Enrichment versus biofilm culture: a functional and phylogenetic comparison of polycyclic aromatic hydrocarbon-degrading microbial communities

Stach, James E.M. and Burns, Richard G. (2002) Enrichment versus biofilm culture: a functional and phylogenetic comparison of polycyclic aromatic hydrocarbon-degrading microbial communities. Environmental Microbiology, 4 (3). pp. 169-182. ISSN 1462-2912 . (The full text of this publication is not available from this repository)

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Abstract

The effect that culture methods have on the diversity of degradative microbial communities is not well understood. We compared conventional batch enrichment with a biofilm culture method for the isolation of polycyclic aromatic hydrocarbon (PAH)-degrading microbial communities from a PAH-contaminated soil. The two methods were assessed by comparing: (i) the diversity of culturable bacteria; (ii) the diversity of PAH-catabolic genes in isolated bacteria; (iii) the inter- and intraspecific diversity of active PAH-catabolic gene classes; (iv) the diversity of bacteria present in 16S rRNA gene libraries generated from RNA extracted from the two communities and soil; and (v) the estimated diversity of active bacteria in the soil and culture systems. Single-strand conformation polymorphism analysis showed that the biofilm culture yielded 36 bacterial and two fungal species compared with 12 bacterial species from the enrichment culture. Application of accumulation and non-parametric estimators to clone libraries generated from 16S rRNA confirmed that the biofilm community contained greater diversity. Sequencing of clones showed that only species from the Proteobacteria were active in the enrichment culture, and that these species were expressing an identical nahAc-like naphthalene dioxygenase. 16S rRNA clones generated from the biofilm community indicated that species from the Cytophaga/Flavobacterium, high G+C bacteria and Proteobacteria were active at the time of sampling, expressing cndA-, nahAc- and phnAc-like naphthalene dioxygenases. The diversity of active species in the biofilm culture system closely matched that in the PAH-contaminated source soil. The results of this study showed that biofilm culture methods are more appropriate for the study of community-level interactions in PAH-degrading microbial communities. The study also indicated that cultivation of microbial communities on solid media might be the primary source of bias in the recovery of diverse species.

Item Type: Article
Additional information: 1462-2912 (Print) Comparative Study Journal Article Research Support, Non-U.S. Gov't
Uncontrolled keywords: Base Sequence *Biofilms Cell Culture Techniques DNA, Bacterial/chemistry/genetics Microbiological Techniques/methods Microscopy, Confocal Molecular Sequence Data *Phylogeny Polycyclic Hydrocarbons, Aromatic/*metabolism Proteobacteria/genetics/growth & development/*metabolism RNA, Bacterial/chemistry/genetics Reverse Transcriptase Polymerase Chain Reaction Sequence Analysis, DNA Soil Microbiology Variation (Genetics)/genetics
Subjects: Q Science
Divisions: Faculties > Science Technology and Medical Studies > School of Biosciences
Depositing User: Sue Davies
Date Deposited: 09 Sep 2008 18:37
Last Modified: 13 May 2014 13:18
Resource URI: http://kar.kent.ac.uk/id/eprint/6749 (The current URI for this page, for reference purposes)
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