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Bacterial diversity of metagenomic and PCR libraries from the Delaware River

Bacterial diversity of metagenomic and PCR libraries from the Delaware River Summary To determine whether metagenomic libraries sample adequately the dominant bacteria in aquatic environments, we examined the phylogenetic make‐up of a large insert metagenomic library constructed with bacterial DNA from the Delaware River, a polymerase chain reaction (PCR) library of 16S rRNA genes, and community structure determined by fluorescence in situ hybridization (FISH). The composition of the libraries and community structure determined by FISH differed for the major bacterial groups in the river, which included Actinobacteria, beta‐proteobacteria and Cytophaga‐like bacteria. Beta‐proteobacteria were underrepresented in the metagenomic library compared with the PCR library and FISH, while Cytophaga‐like bacteria were more abundant in the metagenomic library than in the PCR library and in the actual community according to FISH. The Delaware River libraries contained bacteria belonging to several widespread freshwater clusters, including clusters of Polynucleobacter necessarius, Rhodoferax sp. Bal47 and LD28 beta‐proteobacteria, the ACK‐m1 and STA2‐30 clusters of Actinobacteria, and the PRD01a001B Cytophaga‐like bacteria cluster. Coverage of bacteria with > 97% sequence identity was 65% and 50% for the metagenomic and PCR libraries respectively. Rarefaction analysis of replicate PCR libraries and of a library constructed with re‐conditioned amplicons indicated that heteroduplex formation did not substantially impact the composition of the PCR library. This study suggests that although it may miss some bacterial groups, the metagenomic approach can sample other groups (e.g. Cytophaga‐like bacteria) that are potentially underrepresented by other culture‐independent approaches. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Environmental Microbiology Wiley

Bacterial diversity of metagenomic and PCR libraries from the Delaware River

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References (63)

Publisher
Wiley
Copyright
Copyright © 2005 Wiley Subscription Services, Inc., A Wiley Company
ISSN
1462-2912
eISSN
1462-2920
DOI
10.1111/j.1462-2920.2005.00762.x
pmid
16309387
Publisher site
See Article on Publisher Site

Abstract

Summary To determine whether metagenomic libraries sample adequately the dominant bacteria in aquatic environments, we examined the phylogenetic make‐up of a large insert metagenomic library constructed with bacterial DNA from the Delaware River, a polymerase chain reaction (PCR) library of 16S rRNA genes, and community structure determined by fluorescence in situ hybridization (FISH). The composition of the libraries and community structure determined by FISH differed for the major bacterial groups in the river, which included Actinobacteria, beta‐proteobacteria and Cytophaga‐like bacteria. Beta‐proteobacteria were underrepresented in the metagenomic library compared with the PCR library and FISH, while Cytophaga‐like bacteria were more abundant in the metagenomic library than in the PCR library and in the actual community according to FISH. The Delaware River libraries contained bacteria belonging to several widespread freshwater clusters, including clusters of Polynucleobacter necessarius, Rhodoferax sp. Bal47 and LD28 beta‐proteobacteria, the ACK‐m1 and STA2‐30 clusters of Actinobacteria, and the PRD01a001B Cytophaga‐like bacteria cluster. Coverage of bacteria with > 97% sequence identity was 65% and 50% for the metagenomic and PCR libraries respectively. Rarefaction analysis of replicate PCR libraries and of a library constructed with re‐conditioned amplicons indicated that heteroduplex formation did not substantially impact the composition of the PCR library. This study suggests that although it may miss some bacterial groups, the metagenomic approach can sample other groups (e.g. Cytophaga‐like bacteria) that are potentially underrepresented by other culture‐independent approaches.

Journal

Environmental Microbiology – Wiley

Published: Dec 1, 2005

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