Photobacterium chitinilyticum sp. nov., a marine bacterium isolated from seawater at the bottom of the East China Sea

Chryseobacterium pyrolae sp. nov., isolated from the rhizosphere soil of Pyrola calliantha H

A novel Gram-stain-negative, aerobic, non-motile, rod-shaped bacterium, designated pc2-12T, was isolated from the rhizosphere soil of the herb Pyrola calliantha collected from arid areas of Tibet. The strain grew most vigorously with 1 % (w/v) NaCl, at pH 7.0 and at 25 °C. According to the results of 16S rRNA gene sequence analysis, pc2-12T was closely related to the members of the genus Chryseobacterium, with highest levels of sequence similarity to Chryseobacterium viscerum 687B-08T (98.42 %), Chryseobacterium oncorhynchi 701B-08T (98.11 %) and Chryseobacterium ureilyticum DSM 18017T (97.98 %). The average nucleotide identity values between pc2-12T and C. viscerum 687B-08T, C. oncorhynchi 701B-08T and C. ureilyticum DSM 18017T were 79.71, 79.49 and 79.26 %, respectively. The in silico DNA-DNA hybridisation values between pc2-12T and C. viscerum 687B-08T, C. oncorhynchi 701B-08T and C. ureilyticum DSM 18017T were 23.30, 23.00 and 22.90 %, respectively. The draft genome sequence of pc2-12T was 4.64 Mb long, with DNA G+C content of 37.0 mol%. The fatty acids contained in the cells of pc2-12T were mainly composed of iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c). The main polar lipid was phosphatidylethanolamine. MK-6 was the sole respiratory quinone. On the basis of the results of analysis of all the data described, pc2-12T is considered to represent a novel species of the genus Chryseobacterium, for which the name Chryseobacterium pyrolae sp. nov., is proposed. The type strain is pc2-12T (=GDMCC 1.3256T= JCM 35712T).

Endophytic Bacterium Flexivirga meconopsidis sp. nov. with Plant Growth-Promoting Function, Isolated from the Seeds of Meconopsis integrifolia

Strain Q11T of an irregular coccoid Gram-positive bacterium, aerobic and non-motile, was isolated from Meconopsis integrifolia seeds. Strain Q11T grew optimally in 1% (w/v) NaCl, pH 7, at 30 °C. Strain Q11T is most closely related to Flexivirga, as evidenced by 16S rRNA gene analysis, and shares the highest similarity with Flexivirga aerilata ID2601ST (99.24%). Based on genome sequence analysis, the average nucleotide identity and digital DNA-DNA hybridization values of strains Q11T and D2601ST were 88.82% and 36.20%, respectively. Additionally, strain Q11T showed the abilities of nitrogen fixation and indole acetic acid production and was shown to promote maize growth under laboratory conditions. Its genome contains antibiotic resistance genes (the vanY gene in the vanB cluster and the vanW gene in the vanI cluster) and extreme environment tolerance genes (ectoine biosynthetic gene cluster). Shotgun proteomics also detected antibiotic resistance proteins (class A beta-lactamases, D-alanine ligase family proteins) and proteins that improve plant cold tolerance (multispecies cold shock proteins). Strain Q11T was determined to be a novel species of the genus Flexivirga, for which the name Flexivirga meconopsidis sp. nov. is proposed. The strain type is Q11T (GDMCC 1.3002T = JCM 36020 T).

Comparative Genomic Analyses of the Genus Photobacterium Illuminate Biosynthetic Gene Clusters Associated with Antagonism

The genus Photobacterium is known for its ecophysiological versatility encompassing free-living, symbiotic, and pathogenic lifestyles. Photobacterium sp. CCB-ST2H9 was isolated from estuarine sediment collected at Matang Mangrove, Malaysia. In this study, the genome of CCB-ST2H9 was sequenced, and the pan-genome of 37 Photobacterium strains was analysed. Phylogeny based on core genes showed that CCB-ST2H9 clustered with P. galatheae, forming a distinct clade with P. halotolerans, P. salinisoli, and P. arenosum. The core genome of Photobacterium was conserved in housekeeping functions, while the flexible genome was well represented by environmental genes related to energy production and carbohydrate metabolism. Genomic metrics including 16S rRNA sequence similarity, average nucleotide identity, and digital DNA–DNA hybridization values were below the cut-off for species delineation, implying that CCB-ST2H9 potentially represents a new species. Genome mining revealed that biosynthetic gene clusters (BGCs) involved in producing antimicrobial compounds such as holomycin in CCB-ST2H9 could contribute to the antagonistic potential. Furthermore, the EtOAc extract from the culture broth of CCB-ST2H9 exhibited antagonistic activity against Vibrio spp. Intriguingly, clustering based on BGCs profiles grouped P. galatheae, P. halotolerans, P. salinisoli, P. arenosum, and CCB-ST2H9 together in the heatmap by the presence of a large number of BGCs. These BGCs-rich Photobacterium strains represent great potential for bioactive secondary metabolites production and sources for novel compounds.

Photobacterium arenosum sp. nov., isolated from marine sediment sand

A Gram-stain-negative, aerobic, motile, short rod-shaped, catalase-negative and oxidase-positive bacterium, strain CAU 1568^T, was isolated from marine sediment sand sampled at Sido Island in the Republic of Korea. The optimum conditions for growth were at 25-30 °C, at pH 6.5-8.5 and with 0-4.0 % (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain CAU 1568^T was a member of the genus Photobacterium with high similarity to Photobacterium salinisoli JCM 30852^T (97.7 %), Photobacterium halotolerans KACC 17089^T (97.3 %) and Photobacterium galatheae LMG F28894^T (97.3 %). The predominant cellular fatty acids were C_16 : 0, summed feature 3 (C_16 : 1  ω6c and/or C_16 : 1  ω7c) and summed feature 8 (C_18 : 1  ω7c and/or C_18 : 1  ω6c), with Q-8 as the major of isoprenoid quinone. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerols, phosphatidylcholine, phosphatidylethanolamine, phospholipid, two aminophospholipids and three unidentified lipids. The whole genome size of strain CAU 1568^T was 4.8 Mb with 50.1 mol% G+C content; including 38 contigs and 4233 protein-coding genes. These taxonomic data support CAU 1568^T as representing a novel Photobacterium species, for which the name Photobacterium arenosum sp. nov. is proposed. The type strain of this novel species is CAU 1568^T (=KCTC 82404^T=MCCC 1K05668^T).

Photobacterium salinisoli sp. nov., isolated from a sulfonylurea herbicide-degrading consortium enriched with saline soil

A Gram-stain-negative, aerobic, motile, rod-shaped bacterium, designated strain LAM9072^T, was isolated from a sample of a sulfonylurea herbicide-degrading consortium enriched with saline soil. The optimal temperature and pH for the growth of strain LAM9072^T were 35 °C and 7.0, respectively. Strain LAM9072^T could grow in the presence of NaCl up to 9 % (w/v). Comparative analysis of the 16S rRNA gene sequences revealed that strain LAM9072^T was closely related to members of the family Vibrionaceae, with the highest similarities to Photobacterium halotolerans MACL01^T (97.7 %) and Photobacterium galatheae S2753^T (97.7 %). Strain LAM9072^T formed a distinct phylogenetic subclade within the genus Photobacterium in the 16S rRNA gene phylogenetic trees. The results of multi-locus sequence analysis revealed a distinct lineage with P. halotolerans MACL01^T as its closest relative. The genomic G+C content was 50.2 mol%. The DNA-DNA hybridization values between strain LAM9072^T and P. halotolerans LMG 22194^T and P. galatheae LMG 28894^T were 41.6 and 22.2 %, respectively. The average nucleotide identity values were 90.9 and 78.8 %, respectively, by comparing the draft genome sequences of strain LAM9072^T and P. halotolerans LMG 22194^T and P. galatheae LMG 28894^T. The major fatty acids were summed feature 3 (C_16 : 1ω6c and/or C_16 : 1ω7c), C_16 : 0 and summed feature 8 (C_18 : 1ω7c and/or C_18 : 1ω6c). Ubiquinone 8 was detected as the predominant respiratory quinone. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, aminophospholipid and four unidentified lipids. Based on its phenotypic characteristics and the results of genotypic analyses, we propose that strain LAM9072^T represents a novel species, for which the name Photobacteriumsalinisoli sp. nov. is proposed. The type strain is LAM9072^T (=ACCC 19961^T=JCM 30852^T).