryscale nitrification reactor and a wastewater t reatment plant by 454-pyrosequencing Water Res 45, 4390-4398.
61. Zhang T, Shao MF, Ye L. (2012). 454 Pyrosequencing reveals bacterial diversity of activated sludge from 14 sewage treatment plants. ISME J 6: 1137-1147.
62. Zhao J, Schloss PD, Kalikin LM, Carmody LA, Foster BK, Petrosino JF et al. (2012). Decade-long bacterial community dynamics in cystic fibrosis airways. Proc Natl Acad Sci 109: 5809-5814.