Comparison of the levels of bacterial diversity in freshwater, intertidal wetland, and marine sediments by using millions of illumina tags

Applied and Environmental Microbiology

Volumn 78, Issue 23, 2012, Pages 8264-8271

  Wang, Yu ^a   Sheng, Hua Fang ^a   He, Yan ^a   Wu, Jin Ya ^a   Jiang, Yun Xia ^a   Tam, Nora Fung Yee ^b   Zhou, Hong Wei ^a  

^a SOUTHERN MEDICAL UNIVERSITY   (China)

^b CITY UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

[No Author keywords available]

Indexed keywords

ANAEROBIC CONDITIONS; AQUATIC ENVIRONMENTS; BACTERIAL COMMUNITY; BACTERIAL DIVERSITY; BACTERIAL LINEAGES; BETAPROTEOBACTERIA; FIRMICUTES; FRESHWATER SEDIMENT; GAMMAPROTEOBACTERIA; ILLUMINA; INTERTIDAL SEDIMENTS; INTERTIDAL WETLAND; MARINE SEDIMENTS; MICROBIAL COMMUNITIES; MICROBIAL DIVERSITY; NATURAL SEDIMENTS; NITROSPIRA; PEARL RIVER; PRIMARY PRODUCERS; SULFATE REDUCTION;

BACTERIA; PRINCIPAL COMPONENT ANALYSIS; SEDIMENTOLOGY; SUBMARINE GEOLOGY; WATER; WETLANDS;

SEDIMENTS;

BACTERIAL DNA; FRESH WATER; RIBOSOME DNA; RNA 16S; SEA WATER;

BACTERIUM; COMPARATIVE STUDY; MARINE SEDIMENT; MICROBIAL COMMUNITY; SPECIES DIVERSITY; SPECIES EVENNESS; SPECIES RICHNESS;

ARTICLE; BACTERIUM; BIODIVERSITY; CHEMISTRY; CHINA; CLASSIFICATION; CLUSTER ANALYSIS; DNA SEQUENCE; GENETICS; METAGENOMICS; MICROBIOLOGY; PHYLOGENY; RIVER; SEDIMENT; WETLAND;

BACTERIA; BIODIVERSITY; CHINA; CLUSTER ANALYSIS; DNA, BACTERIAL; DNA, RIBOSOMAL; FRESH WATER; GEOLOGIC SEDIMENTS; METAGENOMICS; PHYLOGENY; RIVERS; RNA, RIBOSOMAL, 16S; SEAWATER; SEQUENCE ANALYSIS, DNA; WETLANDS;

CHINA; GUANGDONG; ZHUJIANG;

ACIDOBACTERIA; ACTINOMYCETALES; ALPHAPROTEOBACTERIA; BACILLARIOPHYTA; BACTERIA (MICROORGANISMS); BACTEROIDETES; BETAPROTEOBACTERIA; CHLOROFLEXI; CHLOROFLEXI (CLASS); DELTAPROTEOBACTERIA; EPSILONPROTEOBACTERIA; FIRMICUTES; GAMMAPROTEOBACTERIA; NITROSPIRA; OTUS; VERRUCOMICROBIA;

EID: 84870834756     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.01821-12     Document Type: Article

References (38)

1. Antje G, Marc M, Henrik S, Heribert C, Martin K. 2008. Identity and abundance of active sulfate-reducing bacteria in deep tidal flat sediments determined by directed cultivation and CARD-FISH analysis. Environ. Microbiol. 10:2645-2658.
2. Auguet JC, Barberan A, Casamayor EO. 2010. Global ecological patterns in uncultured archaea. ISME J. 4:182-190.
3. Barberan A, Casamayor EO. 2010. Global phylogenetic community structure and beta-diversity patterns in surface bacterioplankton metacommunities. Aquat. Microb. Ecol. 59:1-10.
4. Bolhuis H, Stal LJ. 2011. Analysis of bacterial and archaeal diversity in coastal microbial mats using massive parallel 16S rRNA gene tag sequencing. ISME J. 5:1701-1712.
5. Campbell BJ, Engel AS, Porter ML, Takai K. 2006. The versatile ε-proteobacteria: key players in sulphidic habitats. Nat. Rev. Microbiol. 4:458- 468.
6. Chen CP, Tseng CH, Chen CA, Tang SL. 2011. The dynamics of microbial partnerships in the coral Isopora palifera. ISME J. 5:728 -740.
7. dos Santos HF, et al. 2011. Mangrove bacterial diversity and the impact of oil contamination revealed by pyrosequencing: bacterial proxies for oil pollution. PLoS One 6:e16943. doi:10.1371/journal.pone.0016943.
8. Edgar RC. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460.
9. Finkel OM, Burch AY, Lindow SE, Post AF, Belkin S. 2011. Geograph-ical location determines the population structure in phyllosphere microbial communities of a salt-excreting desert tree. Appl. Environ. Microbiol. 77:7647-7655.
10. Huber JA, et al. 2009. Effect of PCR amplicon size on assessments of clone library microbial diversity and community structure. Environ. Microbiol. 11:1292-1302.
11. Huse SM, et al. 2008. Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PLoS Genet. 4:e1000255. doi: 10.1371/journal.pgen.1000255.
12. 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.
13. Jiang XT, et al. 2012. Two-stage-clustering (TSC): a pipeline for selecting operational taxonomic units for the high-throughput sequencing of PCR amplicons. PLoS One 7:e30230. doi:10.1371/journal.pone.0030230.
14. Jones RT, et al. 2009. A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses. ISME J. 3:442- 453.
15. Kim BS, et al. 2008. Rapid phylogenetic dissection of prokaryotic community structure in tidal flat using pyrosequencing. J. Microbiol. 46:357- 363.
16. 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.
17. Lauber CL, Hamady M, Knight R, Fierer N. 2009. Soil pH as a predictor of soil bacterial community structure at the continental scale: a pyrosequencing-based assessment. Appl. Environ. Microbiol. 75:5111-5120.
18. Lenk S, et al. 2011. Novel groups of gammaproteobacteria catalyse sulfur oxidation and carbon fixation in a coastal, intertidal sediment. Environ. Microbiol. 13:758 -774.
19. Li CH, Zhou HW, Wong YS, Tam NFY. 2009. Vertical distribution and anaerobic biodegradation of polycyclic aromatic hydrocarbons in mangrove sediments in Hong Kong, South China. Sci. Tot. Environ. 407:5772- 5779.
20. Lozupone CA, Knight R. 2007. Global patterns in bacterial diversity. Proc. Natl. Acad. Sci. U. S. A. 104:11436 -11440.
21. Mussmann M, Ishii K, Rabus R, Amann R. 2005. Diversity and vertical distribution of cultured and uncultured Deltaproteobacteria in an intertidal mud flat of the Wadden Sea. Environ. Microbiol. 7:405- 418.
22. Newton RJ, Jones SE, Eiler A, McMahon KD, Bertilsson S. 2011. A guide to the natural history of freshwater lake bacteria. Microbiol. Mol. Biol. Rev. 75:14-49.
23. Orcutt BN, Sylvan JB, Knab NJ, Edwards KJ. 2011. Microbial ecology of the dark ocean above, at, and below the seafloor. Microbiol. Mol. Biol. Rev. 75:361- 422.
24. Pires ACC, et al. 2012. Denaturing gradient gel electrophoresis and barcoded pyrosequencing reveal unprecedented archaeal diversity in mangrove sediment and rhizosphere samples. Appl. Environ. Microbiol. 78: 5520-5528.
25. Quince C, et al. 2009. Accurate determination of microbial diversity from 454 pyrosequencing data. Nat. Methods 6:639-641.
26. Quince C, Lanzen A, Davenport R, Turnbaugh P. 2011. Removing noise from pyrosequenced amplicons. BMC Bioinformatics 12:38.
27. Reeder J, Knight R. 2009. The 'rare biosphere': a reality check. Nat. Methods 6:636-637.
28. Roske K, Sachse R, Scheerer C, Roske I. 2012. Microbial diversity and composition of the sediment in the drinking water reservoir Saidenbach (Saxonia, Germany). Syst. Appl. Microbiol. 35:35- 44.
29. Schloss PD, et al. 2009. Introducing mothur: open source, platformindependent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75:7537-7541.
30. Segata N, et al. 2011. Metagenomic biomarker discovery and explanation. Genome Biol. 12:R60.
31. Sogin ML, et al. 2006. Microbial diversity in the deep sea and the underexplored "rare biosphere." Proc. Natl. Acad. Sci. U. S. A. 103:12115-12120.
32. Wu JY, et al. 2010. Effects of polymerase, template dilution and cycle number on PCR based 16S rRNA diversity analysis using the deep sequencing method. BMC Microbiol. 10:255. doi:10.1186/1471-2180-10-255.
33. Zhou HW, Guo CL, Wong YS, Tam NFY. 2006. Genetic diversity of dioxygenase genes in polycyclic aromatic hydrocarbon degrading bacteria isolated from mangrove sediments. FEMS Microbiol. Lett. 262:148 -157.
34. Zhou HW, et al. 2011. BIPES, a cost-effective high-throughput method for assessing microbial diversity. ISME J. 5:741-749.
35. Zhou HW, Luan TG, Zou F, Tam NFY. 2008. Different bacterial groups for biodegradation of three-and four-ring PAHs isolated from a Hong Kong mangrove sediment. J. Hazard. Mater. 152:1179 -1185.
36. Zhou J, et al. 2011. Reproducibility and quantitation of amplicon sequencing-based detection. ISME J. 5:1303-1313.
37. Zimmermann J, Portillo MC, Serrano L, Ludwig W, Gonzalez JM. 2012. Acidobacteria in freshwater ponds at Donana National Park, Spain. Microb. Ecol. 63:844-855.
38. Zinger L, et al. 2011. Global patterns of bacterial beta-diversity in seafloor and seawater ecosystems.PLoSOne6:e24570. doi:10.1371/journal.pone.0024570.