Patiriisocius marinistellae gen. nov., sp. nov., isolated from the starfish Patiria pectinifera, and reclassification of Ulvibacter marinus as a member of the genus Patiriisocius comb. nov.

Abstract

A marine strain, designated KK4T, was isolated from the surface of a starfish, Patiria pectinifera, which was collected from seawater off the coast of Hokkaido, Japan. Strain KK4T is a Gram-stain-negative, non-spore-forming, rod-shaped, aerobic bacterium that forms yellow-pigmented colonies. A phylogenetic relationship analysis, based on 16S rRNA gene sequences, revealed that strain KK4T was closely related to Ulvibacter marinus IMCC12008T, Ulvibacter antarcticus IMCC3101T and Ulvibacter litoralis KMM 3912T, with similarities of 96.9, 95.8 and 95.6 %, respectively, but low sequence similarities (<94 %) among other genera in the family Flavobacteriaceae . Genomic similarities between strain KK4T and the three Ulvibacter type strains based on average nucleotide identity and digital DNA–DNA hybridization values were lower than the species delineation thresholds. Moreover, phylogenetic tree based on genome sequences showed that strain KK4T was clustered with U. marinus IMCC12008T and formed a branch independent from the cluster including type species of the genera Ulvibacter , Marixanthomonas , Marinirhabdus , Aureitalea and Aequorivita . Amino acid identity values between strain KK4T/ U. marinus IMCC12008T and the neighbour type species/strains were 61.9–68.2% and 61.5–67.4 %, which were lower than the genus delineation threshold, implying the novel genus status of strain KK4T. Strain KK4T growth occurred at pH 6.0–9.0, 4–30 °C and in NaCl concentrations of 0.5–5.0 %, and optimally at pH 7.0, 25 °C and 3.0 %, respectively. Unlike Ulvibacter strains, strain KK4T could assimilate glucose, mannose, galactose and acetate. The major quinone and fatty acids were menaquinone-6 and iso-C15 : 0 (27.5 %), iso-C15 : 1 G (22.5 %) and iso-C17 : 0 3-OH (12.8 %), respectively. Based on genetic, phylogenetic and phenotypic properties, strain KK4T represents a novel species of the genus Patiriisocius, for which the name Patiriisocius marinistellae gen. nov., sp. nov. is proposed. The type strain is KK4T (=JCM 33344T=KCTC 72225T). In addition, based on the current data, Ulvibacter marinus should be reclassified as Patiriisocius marinus comb. nov.

Worker-dependent gut symbiosis in an ant

“…For three ants in one colony derived from five populations, using extracted DNA from whole body of each insect as described above, bacterial 16S rRNA gene was directly amplified by PCR using universal primers for bacterial 16S rRNA gene, 27F and 1492R (Table S 3 ), and AmpliTaq Gold 360 master mix (Applied Biosystems, CA, USA) according to the manufacture’s instruction, with the following thermal cycling conditions: initial denaturation at 95 °C for 10 min, followed by 30 cycles of 95 °C for 30 s, 55 °C for 60 s, and 72 °C for 90 s, and a final extension at 72 °C for 120 s. All the PCR products (in total 15) were purified and sequenced using a Sanger sequencer as described previously [ 39 ] (See Supplementary Information). The resulting fragmented sequences were assembled using ATSQ tool version 5.4.1 in genetyx-mac version 19 (Software Development, Tokyo, Japan).…”

Anaeromyxobacter oryzae sp. nov., Anaeromyxobacter diazotrophicus sp. nov. and Anaeromyxobacter paludicola sp. nov., isolated from paddy soils

“…Then, PCR amplification of the 16S rRNA genes of Red232 T , Red267 T and Red630 T was conducted using the primer pair 27F (5′-AGAGTTTGATCMTGGCTCAG-3′) and 1 492R (5′-TACGGYTACCTTGTTACGACTT-3′) [26], with a Q5 Hot Start High-Fidelity 2X Master Mix (New England Biolabs) according to the manufacturer’s instructions. Thermal cycling conditions were as follows: 98 °C for 30 s, followed by 30 cycles of 98 °C for 10 s, 55 °C for 20 s, and 72 °C for 35 s. The resulting PCR amplicons were purified using an ExoSAP-IT Express PCR Product Cleanup Reagent (Thermo Fisher Scientific), followed by sequencing using the BigDye Terminator (version 3.1) Cycle Sequencing Kit and a Sanger sequencer (ABI 3130xl DNA Sequencer, Applied Biosystems) as described previously [27]. Next, the ATGC tool version 7.1.0 in Genetyx-Mac version 20 (jp.co.sdc.genetyx-mac) was used to assemble fragmented sequences, after which the EzBioCloud platform was used to calculate the pairwise similarities between 16S rRNA gene sequences among the three strains, the type strain of Anaeromyxobacter and type species of related genera [28].…”

Geomonas silvestris sp. nov., Geomonas paludis sp. nov. and Geomonas limicola sp. nov., isolated from terrestrial environments, and emended description of the genus Geomonas

“…The prepared genomic DNA was used for sequencing of the 16S rRNA gene and the whole genome as described below. PCR amplification and sequencing of the 16S rRNA gene of strains Red330 T , Red736 T and Red745 T were performed as described previously [9]. The assembly of fragmented sequences was performed using ATSQ tool version 5.4.1 in genetyx-mac version 19 (Software Development, Tokyo, Japan).…”