Antarcticirhabdus aurantiaca gen. nov., sp. nov., isolated from Antarctic gravel soil

Strain R10^T was isolated from a gravel soil sample obtained from Deception Island, Antarctica. The isolate was a Gram-stain-negative, strictly aerobic, motile, short-rod-shaped bacterium, and its colonies were orange yellow in colour. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain R10^T belonged to the family Aurantimonadaceae and shared highest sequence similarity with Jiella aquimaris LZB041^T (96.3 % sequence similarity), Aurantimonas aggregata R14M6^T (96.0 %) and Aureimonas frigidaquae JCM 14755^T (96.0 %). Phylogenetic analysis showed that strain R10^T affiliated with members of the family Aurantimonadaceae and represented an independent lineage. Growth occurred at 10-37 °C (optimum, 28-32 °C), up to 1.0 % (w/v) NaCl (optimum, 0 %) and pH 5.5-9.0 (optimum, pH 7.0). The major respiratory quinone of strain R10^T was Q-10. Its major fatty acids were C_18 : 1 ω7c and C_{16 : 0}. The polar lipid profile of strain R10^T comprised diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, two unknown phospholipids and two unknown aminophospholipids. The genome of strain R10^T was 5.92 Mbp with a G+C content of 69.1 % based on total genome calculations. Average nucleotide identity (ANI) values between R10^T and other related species of the family Aurantimonadaceae were found to be low (ANIm <87.0 %, ANIb <75.0 % and OrthoANIu <77.0 %). Furthermore, digital DNA-DNA hybridization (dDDH) and average amino acid identity (AAI) values between strain R10^T and the closely related species ranged from 19.5-20.6% and from 60.6-64.0 %, respectively. Based on the results of our phylogenetic, phenotypic, genotypic and chemotaxonomic analyses, it is concluded that strain R10^T represents a novel genus and species of the family Aurantimonadaceae, for which the name Antarcticirhabdus aurantiaca gen. nov., sp. nov. is proposed. The type strain is R10^T (=KCTC 72466^T=CGMCC 1.17155^T).

Horsenettle (Solanum carolinense) fruit bacterial communities are not variable across fine spatial scales

Fruit house microbial communities that are unique from the rest of the plant. While symbiotic microbial communities complete important functions for their hosts, the fruit microbiome is often understudied compared to other plant organs. Fruits are reproductive tissues that house, protect, and facilitate the dispersal of seeds, and thus they are directly tied to plant fitness. Fruit microbial communities may, therefore, also impact plant fitness. In this study, we assessed how bacterial communities associated with fruit of Solanum carolinense, a native herbaceous perennial weed, vary at fine spatial scales (<0.5 km). A majority of the studies conducted on plant microbial communities have been done at large spatial scales and have observed microbial community variation across these large spatial scales. However, both the environment and pollinators play a role in shaping plant microbial communities and likely have impacts on the plant microbiome at fine scales. We collected fruit samples from eight sampling locations, ranging from 2 to 450 m apart, and assessed the fruit bacterial communities using 16S rRNA gene amplicon sequencing. Overall, we found no differences in observed richness or microbial community composition among sampling locations. Bacterial community structure of fruits collected near one another were not more different than those that were farther apart at the scales we examined. These fine spatial scales are important to obligate out-crossing plant species such as S. carolinense because they are ecologically relevant to pollinators. Thus, our results could imply that pollinators serve to homogenize fruit bacterial communities across these smaller scales.

Complete Genome and Plasmid Sequences of the Psychrotolerant Aureimonas Strain SA4125, Isolated from Antarctic Moss Vegetation

The complete genome sequences of Aureimonas sp. strain SA4125 and its native plasmid pSA4125 were determined. The genome sequence comprises 4,968,066 bp, with a GC content of 66.0%, and contains 4,691 coding DNA sequences (CDSs), 3 rRNA operons, and 50 tRNAs. The native plasmid comprises 131,777 bp, with a GC content of 62.3%, and contains 138 CDSs.

Aureimonas mangrovi sp. nov., a marine alphaproteobacterium isolated from mangrove sediment in Thailand

Two bacterial strains, designated as 1-4-3^T and 1-4-4, were isolated from a mangrove sediment cultured with coastal seawater. The cells were Gram-stain-negative, motile, short, rod-shaped bacteria with flagella. Growth occurred at 4-37 °C, pH 7.0-9.0, and 0-7% NaCl. The predominant fatty acids of the novel strains were C_18 : 1  ω7c, C_19 : 0 cyclo ω8c, C_18 : 0, and C_16 : 0. A phylogenetic analysis based on 16S rRNA gene sequences and whole genome phylogeny analysis based on distance matrix revealed an affiliation between the two strains and the genus Aureimonas, with closest sequence similarity to A. populi 4M3-2^T (96.41 and 96.64% similarity, respectively) and A. glaciistagni (96.01 and 96.23% similarity, respectively). The DNA G+C content of strain 1-4-3^T was 66.80 mol%. Strain 1-4-3^T displayed low DNA-DNA relatedness to A. populi 4M3-2^T, with an average nucleotide identity value of 77.47 % and digital DNA-DNA hybridization value of 22.83 %. Genotypic, chemotaxonomic, and phenotypic data indicate that strains 1-4-3^T and 1-4-4 represent a novel species of the genus Aureimonas, for which we propose the name Aureimonas mangrovi sp. nov. The type strain is 1-4-3^T (=LMG 31693^T=CGMCC 1.18507^T).

High-throughput sequencing-based analysis of the composition and diversity of endophytic bacterial community in seeds of upland rice

Upland rice is an ecotype crop resulting from the long-term domestication and evolution of rice in dry land without a water layer. Generally, the stems and leaves are thick and luxuriant, while the leaves also typically broad and light. The root system is developed with abundant root hair, and the osmotic pressure of the root and cell juice concentration in the leaves is high, while this plant is drought-resistant, heat-resistant, and water absorbent. This study aims to reveal the "core flora" of the endophytes in upland rice seeds by examining their diversity and community structures. It further intends to reveal the impact of the soil environment on the formation of endophyte community structures in upland rice seeds by comparing the environmental soil microorganisms in upland rice habitats. In this study, high-throughput sequencing technology based on the Illumina Hiseq 2500 platform was used to investigate the structure and diversity of endophytic bacterial communities using upland rice varieties collected from different locations and soil samples from unified planting sites as materials. Here, 42 endophytic OTUs were found to coexist in the 14 samples. At the phylum level, the first dominant phyla in all the samples were Proteobacteria (93.81-99.99%). At the genus level, Pantoea (8.77-87.77%), Pseudomonas (1.15-61.58%), Methylobacterium (0.40-4.64%), Sphingomonas (0.26-3.85%), Microbacterium (0.01-4.67%) and Aurantimonas (0.04-4.34%), which represent the core microflora in upland rice seeds, served as the dominant genera that coexisted in all the upland rice seeds tested. This study significant for the isolation, screening, functional evaluation, and re-action of various functional microorganisms in upland rice to improve its agronomic traits. It also provides a specific reference for the interaction between microorganisms and plants.

Aureimonas fodinaquatilis sp. nov., isolated from coal mine wastewater

A Gram stain-negative, aerobic, non-motile, short, rod-shaped bacterial strain CAU 1482^T was isolated from coal mine wastewater in Hongcheon, Korea. It grew well at 30 °C, pH 8.5, 2% NaCl (w/v). 16S rRNA-based phylogeny indicated that CAU 1482^T forms a distinct lineage within Aureimonas with high similarity to Aureimonas frigidaquae CW5^T (98.2%), Aureimonas altamirensis S21B^T (98.0%), and Aureimonas glaciei B5-2^T (96.3%). The predominant cellular fatty acids were C_18:1 2-OH, C_16:0, C_18:1 ω7c, and/or C_18:1 ω6c (summed feature 8), with Q-10 as the major isoprenoid quinone. The polar lipid profile comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, two unidentified aminolipids, and three unidentified lipids. The 3.9-Mb genome included 8 contigs and 3599 protein-coding genes with a 56.7 mol% G + C content. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain CAU 1482^T and closely related strains of A. frigidaquae CW5^T and A. altamirensis S21B^T were 72.2‒72.4% and 18.7‒18.8%, respectively. These phenotypic, chemotaxonomic, and phylogenetic data support CAU 1482^T as a novel Aureimonas species, for which the name Aureimonas fodinaquatilis sp. nov. is proposed. The type strain is CAU 1482^T (= KCTC 62995^T = NBRC 113692^T).

Aureimonas leprariae sp. nov., Isolated from a Lepraria sp. Lichen

A Gram-negative, motile, aerobic and coccoid rod-shaped bacterium, designated strain YIM132180^T, was isolated from a Lepraria sp. lichen collected from Pu'er, Yunnan Province, China. The strain grew at 15-35 °C (optimum, 25-28 °C), at 0-2% (w/v) NaCl (optimum, 0-1%) and at pH 6.0-9.0 (optimum, pH 7.0). The 16S rRNA gene sequence showed that strain YIM132180^T had highest similarity (96.4%) with Aureimonas endophytica 2T4P-2-4^T, followed by Aureimonas ureilytica NBRC 106430^T (95.7%) and Aureimonas rubiginis CC-CFT034^T (95.6%). Phylogenetic analysis showed that the strain grouped with species of the genus Aureimonas. The genomic sequence was 4,779,519 bp and contained 4584 coding sequences (CDSs), 54 RNA genes, 3 complete rRNA genes and 47 tRNA genes. The major fatty acids (>10%) of strain YIM132180^T were C_18:1ω7c, C-_16:0 and C_19:0 cyclo ω8c. The predominant menaquinone was ubiquinone 10 (Q-10). The polar lipid profile comprised diphosphatidylglycerol, phosphatidylcholine, phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, unidentified phospholipid, amino lipid, lipid and most importantly sulfoquinovosyldiacylglycerol (SQDG). Based on the draft genome sequence, the G +C content of strain YIM132180^T was 68.4 mol%. The results of the polyphasic taxonomic study, including phenotypic, chemotaxonomic, and phylogenetic analyses, showed that strain YIM132180^T represents a novel species of the genus Aureimonas, for which the name Aureimonas leprariae sp. nov. is proposed. The type strain is YIM 132180^T (=KCTC 72462^T = CGMCC 1.17389^T).