Metagenomics

Prior work had identified undescribed genes putatively involved in the metabolism of archaeal methanotrophs on fosmids carrying a 16S rRNA gene of ANME-1b and ANME-2a (Meyerdierks et al. 2005). In the past two years, our focus, in collaboration with the MPI for Molecular Genetics in Berlin (sequencing group of Richard Reinhardt), was on the ANME-1b genome. Currently we analyse about 3 Mbp non-redundant sequence information. The data set originates from ~13,000 fosmid clones constructed from a Black Sea microbial mat sample. We determined ~20,000 fosmid insert end sequences. A total of 143 fosmids were completely sequenced and assigned to ANME-1 based on TETRA (Teeling et al. 2004). Of these 127 assembled into contigs of up to 459 kbp length. In overlaps of 1.68 Mbp only 334 nucleotide polymorphisms were detected, resulting in a polymorphism rate of ~0.02%. Additionally, five regions of up to 4.3 kbp were detected in which the assembled fosmids did not show any similarity to each other (insertions, deletions, transpositions) due to the presence of closely related strains. Thus, the effort to close the genome would be at least disproportionately high or even impossible. We therefore work towards publication of a draft composite genome.

Annotation identified all genes of the (reverse) methanogenesis pathway, except for one of the key enzymes, the methylenetetrahydromethanopterin reductase (mer). Hydrogenases/ dehydrogenases known from methanogens were not found. This supports the hypothesis of Hallam et al. (2004) that alternative proteins might be involved in oxidoreductase reactions and electron transport coupled to methane oxidation in ANME-1.

There are no indications for the presence of genes of the dissimilatory sulfate reduction pathway in ANME-1. In collaboration with Martin Kruger (BGR Hannover) and the group around Rolf Thauer (MPI Marburg) the analysis of MCR protein from Black Sea microbial mats was continued. The ANME-1 genome data were used for a more efficient assignment of peptide fragments to certain genes. Studies on mRNA expression have been initiated and indicate expression of most of single genes out of interesting ORF clusters putatively involved in oxidoreductase reactions.

Within the DFG-Priority Program 1144 “RIDGE” another metagenome project is targeting the biochemical potential of free-living microorganisms in sediments of the Logatchev hydrothermal vent field (PhD thesis, Regina Schauer). This is combined with in situ characterization of hydrothermal sediments covered by a white mat. There is a steep increase of temperature reaching 100°C in 28 cm depth. Diversity is analyzed by DGGE fingerprinting, and the rRNA approach indicating dominance of Epsilon- and Deltaproteobacteria suggesting that reduced sulfur compounds are the primary electron donors for chemolithotrophic life in these sediments.