Journal Article

Characterization and Genomic Analysis of IFererhizobium litorale/I gen. nov., sp. nov., Isolated from the Sandy Sediments of the Sea of Japan Seashore

Mikhailov, Valery, Otstavnykh, Nadezhda, Isaeva, Marina, Romanenko, Lyudmila, Tanaka, Naoto, Kurilenko, Valeriya, Tekutyeva, Liudmila, Svetashev, Vasily

2023

Overview

The taxonomic status of two gram-negative, whitish-pigmented motile bacteria KMM 9576[sup.T] and KMM 9553 isolated from a sandy sediment sample from the Sea of Japan seashore was defined. Phylogenetic analysis revealed that strains KMM 9576[sup.T] and KMM 9553 represent a distinct lineage within the family Rhizobiaceae, sharing 100% 16S rRNA sequence similarity and 99.5% average nucleotide identity (ANI) to each other. The strains showed the highest 16S rRNA sequence similarities of 97.4% to Sinorhizobium garamanticum LMG 24692[sup.T] , 96.9% to Ensifer adhaerens NBRC 100388[sup.T] , and 96.8% to Pararhizobium giardinii NBRC 107135[sup.T] . The ANI values between strain KMM 9576[sup.T] and Ensifer adhaerens NBRC 100388[sup.T] , Sinorhizobium fredii USDA 205[sup.T] , Pararhizobium giardinii NBRC 107135[sup.T] , and Rhizobium leguminosarum NBRC 14778[sup.T] were 79.9%, 79.6%, 79.4%, and 79.2%, respectively. The highest core-proteome average amino acid identity (cpAAI) values of 82.1% and 83.1% were estimated between strain KMM 9576[sup.T] and Rhizobium leguminosarum NBRC 14778[sup.T] and ‘Rhizobium album’ NS-104, respectively. The DNA GC contents were calculated from a genome sequence to be 61.5% (KMM 9576[sup.T] ) and 61.4% (KMM 9553). Both strains contained the major ubiquinone Q-10 and C[sub.18:1] ω7c as the dominant fatty acid followed by 11-methyl C[sub.18:1] ω7c and C[sub.19:0] cyclo, and polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminophospholipid, and two unidentified phospholipids. Based on phylogenetic and phylogenomic analyses, and phenotypic characterization, strains KMM 9576[sup.T] and KMM 9553 are concluded to represent a novel genus and species, for which the name Fererhizobium litorale gen. nov., sp. nov. is proposed. The type strain of the type species is strain KMM 9576[sup.T] (=NRIC 0957[sup.T] ).

• Publisher: MDPI AG
• Subject: Environmental aspects / Genetic aspects / Gram-negative bacteria / Identification and classification / Intertidal zonation / Marine bacteria / Marine sediments