Mariluticola halotolerans gen. nov., sp. nov., a novel member of the family Devosiaceae isolated from South China Sea sediment

A novel member of class Alphaproteobacteria was isolated from marine sediment of the South China Sea. Cells of strain LMO-2^T were Gram-stain negative, greyish in colour, motile, with a single lateral flagellum and short rod in shape with a slight curve. Strain LMO-2^T was positive for oxidase and negative for catalase. The bacterium grew aerobically at 10-40 °C (optimum, 25-30 °C), pH 5.5-10.0 (optimum, pH 7.0) and 0-9 % NaCl (w/v; optimum, 2-3 %). Phylogenetic analysis of the 16S rRNA gene sequence and phylogenomic analysis of the whole genome sequence indicated that strain LMO-2^T represents a new genus and a new species within the family Devosiaceae, class Alphaproteobacteria, phylum Pseudomonadota. Comparisons of the 16S rRNA gene sequences of strain LMO-2^T showed 94.8 % similarity to its closest relative. The genome size is ~3.45 Mbp with a DNA G+C content of 58.17 mol%. The strain possesses potential capability for the degradation of complex organic matter, i.e. fatty acid and benzoate. The predominant cellular fatty acids (>10 %) were C_16 : 0 and C_18 : 1 ω7c 11-methyl. The sole respiratory quinone was ubiquinone-10. The major identified polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phospholipid. Based on the polyphasic taxonomic data, strain LMO-2^T represents a novel genus and a novel species for which the name Mariluticola halotolerans gen. nov., sp. nov., was proposed in the family Devosiaceae. The type strain is LMO-2^T (=CGMCC 1.19273^T=JCM 34934^T).

Complete Genome Sequence of Paradevosia shaoguanensis Type Strain J5-3, Obtained Using Nanopore and Illumina Sequencing Technologies

The complete genome sequence of Paradevosia shaoguanensis J5-3^T (China General Microbiological Culture Collection Center [CGMCC] 1.12430^T) is presented here. The complete genome sequence of P. shaoguanensis J5-3^T will provide valuable references for classification and comparative genome analysis.

Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria

The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.

Complete Genome Sequence of Potential Deoxynivalenol-Degrading Bacterium Youhaiella tibetensis Type Strain F4

Here, we report the first complete genome sequence of the potential deoxynivalenol-degrading strain Youhaiella tibetensis F4^T (China General Microbiological Culture Collection Center [CGMCC] 1.12719^T). To the best of our knowledge, this is also the first announcement of the complete genome sequence of a Youhaiella species.

Here, we report the first complete genome sequence of the potential deoxynivalenol-degrading strain Youhaiella tibetensis F4^T (China General Microbiological Culture Collection Center [CGMCC] 1.12719^T). To the best of our knowledge, this is also the first announcement of the complete genome sequence of a Youhaiella species.

Hymenobacter bucti sp. nov., isolated from subsurface sandstone sediment

A Gram-reaction-negative, strictly aerobic, non-motile, non-spore-forming bacterial strain, designated DK6-66^T, was isolated from subsurface sandstone sediment located in the Qilian Mountains in Qinghai Province, Northwest China. Strain DK6-66^T was found to grow optimally at pH 7.0 and 22 °C. The 16S rRNA gene sequence analysis indicated that strain DK6-66^T belonged to the genus Hymenobacter and clustered with the type strain of Hymenobacter arcticus, with which it exhibited a 16S rRNA gene sequence similarity value of 98.2 %. The DNA G+C content was 60.4 mol%. The major respiratory quinone was MK-7 and the major polar lipid was phosphatidylethanolamine. The major fatty acids were C16 : 1ω7c and/or C16 : 1ω6c, anteiso-C17 : 1 B and/or iso-C17 : 1 I, iso-C15 : 0, anteiso-C15 : 0 and C16 : 1ω5c. On the basis of phylogenetic and phenotypic data, strain DK6-66^T was classified in the genus Hymenobacter as a member of a novel species, for which the name Hymenobacterbucti sp. nov. is proposed. The type strain is DK6-66^T (=CGMCC 1.15795^T=KCTC 52629^T).

Sphingomonas qilianensis sp. nov., Isolated from Surface Soil in the Permafrost Region of Qilian Mountains, China

A Gram-stain-negative, strictly aerobic, non-motile and rod-shaped bacterial strain, designated X1(T), was isolated from the permafrost region of Qilian Mountains in northwest of China. Phylogenetic analyses of 16S rRNA gene sequence revealed that strain X1(T) was a member of the genus Sphingomonas and shared the highest 16S rRNA gene sequence similarity with Sphingomonas oligophenolica JCM 12082(T) (96.9%), followed by Sphingomonas glacialis CGMCC 1.8957(T) (96.7%) and Sphingomonas alpina DSM 22537(T) (96.4%). Strain X1(T) was able to grow at 15-30 °C, pH 6.0-10.0 and with 0-0.3% NaCl (w/v). The DNA G+C content of the isolate was 64.8 mol%. Strain X1(T)-contained Q-10 as the dominant ubiquinone and C(18:1)ω7c, C(16:1)ω7c, C(16:0) and C(14:0) 2-OH as the dominant fatty acids. The polar lipid profile of strain XI(T)-contained sphingoglycolipid, phosphatidylglycerol, phosphatidylethanolamine, one unidentified glycolipid and two unidentified phospholipid. Due to the phenotypic and genetic distinctiveness and other characteristic studied in this article, we consider X1(T) as a novel species of the genus Sphingomonas and propose to name it Sphingomonas qilianensis sp. nov. The type strain is X1(T) (=CGMCC 1.15349(T) = KCTC 42862(T)).