Fosmids of novel marine Planctomycetes from the Namibian and Oregon coast upwelling systems and their cross-comparison with planctomycete genomes

Abstract

Planctomycetes are widely distributed in marine environments, where they supposedly play a role in carbon recycling. To deepen our understanding about the ecology of this sparsely studied phylum six planctomycete fosmids from two marine upwelling systems were investigated and compared with all available planctomycete genomic sequences including the as yet unpublished nearcomplete genomes of Blastopirellula marina DSM 3645 T and Planctomyces maris DSM 8797 T . High numbers of sulfatase genes (41-109) were found on all marine planctomycete genomes and on two fosmids (2). Furthermore, C1 metabolism genes otherwise only known from methanogenic Archaea and methylotrophic Proteobacteria were found on two fosmids and all planctomycete genomes, except for 'Candidatus Kuenenia stuttgartiensis'. Codon usage analysis indicated high expression levels for some of these genes. In addition, novel large families of planctomycete-specific paralogs with as yet unknown functions were identified, which are notably absent from the genome of 'Candidatus Kuenenia stuttgartiensis'. The high numbers of sulfatases in marine planctomycetes characterizes them as specialists for the initial breakdown of sulfatated heteropolysaccharides and indicate their importance for recycling carbon from these compounds. The almost ubiquitous presence of C1 metabolism genes among Planctomycetes together with codon usage analysis and information from the genomes suggest a general importance of these genes for Planctomycetes other than formaldehyde detoxification. The notable absence of these genes in Candidatus K. stuttgartiensis plus the surprising lack of almost any planctomycete-specific gene within this organism reveals an unexpected distinctiveness of anammox bacteria from all other Planctomycetes.

Genome sequencing of a single cell of the widely distributed marine subsurface Dehalococcoidia, phylum Chloroflexi

“…Organosulphur compounds can be particularly abundant in the pelagic marine environment (Glö ckner et al, 2003) and may further arise from sulphurisation of organic compounds through diagenetic reactions during burial in marine sediments (Schmidt et al, 2009). Genes encoding sulfatases are well represented in marine sediment metagenomes (Quaiser et al, 2011) and are highly represented in the genomes of marine versus freshwater Planctomycetes (Woebken et al, 2007). Sulfatases may therefore be a particular adaptation of DEH-J10 to organosulphur compounds found in marine sediment environments.…”

“…In addition, a gene encoding a sulfatase-maturating enzyme was identified, which is critical for post-translational modification and functionality of sulfatases (Benjdia et al, 2011). Sulfatases catalyse the removal of sulphate groups from organic molecules and thereby enable further catabolism of the carbon backbones of various organic compounds (Kertesz, 2000;Glö ckner et al, 2003;Woebken et al, 2007). Organosulphur compounds can be particularly abundant in the pelagic marine environment (Glö ckner et al, 2003) and may further arise from sulphurisation of organic compounds through diagenetic reactions during burial in marine sediments (Schmidt et al, 2009).…”

Bacterial diversity in relation to secondary production and succession on surfaces of the kelp Laminaria hyperborea

“…There are no close cultured relatives of these Planctomycetes, and their roles on kelp surfaces are yet unknown. Other marine Planctomycetes are presumably degraders of sulfated polysaccharides (Woebken et al, 2007). Such substances are produced by kelps (Evans et al, 1973), and may possibly be utilized by kelp surface Planctomycetes.…”

Comparative metagenomics of bathypelagic plankton and bottom sediment from the Sea of Marmara

“…Correlating with a relative high abundance of Planctomycetes in Marmara sediment, we also detected a high number of sulfatases (Figure 6 and Supplementary Table S2). Sulfatases are abundant in the genome of R. baltica (109 hits; Glockner et al, 2003) and, in general, marine planctomycetes possess a large number of these enzymes, which they might use for the initial breakdown of sulfated heteropolysaccharides, thus having an important role in recycling these abundant oceanic compounds (Woebken et al, 2007).…”