Sinomicrobium kalidii sp. nov., an indole-3-acetic acid-producing endophyte from a shoot of halophyte Kalidium cuspidatum

To better understand the effects of endophytic bacteria on halophytes, a bacteria that produced indole-3-acetic acid and 1-aminocyclopropane-1-carboxylic acid deaminase, designated HD2P242^T, was isolated from a shoot of Kalidium cuspidatum collected in Tumd Right Banner, Inner Mongolia, PR China. The cells of strain HD2P242^T were Gram-stain-negative, strictly aerobic, motile by gliding, non-spore-forming and rod-shaped. Strain HD2P242^T grew at pH 6.0-9.0 (optimum, pH 7.0) and 10-45 °C (optimum 37 °C), in the presence of 0-8 % (w/v) NaCl (optimum, 4 %). The strain was positive for oxidase and catalase. The phylogenetic trees based on the 16S rRNA gene sequences and the whole genome sequences both showed that strain HD2P242^T clustered with Sinomicrobium pectinilyticum 5DNS001^T and S. oceani SCSIO 03483^T, and had 95.6, 94.3 and <94.3 % 16S rRNA gene similarities to S. pectinilyticum 5DNS001^T, S. oceani SCSIO 03483^T and all the other current type strains. Strain HD2P242^T contained menaquinone 6 as its sole respiratory quinone. Its major polar lipids were phosphatidylethanolamine, two unidentified aminolipids, two unidentified phospholipids and an unidentified lipid. The major fatty acids were iso-C_17 : 0, iso-C_16 : 0 3-OH, anteiso-C_17 : 0 and summed feature 6 (C_19 : 1  ω9c and/or C_19 : 1  ω11c). The genome consisted of a 5 364 211 bp circular chromosome, with a G+C content of 45.1 mol%, predicting 4391 coding sequence genes, 47 tRNA genes and two rRNA operons. The average nucleotide identity based on blast and the digital DNA-DNA hybridization values of strain HD2P242^T with S. oceani SCSIO 03483^T and S. pectinilyticum 5DNS001^T were 73.8 and 77.0%, and 22.3 and 22.2%, respectively. The comparative genome analysis showed that the pan-genomes of strain HD2P242^T and three Sinomicrobium type strains possessed 4236 clusters, whereas the core genome possessed 2162 clusters, which accounted for 52.3 % of all the clusters. The genomic analysis revealed that all four Sinomicrobium members could utilize d-glucose by the glycolysis-gluconeogenesis pathway or the pentose phosphate pathway. The tricarboxylic acid cycle was utilized as a metabolic centre. The phylogenetic, physiological and phenotypic characteristics allowed the discrimination of strain HD2P242^T from its phylogenetic relatives. Therefore, Sinomicrobium kalidii sp. nov. is proposed, and the type strain is HD2P242^T (=CGMCC 1.19025^T=KCTC 92136^T).

Sinomicrobium weinanense sp. nov., a halophilic bacterium isolated from saline-alkali soil

A Gram-stain-negative, facultative anaerobic, non-motile, rod-shaped strain was isolated from saline-alkali soil collected in PR China, and it was designated as strain FJxs T . Its optimal growth was observed at 37–40 °C in the presence of 0–3 % (w/v) NaCl (pH 7.0). The major fatty acids of strain FJxs T were iso-C15 : 0, iso-C17 : 0 3OH, summed feature 3, C16 : 0 and iso-C15 : 1 G. The predominant respiratory quinone was menaquinone 6. The DNA G+C content of the strain was 45.18 mol%. Whole genome and 16S rRNA gene sequence analyses indicated that strain FJxs T exhibited 94.78 % sequence identity (the maximum) with Sinomicrobium soli N-1-3-6T, 94.36 % with Sinomicrobium pectinilyticum 5DNS001T, and 93.52 % with Sinomicrobium oceani SCSIO 03483T. Analyses of genotypic, phenotypic, phylogenetic and chemotaxonomic characteristics indicated that strain FJxs T represented a novel species of the genus Sinomicrobium . This novel species was named Sinomicrobium weinanense sp. nov. with its type strain as FJxs T (=CCTCC AB 2019251T=KCTC 72740T).

Jannaschia marina sp. nov., isolated from the gut of a gastropod, Onchidium reevesii

A taxonomic study was carried out on strain SHC163^T, which was isolated from the gut of Onchidium reevesii. The bacterium was Gram-stain-negative, oxidase-positive, catalase-negative and rod-shaped. Growth was observed at salinities of 0-4.0 % NaCl and at temperatures of 15-35 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SHC163^T belonged to the genus Jannaschia, with the highest sequence similarity to Jannaschia seosinensis CL-SP26^T (97.9%), followed by Jannaschia faecimaris DSM 100420^T (97.8 %), Jannaschia rubra CECT 5088^T (97.5%) and eight species of the genus Jannaschia (94.7-97.1 %). The average amino acid identity, average nucleotide identity and the digital DNA-DNA hybridization estimate values between strain SHC163^T and the type strains of the genus Jannaschia were 64.33-79.78 %, 71.0-78.4 % and 19.2-21.0%, respectively. The principal fatty acids (>5 %) were summed feature 8 (C_18 : 1  ω7c/C_18 : 1  ω6c, 56.5 %), C_18 : 1  ω7c 11-methyl (23.1 %), C_18 : 0 (8.7 %). The G+C content of the chromosomal DNA was 67.8 mol%. The respiratory quinone was determined to be Q-10 (100 %). The polar lipids were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an unidentified phospholipid, an unidentified aminolipid and aminophospholipid. The combined genotypic and phenotypic data show that strain SHC163^T represents a novel species within the genus Jannaschia, for which the name Jannaschia marina sp. nov. is proposed, with the type strain SHC163^T (=MCCC 1K04032^T=KCTC 72524^T).

Solimonas marina sp. nov., isolated from deep seawater of the Pacific Ocean

A taxonomic study was carried out on strain C16B3^T, which was isolated from deep seawater of the Pacific Ocean. The bacterium was Gram-stain-negative, oxidase- and catalase- positive and rod-shaped. Growth was observed at salinities of 0-8.0 % and at temperatures of 10-45 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain C16B3^T belonged to the genus Solimonas, with the highest sequence similarity to Solimonas terrae KIS83-12^T (97.2 %), followed by Solimonas variicoloris MN28^T (97.0 %) and the other four species of the genus Solimonas (94.5 -96.8 %). The average nucleotide identity and estimated DNA-DNA hybridization values between strain C16B3^T and the type strains of the genus Solimonas were 74.05-79.48 % and 19.5-22.5 %, respectively. The principal fatty acids (>5 %) were summed feature 8 (C_18 : 1  ω7c/C_18 : 1  ω6c; 20.9 %), iso-C_16 : 0 (14.6 %), C_16 : 1  ω5c (9.4 %), iso-C_12 : 0 (8.4 %), summed feature 2 (C_14 : 0 3-OH/iso I-C_16 : 1 and C_12 : 0 aldehyde; 6.8 %) and C_16 : 0 (5.5 %). The G+C content of the chromosomal DNA was 65.37 mol%. The respiratory quinone was determined to be Q-8 (100 %). The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, four unidentified aminolipids, six unidentified phospholipids and one unidentified polar lipid. The combined genotypic and phenotypic data show that strain C16B3^T represents a novel species within the genus Solimonas, for which the name Solimonas marina sp. nov. is proposed, with the type strain C16B3^T (=MCCC 1A04678^T=KCTC 52314^T).