Genome sequence and emended description of Leisingera nanhaiensis strain DSM 24252(T) isolated from marine sediment

Complete Genome Sequence of Leisingera aquamixtae R2C4, Isolated from a Self-Regenerating Biocathode Consortium

Here, we present the complete genome sequence of Leisingera aquamixtae R2C4, isolated from the electroautotrophic microbial consortium biocathode MCL (Marinobacter-Chromatiaceae-Labrenzia). As an isolate of a current-producing system, the genome sequence of L. aquamixtae will yield insights regarding electrode-associated microorganisms and communities. A dark pigment is also observed during cultivation.

Here, we present the complete genome sequence of Leisingera aquamixtae R2C4, isolated from the electroautotrophic microbial consortium biocathode MCL (Marinobacter-Chromatiaceae-Labrenzia). As an isolate of a current-producing system, the genome sequence of L. aquamixtae will yield insights regarding electrode-associated microorganisms and communities. A dark pigment is also observed during cultivation.

Sedimentitalea todarodis sp. nov., isolated from the intestinal tract of a Japanese flying squid

A novel Gram-stain-negative, motile, aerobic and rod-shaped alphaproteobacterium, designated strain KHS03T, was isolated from the intestinal tract of a Japanese flying squid, Todarodes pacificus, which was collected from the East Sea, Korea. The new isolate shared 97.4 % 16S rRNA gene sequence similarity with Sedimentitalea nanhaiensis NH52FT. The isolate grew optimally at 25 °C and pH 7 in the presence of 1-2 % (w/v) NaCl, and had an absolute requirement of sodium ions for growth. The major cellular fatty acid was C18 : 1ω7c. The primary isoprenoid quinone was ubiquinone-10. Polar lipids comprised diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminolipid and two unidentified lipids. Genotypic analyses indicated that the whole genomic DNA of the isolate had a G+C content of 59.9 mol%. DNA-DNA hybridization showed that the isolate shared 17.1±2.3 % (reciprocal 17.0±1.9 %) genomic relatedness with the closest related type strain, S. nanhaiensis NH52FT. Strain KHS03T is thus suggested to represent a novel species of the genus Sedimentitalea, for which the name Sedimentitalea todarodis sp. nov. is proposed. The type strain is KHS03T (=KCTC 42412T=JCM 31160T).

Genome sequence of Shimia str. SK013, a representative of the Roseobacter group isolated from marine sediment

Shimia strain SK013 is an aerobic, Gram-negative, rod shaped alphaproteobacterium affiliated with the Roseobacter group within the family Rhodobacteraceae. The strain was isolated from surface sediment (0–1 cm) of the Skagerrak at 114 m below sea level. The 4,049,808 bp genome of Shimia str. SK013 comprises 3,981 protein-coding genes and 47 RNA genes. It contains one chromosome and no extrachromosomal elements. The genome analysis revealed the presence of genes for a dimethylsulfoniopropionate lyase, demethylase and the trimethylamine methyltransferase (mttB) as well as genes for nitrate, nitrite and dimethyl sulfoxide reduction. This indicates that Shimia str. SK013 is able to switch from aerobic to anaerobic metabolism and thus is capable of aerobic and anaerobic sulfur cycling at the seafloor. Among the ability to convert other sulfur compounds it has the genetic capacity to produce climatically active dimethyl sulfide. Growth on glutamate as a sole carbon source results in formation of cell-connecting filaments, a putative phenotypic adaptation of the surface-associated strain to the environmental conditions at the seafloor. Genome analysis revealed the presence of a flagellum (fla1) and a type IV pilus biogenesis, which is speculated to be a prerequisite for biofilm formation. This is also related to genes responsible for signalling such as N-acyl homoserine lactones, as well as quip-genes responsible for quorum quenching and antibiotic biosynthesis. Pairwise similarities of 16S rRNA genes (98.56 % sequence similarity to the next relative S. haliotis) and the in silico DNA-DNA hybridization (21.20 % sequence similarity to S. haliotis) indicated Shimia str. SK013 to be considered as a new species. The genome analysis of Shimia str. SK013 offered first insights into specific physiological and phenotypic adaptation mechanisms of Roseobacter-affiliated bacteria to the benthic environment.

Distinct compositions of free-living, particle-associated and benthic communities of the Roseobacter group in the North Sea

The Roseobacter group is one of the predominant lineages in the marine environment. While most investigations focus on pelagic roseobacters, the distribution and metabolic potential of benthic representatives is less understood. In this study, the diversity of the Roseobacter group was characterized in sediment and water samples along the German/Scandinavian North Sea coast by 16S rRNA gene analysis and cultivation-based methods. Molecular analysis indicated an increasing diversity between communities of the Roseobacter group from the sea surface to the seafloor and revealed distinct compositions of free-living and attached fractions. Culture media containing dimethyl sulfide (DMS), dimethyl sulfonium propionate (DMSP) or dimethyl sulfoxide (DMSO) stimulated growth of roseobacters showing highest most probable numbers (MPN) in DMSO-containing dilutions of surface sediments (2.1 × 10(7) roseobacters cm(-3)). Twenty roseobacters (12 from sediments) were isolated from DMSP- and DMS-containing cultures. Sequences of the isolates represented 0.04% of all Bacteria and 4.7% of all roseobacters in the pyrosequencing dataset from sediments. Growth experiments with the isolate Shimia sp. SK013 indicated that benthic roseobacters are able to switch between aerobic and anaerobic utilization of organic sulfur compounds. This response to changing redox conditions might be an adaptation to specific environmental conditions on particles and in sediments.

Genome-scale data suggest reclassifications in the Leisingera-Phaeobacter cluster including proposals for Sedimentitalea gen. nov. and Pseudophaeobacter gen. nov

Earlier phylogenetic analyses of the marine Rhodobacteraceae (class Alphaproteobacteria) genera Leisingera and Phaeobacter indicated that neither genus might be monophyletic. We here used phylogenetic reconstruction from genome-scale data, MALDI-TOF mass-spectrometry analysis and a re-assessment of the phenotypic data from the literature to settle this matter, aiming at a reclassification of the two genera. Neither Phaeobacter nor Leisingera formed a clade in any of the phylogenetic analyses conducted. Rather, smaller monophyletic assemblages emerged, which were phenotypically more homogeneous, too. We thus propose the reclassification of Leisingera nanhaiensis as the type species of a new genus as Sedimentitalea nanhaiensis gen. nov., comb. nov., the reclassification of Phaeobacter arcticus and Phaeobacter leonis as Pseudophaeobacter arcticus gen. nov., comb. nov. and Pseudophaeobacter leonis comb. nov., and the reclassification of Phaeobacter aquaemixtae, Phaeobacter caeruleus, and Phaeobacter daeponensis as Leisingera aquaemixtae comb. nov., Leisingera caerulea comb. nov., and Leisingera daeponensis comb. nov. The genera Phaeobacter and Leisingera are accordingly emended.