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Identification of novel perchloroethene‐respiring microorganisms in anoxic river sediment by RNA‐based stable isotope probing
Author(s) -
Kittelmann Sandra,
Friedrich Michael W.
Publication year - 2008
Publication title -
environmental microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.954
H-Index - 188
eISSN - 1462-2920
pISSN - 1462-2912
DOI - 10.1111/j.1462-2920.2007.01427.x
Subject(s) - stable isotope probing , terminal restriction fragment length polymorphism , dehalococcoides , biology , microcosm , proteobacteria , microorganism , microbial population biology , population , chloroflexi (class) , environmental chemistry , 16s ribosomal rna , microbiology and biotechnology , bacteria , enrichment culture , ribosomal rna , chemocline , anoxic waters , ecology , chemistry , biochemistry , restriction fragment length polymorphism , sociology , genetics , polymer , vinyl chloride , polymerase chain reaction , demography , organic chemistry , copolymer , gene
Summary The halogenated compound tetrachloroethene (perchloroethene, PCE) is a persistent contaminant of aquifers, soils and sediments. Although a number of microorganisms are known to reductively dechlorinate PCE by dehalorespiration, their diversity and community structure especially in pristine environments remain elusive. In this study, we report on the detection of a novel group of dehalorespiring bacteria that reductively dechlorinate PCE to cis ‐dichloroethene by RNA‐based stable isotope probing. Pristine river sediment was incubated at 15°C with PCE at low aqueous concentration. Upon formation of dechlorination products, the microbial community was probed with 13 C‐labelled acetate as electron donor and carbon source. Terminal restriction fragment length polymorphism (T‐RFLP) analysis of density‐separated 16S rRNA revealed a predominantly 13 C‐labelled bacterial population only in the microcosm with PCE in high‐density gradient fractions, whereas in the control without PCE Bacteria‐specific rRNA was restricted to light gradient fractions. By cloning and sequence analysis of 16S rRNA, the predominant population was identified as a novel group of bacteria within the phylum Chloroflexi . These microorganisms, designated Lahn Cluster (LC), were only distantly related to cultivated dehalorespiring Dehalococcoides spp. (92–94% sequence identity). Minor clone groups detected 13 C‐labelled and thus, potentially involved in PCE dehalorespiration, were related to β‐proteobacterial Dechloromonas spp., and δ‐ Proteobacteria ( Geobacteraceae , Desulfobacteraceae , Desulfobulbaceae ). In contrast, clones from an ethene‐producing microcosm incubated at 20°C grouped with known Dehalococcoides spp. Our results show that stable isotope probing allows targeting dehalorespiring bacteria as functional guild, and to identify novel PCE‐respiring populations previously not recognized.