Harenicola maris gen. nov., sp. nov. isolated from the Sea of Japan shallow sediments

Genomic potential for inorganic carbon sequestration and xenobiotic degradation in marine bacterium Youngimonas vesicularis CC-AMW-ET affiliated to family Paracoccaceae

Ecological studies on marine microbial communities largely focus on fundamental biogeochemical processes or the most abundant constituents, while minor biological fractions are frequently neglected. Youngimonas vesicularis CC-AMW-ET, isolated from coastal surface seawater in Taiwan, is an under-represented marine Paracoccaceae (earlier Rhodobacteraceae) member. The CC-AMW-ET genome was sequenced to gain deeper insights into its role in marine carbon and sulfur cycles. The draft genome (3.7 Mb) contained 63.6% GC, 3773 coding sequences and 51 RNAs, and displayed maximum relatedness (79.06%) to Thalassobius litoralis KU5D5T, a Roseobacteraceae member. While phototrophic genes were absent, genes encoding two distinct subunits of carbon monoxide dehydrogenases (CoxL, BMS/Form II and a novel form III; CoxM and CoxS), and proteins involved in HCO3- uptake and interconversion, and anaplerotic HCO3- fixation were found. In addition, a gene coding for ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO, form II), which fixes atmospheric CO2 was found in CC-AMW-ET. Genes for complete assimilatory sulfate reduction, sulfide oxidation (sulfide:quinone oxidoreductase, SqrA type) and dimethylsulfoniopropionate (DMSP) cleavage (DMSP lyase, DddL) were also identified. Furthermore, genes that degrade aromatic hydrocarbons such as quinate, salicylate, salicylate ester, p-hydroxybenzoate, catechol, gentisate, homogentisate, protocatechuate, 4-hydroxyphenylacetic acid, N-heterocyclic aromatic compounds and aromatic amines were present. Thus, Youngimonas vesicularis CC-AMW-ET is a potential chemolithoautotroph equipped with genetic machinery for the metabolism of aromatics, and predicted to play crucial roles in the biogeochemical cycling of marine carbon and sulfur.

Gymnodinialimonas phycosphaerae sp. nov., a phycosphere bacterium isolated from Karlodinium veneficum

A facultative anaerobic, Gram-negative, non-motile, rod-shaped bacterial strain, designated N5^T, was obtained from the phycosphere microbiota of the marine planktonic dinoflagellate, Karlodinium veneficum. Strain N5^T showed growth on marine agar at 25 °C, pH 7 and 1 % (w/v) NaCl and produced a yellow colour. According to a phylogenetic study based on 16S rRNA gene sequences, strain N5^T has a lineage within the genus Gymnodinialimonas. The G+C content in the genome of strain N5^T is 62.9 mol% with a total length of 4 324 088 bp. The NCBI Prokaryotic Genome Annotation Pipeline revealed that the N5^T genome contained 4230 protein-coding genes and 48 RNA genes, including a 5S rRNA, 16S rRNA, 23S rRNA, 42 tRNA, and three ncRNAs. Genome-based calculations (genome-to-genome distance, average nucleotide identity and DNA G+C content) clearly indicated that the isolate represents a novel species within the genus Gymnodinialimonas. The predominant fatty acids were C_19 : 0 cyclo ω8c and feature 8 (comprising C_18 : 1 ω6c and/or C_18 : 1 ω7c). The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. The main respiratory quinone was Q-10. Based on its phenotypic, phylogenetic, genomic and chemotaxonomic features, strain N5^T represents a novel species of the genus Gymnodinialimonas, for which the name Gymnodinialimonas phycosphaerae sp. nov. is proposed. The type strain is N5^T (=KCTC 82362^T=NBRC 114899^T).

Limibaculum sediminis sp. nov., isolated from mangrove sediment

A Gram-stain-negative, cream-coloured, aerobic, motile and ovoid- to rod-shaped bacterium, designated as FT325^T, was isolated from mangrove sediment collected in Shenzhen, PR China. The taxonomic position of strain FT325^T was established by phylogenetic, physiological, biochemical and chemotaxonomic analyses. Strain FT325^T grew optimally at 37-40 °C and pH 6.0 in the presence of 0 % (w/v) NaCl. Results of 16S rRNA gene sequence analysis showed that strain FT325^T was most similarly related to Limibaculum halophilum CAU 1123^T (96.2 %), Phaeovulum vinaykumarii DSM 18714^T (93.9%) and Amaricoccus solimangrovi HB 172011^T (93.7 %). The major fatty acids (>10 %) were C_18 : 1  ω7c (60.0 %) and 11-methyl C_18 : 1  ω7c (16.7 %). The sole respiratory quinone was Q-10. The polar lipids were phosphatidylglycerol, one unidentified glycolipid, three unidentified aminolipids and three unidentified phospholipids. Its estimated genome size was 4 318 768 bp and the genomic DNA G+C content was 69.6 mol%. Based on its distinct phenotypic, chemotaxonomic and phylogenetic characteristics, strain FT325^T represents a novel species of the genus Limibaculum, for which the name Limibaculum sediminis sp. nov. is proposed (=MCCC 1K07397^T=KCTC 92313^T).