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Microbiology of Dehalococcoides-like Chloroflexi

Final Report Summary - MICROFLEX (Microbiology of Dehalococcoides-like Chloroflexi)

The Microflex project focuses on the detection and characterization of bacteria of the Dehalococcoides-related Chloroflexi. This group of bacteria is deeply rooting in the phylogenetic tree and is composed mainly of a wide variety of environmental sequences from uncultivated organisms. Such sequences were mostly found in anaerobic sediments both from marine and terrestrial sites. In addition, the bacterial group encompasses the strains of the Dehalococcoides cluster, bacteria that are unique in their capacity to transform highly toxic halogenated compounds such as polychlorinated dibenzodioxins (PCDD), polychlorinated biphenyls (PCBs) or chlorobenzenes. In the Microflex project characteristics of Dehalococcoides species are being compared with results obtained for Chloroflexi from anaerobic sediments. Comparisons include encoded open reading frames, expressed mRNA, proteins, marker lipids, enzyme activities, and small metabolites.

Major achievements of the project include further characterization of Dehalococcoides species in respect to membrane composition, protein inventory, substrate range, isotopic fractionation during the dehalogenating reactions, physiology and biochemical characterization of the reductive dehalogenating enzymes. On the other hand, many new methods were established and/or optimized for anaerobic cultivation of Dehalococcoides-related Chloroflexi, cell detection, quantification, and DNA separation. Also molecular techniques were optimized and adapted for the work with fine sediments containing a multitude of organic components. The methods now allow for the enrichment of Dehalococcoides-related Chloroflexi and assessment of reductive dehalogenation activity in marine sediments. We have also developed a primer set with which we can determine the abundance, distribution and diversity of DRC in marine sediments. With this primer set we have studied samples in the Baffin Bay (Arctic) in different transects and correlate occurrence of DRC with geochemical parameters. These studies show that DRC are very abundant throughout most sediments and sediment layers but that increased numbers are found in organic-high layers. Diversity studies show that the Dehalococcoides-related Chloroflexi are composed of tens of different subgroups and the distribution and correlation with biogeochemical parameters suggests that the different subgroups have different physiologies and ecological roles.

We obtained ~70% of the genome sequence of a single Dehalococcoides-related Chloroflexi after isolating a single cell from marine sediment. The comparison of this genome with Dehalococcoides genomes suggests a less specific physiology of the Dehalococcoides-related Chloroflexi compared to Dehalococcoides species and indicates a life style independent from reductive dehalogenation in marine sediments. However, major structural features of the genome and genes are conserved.