Bacterial communities of Beijing surface waters as revealed by 454 pyrosequencing of the 16S rRNA gene

Environmental Science and Pollution Research

Volumn 22, Issue 16, 2015, Pages 12605-12614

  Wei, Yu Mei ^a,b   Wang, Jing Qi ^a   Liu, Ting Ting ^a   Kong, Wei Wen ^a   Chen, Nan ^a   He, Xiao Qing ^a   Jin, Yi ^a  

^a BEIJING FORESTRY UNIVERSITY   (China)

^b RESEARCH CENTER FOR ECO ENVIRONMENTAL SCIENCES   (China)

Author keywords

Bacterial communities; Pyrosequencing; Surface waters

Indexed keywords

ABUNDANCE; CLASSIFICATION; GENE FLOW; GENETIC ANALYSIS; GENETIC DIFFERENTIATION; GEOGRAPHICAL REGION; MICROBIAL COMMUNITY; PHYLOGENETICS; RNA; SAMPLING; SURFACE WATER; TAXONOMY; WATER QUALITY;

BEIJING [CHINA]; CHINA;

BACTERIA (MICROORGANISMS);

FRESH WATER; RNA 16S;

BACTERIUM; CHINA; DNA SEQUENCE; GENETICS; GEOGRAPHY; MICROBIOLOGY; MICROFLORA; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE;

BACTERIA; BASE SEQUENCE; BEIJING; FRESH WATER; GEOGRAPHY; MICROBIOTA; MOLECULAR SEQUENCE DATA; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA;

EID: 84937976705     PISSN: 09441344     EISSN: 16147499     Source Type: Journal    
DOI: 10.1007/s11356-015-4534-3     Document Type: Article

References (54)

1. Alegría Á, Szczesny P, Mayo B, Bardowski J, Kowalczyk M (2012) Biodiversity in Oscypek, a traditional Polish cheese, determined by culture-dependent and-independent approaches. Appl Environ Microbiol 78:1890–1898
2. Beloshapka AN, Dowd SE, Suchodolski JS, Steiner JM, Duclos L, Swanson KS (2013) Fecal microbial communities of healthy adult dogs fed raw meat‐based diets with or without inulin or yeast cell wall extracts as assessed by 454 pyrosequencing. FEMS Microbiol Ecol 84:532–541
3. Cébron A, Coci M, Garnier J, Laanbroek HJ (2004) Denaturing gradient gel electrophoretic analysis of ammonia-oxidizing bacterial community structure in the lower Seine River: impact of Paris wastewater effluents. Appl Environ Microbiol 70:6726–6737
4. Cazalet C, Gomez-Valero L, Rusniok C, Lomma M, Dervins-Ravault D, Newton HJ, Sansom FM, Jarraud S, Zidane N, Ma L (2010) Analysis of the Legionella longbeachae genome and transcriptome uncovers unique strategies to cause Legionnaires’ disease. PLoS Genet 6:e1000851
5. Claesson MJ, O’Sullivan O, Wang Q, Nikkilä J, Marchesi JR, Smidt H, de Vos WM, Ross RP, O’Toole PW (2009) Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine. PLoS ONE 4:e6669
6. Crump EM, Perry MB, Clouthier SC, Kay WW (2001) Antigenic characterization of the fish pathogen Flavobacterium psychrophilum. Appl Environ Microbiol 67:750–759
7. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27:2194–2200
8. Eichler S, Christen R, Höltje C, Westphal P, Bötel J, Brettar I, Mehling A, Höfle MG (2006) Composition and dynamics of bacterial communities of a drinking water supply system as assessed by RNA-and DNA-based 16S rRNA gene fingerprinting. Appl Environ Microbiol 72:1858–1872
9. Eilers KG, Debenport S, Anderson S, Fierer N (2012) Digging deeper to find unique microbial communities: the strong effect of depth on the structure of bacterial and archaeal communities in soil. Soil Biol Biochem 50:58–65
10. Ferrando L, Mañay JF, Scavino AF (2012) Molecular and culture‐dependent analyses revealed similarities in the endophytic bacterial community composition of leaves from three rice (Oryza sativa) varieties. FEMS Microbiol Ecol 80:696–708
11. Garrido L, Sánchez O, Ferrera I, Tomàs N, Mas J (2014) Dynamics of microbial diversity profiles in waters of different qualities. Approximation to an ecological quality indicator. Sci Total Environ 468:1154–1161
12. Gihring TM, Green SJ, Schadt CW (2012) Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes. Environ Microbiol 14:285–290
13. Glenn TC (2011) Field guide to next‐generation DNA sequencers. Mol Ecol Resour 11:759–769
14. González-Arenzana L, López R, Santamaría P, López-Alfaro I (2013) Dynamics of lactic acid bacteria populations in Rioja wines by PCR-DGGE, comparison with culture-dependent methods. Appl Microbiol Biotechnol 97:6931–6941
15. He X, Wei Y, Cheng L, Zhang D, Wang Z (2012) Molecular detection of three gastroenteritis viruses in urban surface waters in Beijing and correlation with levels of fecal indicator bacteria. Environ Monit Assess 184:5563–5570
16. Holmfeldt K, Dziallas C, Titelman J, Pohlmann K, Grossart HP, Riemann L (2009) Diversity and abundance of freshwater Actinobacteria along environmental gradients in the brackish northern Baltic Sea. Environ Microbiol 11:2042–2054
17. Hong P, Hwang C, Ling F, Andersen GL, LeChevallier MW, Liu W (2010) Pyrosequencing analysis of bacterial biofilm communities in water meters of a drinking water distribution system. Appl Environ Microbiol 76:5631–5635
18. Hou W, Wang S, Dong H, Jiang H, Briggs BR, Peacock JP, Huang Q, Huang L, Wu G, Zhi X (2013) A comprehensive census of microbial diversity in hot springs of Tengchong, Yunnan Province China using 16S rRNA gene pyrosequencing. PLoS ONE 8:e53350
19. Hughes JB, Hellmann JJ, Ricketts TH, Bohannan BJ (2001) Counting the uncountable: statistical approaches to estimating microbial diversity. Appl Environ Microbiol 67:4399–4406
20. Ibarbalz FM, Figuerola EL, Erijman L (2013) Industrial activated sludge exhibit unique bacterial community composition at high taxonomic ranks. Water Res 47:3854–3864
21. Jackson SA, Kennedy J, Morrissey JP, O’Gara F, Dobson AD (2012) Pyrosequencing reveals diverse and distinct sponge-specific microbial communities in sponges from a single geographical location in Irish waters. Microb Ecol 64:105–116
22. Jia A, Wan Y, Xiao Y, Hu J (2012) Occurrence and fate of quinolone and fluoroquinolone antibiotics in a municipal sewage treatment plant. Water Res 46:387–394
23. Jones SE, Newton RJ, McMahon KD (2009) Evidence for structuring of bacterial community composition by organic carbon source in temperate lakes. Environ Microbiol 11:2463–2472
24. Kasalický V, Jezbera J, Šimek K, Hahn MW (2010) Limnohabitans planktonicus sp. nov. and Limnohabitans parvus sp. nov., planktonic betaproteobacteria isolated from a freshwater reservoir, and emended description of the genus Limnohabitans. Int J Syst Evol Microbiol 60:2710–2714
25. Khan ST, Horiba Y, Yamamoto M, Hiraishi A (2002) Members of the family Comamonadaceae as primary poly (3-hydroxybutyrate-co-3-hydroxyvalerate)-degrading denitrifiers in activated sludge as revealed by a polyphasic approach. Appl Environ Microbiol 68:3206–3214
26. Kim TS, Jeong J, Wells GF, Park H (2013) General and rare bacterial taxa demonstrating different temporal dynamic patterns in an activated sludge bioreactor. Appl Microbiol Biotechnol 97:1755–1765
27. Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD (2013) Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ Microbiol 79:5112–5120
28. Ma B, Peng Y, Zhang S, Wang J, Gan Y, Chang J, Wang S, Wang S, Zhu G (2013) Performance of anammox UASB reactor treating low strength wastewater under moderate and low temperatures. Bioresour Technol 129:606–611
29. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen Y-J, Chen Z (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380
30. Meyer RD (1983) Legionella infections: a review of five years of research. Rev Infect Dis 5:258–278
31. Miller SR, Strong AL, Jones KL, Ungerer MC (2009) Bar-coded pyrosequencing reveals shared bacterial community properties along the temperature gradients of two alkaline hot springs in Yellowstone National Park. Appl Environ Microbiol 75:4565–4572
32. Moller AK, Soborg DA, Al-Soud WA, Sorensen SJ, Kroer N (2013) Bacterial community structure in High-Arctic snow and freshwater as revealed by pyrosequencing of 16S rRNA genes and cultivation. Polar Research 32
33. Newton RJ, Jones SE, Helmus MR, McMahon KD (2007) Phylogenetic ecology of the freshwater Actinobacteria acI lineage. Appl Environ Microbiol 73:7169–7176
34. Normand P (2006) The families Frankiaceae, Geodermatophilaceae, Acidothermaceae and Sporichthyaceae, The Prokaryotes. Springer, pp. 669–681
35. Pérez-Pantoja D, Donoso R, Agulló L, Córdova M, Seeger M, Pieper DH, González B (2012) Genomic analysis of the potential for aromatic compounds biodegradation in Burkholderiales. Environ Microbiol 14:1091–1117
36. Peng J-F, Liu J-F, Hu X-L, Jiang G-B (2007) Direct determination of chlorophenols in environmental water samples by hollow fiber supported ionic liquid membrane extraction coupled with high-performance liquid chromatography. J Chromatogr A 1139:165–170
37. Qian P, Wang Y, Lee OO, Lau SC, Yang J, Lafi FF, Al-Suwailem A, Wong TY (2011) Vertical stratification of microbial communities in the Red Sea revealed by 16S rDNA pyrosequencing. ISME J 5:507–518
38. Sánchez O, Ferrera I, González JM, Mas J (2013) Assessing bacterial diversity in a seawater‐processing wastewater treatment plant by 454‐pyrosequencing of the 16S rRNA and amoA genes. Microb Biotechnol 6:435–442
39. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541
40. 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
41. Schloss PD, Westcott SL, Jenior ML, Highlander SK (2015) Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system. PeerJ PrePrints 3:e778v1
42. Sekar R, Pernthaler A, Pernthaler J, Warnecke F, Posch T, Amann R (2003) An improved protocol for quantification of freshwater Actinobacteria by fluorescence in situ hybridization. Appl Environ Microbiol 69:2928–2935
43. Struthers M, Wong J, Janda JM (1996) An initial appraisal of the clinical significance of Roseomonas species associated with human infections. Clin Infect Dis 23:729–733
44. Sun S, Guo Z, Yang R, Sheng Z, Cao P (2013) Analysis of microbial diversity in tomato paste wastewater through PCR-DGGE. Biotechnol Bioprocess Eng 18:111–118
45. Vandecandelaere I, Matthijs N, Van Nieuwerburgh F, Deforce D, Vosters P, De Bus L, Nelis HJ, Depuydt P, Coenye T (2012) Assessment of microbial diversity in biofilms recovered from endotracheal tubes using culture dependent and independent approaches. PLoS ONE 7:e38401
46. Wakelin SA, Colloff MJ, Kookana RS (2008) Effect of wastewater treatment plant effluent on microbial function and community structure in the sediment of a freshwater stream with variable seasonal flow. Appl Environ Microbiol 74:2659–2668
47. Wang T, Cai G, Qiu Y, Fei N, Zhang M, Pang X, Jia W, Cai S, Zhao L (2012a) Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers. ISME J 6:320–329
48. Wang X, Hu M, Xia Y, Wen X, Ding K (2012b) Pyrosequencing analysis of bacterial diversity in 14 wastewater treatment systems in China. Appl Environ Microbiol 78:7042–7047
49. Wu S, Wang G, Angert ER, Wang W, Li W, Zou H (2012) Composition, diversity, and origin of the bacterial community in grass carp intestine. PLoS ONE 7:e30440
50. Ye L, Zhang T (2013) Bacterial communities in different sections of a municipal wastewater treatment plant revealed by 16S rDNA 454 pyrosequencing. Appl Microbiol Biotechnol 97:2681–2690
51. Yu K, Zhang T (2012) Metagenomic and metatranscriptomic analysis of microbial community structure and gene expression of activated sludge. PLoS ONE 7:e38183
52. Zhang R, Wu Q, Piceno YM, Desantis TZ, Saunders FM, Andersen GL, Liu WT (2013a) Diversity of bacterioplankton in contrasting Tibetan lakes revealed by high‐density microarray and clone library analysis. FEMS Microbiol Ecol 86:277–287
53. Zhang W, Long X, Huo X, Chen Y, Lou K (2013b) 16S rRNA-Based PCR-DGGE analysis of Actinomycete communities in fields with continuous cotton cropping in Xinjiang, China. Microb Ecol 66:385–393
54. Zhou J, Bruns MA, Tiedje JM (1996) DNA recovery from soils of diverse composition. Appl Environ Microbiol 62:316–322