Cryobacterium tepidiphilum sp. nov., isolated from rhizosphere soil of lettuce (var. ramosa Hort.)

Cryobacterium zhongshanensis sp. nov., an actinobacterium isolated from Antarctic soil

A Gram-staining-positive, heterotrophic, non-spore-forming, non-motile, rod-shaped, strain ZS14-85^T belonging to the genus Cryobacterium was isolated from soil in Antarctica. Growth was observed in the presence of 0-2% (w/v) NaCl, at pH 7.0-9.0 (optimum, pH 7.0) and 4-30 ℃ (optimum, 20 ℃). Phylogenetic analysis showed that strain ZS14-85^T formed a lineage in the genus Cryobacterium. The digital DNA-DNA hybridization (dDDH) values between strain ZS14-85^T and its close relatives Cryobacterium psychrotolerans CGMCC 1.5382^T, Cryobacterium soli MCCC 1K03549^T and Cryobacterium breve NBRC 113800^T were 22.5, 22.3 and 22.2%, respectively. Orthologous Average Nucleotide Identity (OrthoANI) scores between strain ZS14-85^T and C. psychrotolerans CGMCC 1.5382^T, C. breve NBRC 113800^T and C. soli MCCC 1K03549^T were 78.7, 78.1 and 77.7%, respectively. The polar lipids of strain ZS14-85^T were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), one unidentified glycolipid (GL) and two unidentified lipids (L). The major fatty acids were anteiso-C_15:0 (60.7%), iso-C_16:0 (17.0%) and anteiso-C_17:0 (15.2%). MK-10, MK-11 and MK-9 were the predominant respiratory menaquinones. Based on phenotypic, phylogenetic and genotypic data, a novel species, Cryobacterium zhongshanensis sp. nov. is proposed. The type strain is ZS14-85^T (= CCTCC AB 2019396^T = KCTC 49384^T).

Diversity of the genus Cryobacterium and proposal of 19 novel species isolated from glaciers

The bacterial genus Cryobacterium includes at present 14 species that live in cryospheric environments. In this study, we analyzed 101 genomes of Cryobacterium with pure cultures obtained from GenBank. They could be classified into 44 species based on average nucleotide identity (ANI) analysis, showing the diversity of Cryobacterium. Among these, 19 strains in our laboratory were isolated from the glacier samples in China. The pairwise ANI values of these 19 strains and known species were <95%, indicating that they represented 19 novel species. The comparative genomic analysis showed significant differences in gene content between the two groups with a maximum growth temperature (T _max) of ≤ 20°C and a T _max of >20°C. A comprehensive and robust phylogenetic tree, including 14 known species and 19 novel species, was constructed and showed five phylogenetic branches based on 265 concatenated single-copy gene sequences. The T _max parameter had a strong phylogenetic signal, indicating that the temperature adaptation of Cryobacterium was largely through vertical transfer rather than horizontal gene transfer and was affected by selection. Furthermore, using polyphasic taxonomy combined with phylogenomic analysis, we proposed 19 novel species of the genus Cryobacterium by the following 19 names: Cryobacterium serini sp. nov., Cryobacterium lactosi sp. nov., Cryobacterium gelidum sp. nov., Cryobacterium suzukii sp. nov., Cryobacterium fucosi sp. nov., Cryobacterium frigoriphilum sp. nov., Cryobacterium cryoconiti sp. nov., Cryobacterium lyxosi sp. nov., Cryobacterium sinapicolor sp. nov., Cryobacterium sandaracinum sp. nov., Cryobacterium cheniae sp. nov., Cryobacterium shii sp. nov., Cryobacterium glucosi sp. nov., Cryobacterium algoritolerans sp. nov., Cryobacterium mannosilyticum sp. nov., Cryobacterium adonitolivorans sp. nov., Cryobacterium algoricola sp. nov., Cryobacterium tagatosivorans sp. nov., and Cryobacterium glaciale sp. nov. Overall, the taxonomy and genomic analysis can improve our knowledge of phenotypic diversity, genetic diversity, and evolutionary characteristics of Cryobacterium.

Deep mining decreases the microbial taxonomic and functional diversity of subsurface oil reservoirs

Microbes in subsurface oil reservoirs play important roles in elemental cycles and biogeochemical processes. However, the community assembly pattern of indigenous microbiome and their succession under long-term human activity remain poorly understood. Here we studied the microbial community assembly in underground sandstone cores from 190 to 2050 m in northeast China and their response to long-term oil recovery (10-50 years). Indigenous microbiome in subsurface petroleum reservoirs were dominated by Gammaproteobacteria, Firmicutes, Alphaproteobacteria, Bacteroidetes, and Actinobacteria, which exhibited a higher contribution of homogenizing dispersal assembly and different taxonomy distinct ecological modules when compared with perturbed samples. Specifically, the long-term oil recovery reduced the bacterial taxonomic- and functional-diversity, and increased the community co-occurrence associations in subsurface oil reservoirs. Moreover, distinguished from the perturbed samples, both variation partition analysis and structural equation model revealed that the contents of quartz, NO₃^- and Cl^- significantly structured the α- and β-diversity in indigenous subsurface bacterial communities. These findings first provide the holistic picture of microbiome in the deep oil reservoirs, which demonstrate the significant impact of human activity on microbiome in deep continental subsurface.

Aurantimicrobium photophilum sp. nov., a non-photosynthetic bacterium adjusting its metabolism to the diurnal light cycle and reclassification of Cryobacterium mesophilum as Terrimesophilobacter mesophilus gen. nov., comb. nov

The aerobic primarily chemoorganotrophic actinobacterial strain MWH-Mo1^T was isolated from a freshwater lake and is characterized by small cell lengths of less than 1 µm, small cell volumes of 0.05-0.06 µm³ (ultramicrobacterium), a small genome size of 1.75 Mbp and, at least for an actinobacterium, a low DNA G+C content of 54.6 mol%. Phylogenetic analyses based on concatenated amino acid sequences of 116 housekeeping genes suggested the type strain of Aurantimicrobium minutum affiliated with the family Microbacteriaceae as its closest described relative. Strain MWH-Mo1^T shares with the type strain of that species a 16S rRNA gene sequence similarity of 99.6 % but the genomes of the two strains share an average nucleotide identity of only 79.3 %. Strain MWH-Mo1^T is in many genomic, phenotypic and chemotaxonomic characteristics quite similar to the type strain of A. minutum. Previous intensive investigations revealed two unusual traits of strain MWH-Mo1^T. Although the strain is not known to be phototrophic, the metabolism is adjusted to the diurnal light cycle by up- and down-regulation of genes in light and darkness. This results in faster growth in the presence of light. Additionally, a cell size-independent protection against predation by bacterivorous flagellates, most likely mediated by a proteinaceous cell surface structure, was demonstrated. For the previously intensively investigated aerobic chemoorganotrophic actinobacterial strain MWH-Mo1^T (=CCUG 56426^T=DSM 107758^T), the establishment of the new species Aurantimicrobium photophilum sp. nov. is proposed.