Pyrosequencing analysis of bacterial community and assembly in activated sludge samples from different geographic regions in China

Applied Microbiology and Biotechnology

Volumn 98, Issue 21, 2014, Pages 9119-9128

  Zhao, Dayong ^a   Huang, Rui ^a   Zeng, Jin ^b   Yu, Zhongbo ^a   Liu, Peng ^a   Cheng, Shupei ^c   Wu, Qinglong L ^b  

^a HOHAI UNIVERSITY   (China)

^b NANJING INSTITUTE OF GEOGRAPHY AND LIMNOLOGY   (China)

^c NANJING UNIVERSITY   (China)

Author keywords

Activated sludge; Bacterial community composition; Geographic locations; Network analysis; Pyrosequencing

Indexed keywords

BACTERIA; BACTERIOLOGY; ELECTRIC NETWORK ANALYSIS; SEWAGE PUMPING PLANTS; SEWAGE TREATMENT PLANTS; WASTEWATER TREATMENT; WATER TREATMENT PLANTS;

ACTIVATED SLUDGE; BACTERIAL COMMUNITY COMPOSITION; BIOINFORMATICS ANALYSIS; GEOGRAPHIC LOCATION; MUNICIPAL WASTEWATER TREATMENT PLANTS; NON-METRIC MULTIDIMENSIONAL SCALING; PYROSEQUENCING; WASTEWATER TREATMENT PLANTS;

ACTIVATED SLUDGE PROCESS;

ACTIVATED SLUDGE; BIOINFORMATICS; COMMUNITY COMPOSITION; MICROBIAL COMMUNITY; NETWORK ANALYSIS; TAXONOMY; WASTEWATER; WATER TREATMENT;

ACTIVATED SLUDGE; ARTICLE; BACTERIAL ASSEMBLY; BACTERIAL GENETICS; BACTERIAL PHENOMENA AND FUNCTIONS; BIOGEOGRAPHY; BIOINFORMATICS; CHINA; CLASSIFIER; GENETIC CORRELATION; GENETIC IDENTIFICATION; GENETIC SIMILARITY; GEOGRAPHIC DISTRIBUTION; HIGH THROUGHPUT SEQUENCING; MICROBIAL COMMUNITY; NONHUMAN; PYROSEQUENCING; SEQUENCE ANALYSIS; TAXONOMY; WASTE WATER TREATMENT PLANT; BACTERIUM; BIOLOGY; BIOTA; CITY; CLASSIFICATION; GENETICS; GEOGRAPHY; MICROBIOLOGY; SEWAGE; WATER MANAGEMENT;

CHINA;

BACTERIA (MICROORGANISMS);

SEWAGE;

BACTERIA; BIOTA; CHINA; CITIES; COMPUTATIONAL BIOLOGY; GEOGRAPHY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; SEWAGE; WATER PURIFICATION;

EID: 84919935308     PISSN: 01757598     EISSN: 14320614     Source Type: Journal    
DOI: 10.1007/s00253-014-5920-3     Document Type: Article

References (35)

1. Barberán A, Bates ST, Casamayor EO, Fierer N (2011) Using network analysis to explore co-occurrence patterns in soil microbial communities. ISME J 6:343–351
2. Bastian M, Heymann S, Jacomy M (2009) Gephi: an open source software for exploring and manipulating networks. In: International AAAI conference on weblogs and social media: San Jose, California
3. Blackall LL, Burrell PC, Gwilliam H, Bradford D, Bond PL, Hugenholtz P (1998) The use of 16S rDNA clone libraries to describe the microbial diversity of activated sludge communities. Water Sci Technol 37:451–454
4. Harrell Jr FE (2008) Hmisc: harrell miscellaneous. R package version: 3.5-2
5. Hu M, Wang X, Wen X, Xia Y (2012) Microbial community structures in different wastewater treatment plants as revealed by 454-pyrosequencing analysis. Bioresour Technol 117:72–79
6. Huse SM, Welch DM, Morrison HG, Sogin ML (2010) Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ Microbiol 12:1889–1898
7. Ju F, Xia Y, Guo F, Wang Z, Zhang T (2014) Taxonomic relatedness shapes bacterial assembly in activated sludge of globally distributed wastewater treatment plants. Environ Microbiol (in press)
8. Kim TS, Kim HS, Kwon S, Park HD (2011) Nitrifying bacterial community structure of a full-scale integrated fixed-film activated sludge process as investigated by pyrosequencing. J Microbiol Biotechnol 21:293–298
9. Kim TS, Jeong JY, Wells GF, Park HD (2013) General and rare bacterial taxa demonstrating different temporal dynamic patterns in an activated sludge bioreactor. Appl Microbial Biot 97:1755–1765
10. Kunin V, Engelbrektson A, Ochman H, Hugenholtz P (2010) Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ Microbiol 12:118–123
11. Kwon S, Kim TS, Yu GH, Jung JH, Park HD (2010) Bacterial community composition and diversity of a full-scale integrated fixed-film activated sludge system as investigated by pyrosequencing. J Microbiol Biotechnol 20:1717–1723
12. Lim JH, Baek SH, Lee ST (2009) Ferruginibacter alkalilentus gen. nov., sp. nov. and Ferruginibacter lapsinanis sp. nov., novel members of the family ‘Chitinophagaceae’ in the phylum Bacteroidetes, isolated from freshwater sediment. Int J Syst Evol Micr 59:2394–2399
13. Low EW, Chase HA, Milner MG, Curtis TP (2000) Uncoupling of metabolism to reduce biomass production in the activated sludge process. Water Res 34:3204–3212
14. Madoni P, Davoli D, Gibin G (2000) Survey of filamentous microorganisms from bulking and foaming activated-sludge plants in Italy. Water Res 34:1767–1772
15. Newman MEJ (2003) The structure and function of complex networks. SIAM Rev 45:167–256
16. Newman MEJ (2006) Modularity and community structure in networks. Proc Natl Acad Sci U S A 103:8577–8582
17. Park M, Ryu SH, Vu THT, Ro HS, Yun PY, Jeon CO (2007) Flavobacterium defluvii sp. nov., isolated from activated sludge. Int J Syst Evol Micr 57:233–237
18. Roesch LF, Fulthorpe RR, Riva A, Casella G, Hadwin AK, Kent AD, Daroub SM, Camargo FAO, Farmerie WG, Triplett EW (2007) Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J 1:283–290
19. Schloss PD (2010) 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
20. Schloss PD, Handelsman J (2005) Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71:1501–1506
21. Schloss PD, Gevers D, Westcott SL (2011) Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS One 6:e27310
22. Snaidr J, Amann R, Huber I, Ludwig W, Schleifer KH (1997) Phylogenetic analysis and in situ identification of bacteria in activated sludge. Appl Environ Microbiol 63:2884–2896
23. Steele JA, Countway PD, Xia L, Vigil PD, Beman JM, Kim DY, Chou CT, Sachdeva R, Jones AC, Schwalbach MS, Rose JM, Hewson I, Patel A, Sun FZ, Caron DA, Fuhrman JA (2011) Marine bacterial, archaeal and protistan association networks reveal ecological linkages. ISME J 5:1414–1425
24. Tezuka Y (1969) Cation-dependent flocculation in a flavobacterium species predominant in activated sludge. Appl Microbial 17:222–226
25. Thomsen TR, Nielsen JL, Ramsing NB, Nielsen PH (2004) Micromanipulation and further identification of FISH-labelled microcolonies of a dominant denitrifying bacterium in activated sludge. Environ Microbiol 6:470–479
26. Timmermans P, Van Haute A (1983) Denitrification with methanol: fundamental study of the growth and denitrification capacity of Hyphomicrobium sp. Water Res 17:1249–1255
27. Wagner M, Loy A (2002) Bacterial community composition and function in sewage treatment systems. Curr Opin Biotechnol 13:218–227
28. Wang Q, Garrity G, Tiedje J, Cole J (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:5261–5267
29. Wang XH, Hu M, Xia Y, Wen XH, Ding K (2012) Pyrosequencing analysis of bacterial diversity in 14 wastewater treatment systems in China. Appl Environ Microbiol 73:7042–7047
30. Xia S, Duan L, Song Y, Li J, Piceno Y, Andersen GL, Alvarez-Cohen L, Moreno-Andrade I, Huang CL, Hermanowicz SW (2010) Bacterial community structure in geographically distributed biological wastewater treatment reactors. Environ Sci Technol 44:1043–1045
31. Ye L, Shao MF, Zhang T, Tong AHY, Lok S (2011) Analysis of the bacterial community in a laboratory-scale nitrification reactor and a wastewater treatment plant by 454-pyrosequencing. Water Res 45:4390–4398
32. Yoon DN, Park SJ, Kim SJ, Jeon CO, Chae JC, Rhee SK (2010) Isolation, characterization, and abundance of filamentous members of Caldilineae in activated sludge. J Microbiol 48:275–283
33. Zhang T, Shao MF, Ye L (2011a) 454 Pyrosequencing reveals bacterial diversity of activated sludge from 14 sewage treatment plants. ISME J 6:1137–1147
34. Zhang SY, Wang QF, Wan R, Xie SG (2011b) Changes in bacterial community of anthracene bioremediation in municipal solid waste composting soil. J Zhejiang Univ (Sci) 12:760–768
35. Zhou JZ, Bruns MA, Tiedje JM (1996) DNA recovery from soils of diverse composition. Appl Environ Microbiol 62:316–322