Phylogenomic evaluation of Mangrovimicrobium sediminis gen. nov. sp. nov., the first nitrogen fixing member of the family Halieaceae adapted to mangrove habitat and reclassification of Halioglobus pacificus to Pseudohaliglobus pacificus comb. nov

Pravin Kumar; Ashish Verma; Pooja Yadav; Joyasree Das; Lalit Kumar; Srinivasan Krishnamurthi

doi:10.1016/j.scitotenv.2024.172995

Phylogenomic evaluation of Mangrovimicrobium sediminis gen. nov. sp. nov., the first nitrogen fixing member of the family Halieaceae adapted to mangrove habitat and reclassification of Halioglobus pacificus to Pseudohaliglobus pacificus comb. nov

Sci Total Environ. 2024 Jul 10:933:172995. doi: 10.1016/j.scitotenv.2024.172995. Epub 2024 May 6.

Authors

Pravin Kumar¹, Ashish Verma², Pooja Yadav¹, Joyasree Das¹, Lalit Kumar¹, Srinivasan Krishnamurthi³

Affiliations

¹ Microbial Type Culture Collection & Gene Bank (MTCC), CSIR- Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India.
² Microbial Type Culture Collection & Gene Bank (MTCC), CSIR- Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India; Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden; Umeå Marine Sciences Centre, Hörnefors, Sweden.
³ Microbial Type Culture Collection & Gene Bank (MTCC), CSIR- Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India. Electronic address: kmurthi@imtech.res.in.

PMID: 38719044
DOI: 10.1016/j.scitotenv.2024.172995

Abstract

The taxonomic position and genomic characteristics of a nitrogen fixing and polymer degrading marine bacterium, strain SAOS 164 isolated from a mangrove sediment sample was investigated. Sequence analysis based on 16S rRNA gene identified it as a member of family Halieaceae with closest similarity to Haliea salexigens DSM 19537^T (96.3 %), H. alexandrii LZ-16-2^T (96.2 %) and Parahaliea maris HSLHS9^T (96.0 %) but was distantly related to the genera Haliea, Parahaliea and Halioglobus in phylogenetic trees. In order to ascertain the exact taxonomic position, phylogeny based on RpoBC proteins, whole genome, core and orthologous genes, and comparative analysis of metabolic potential retrieved the strain in an independent lineage clustering along with the genera Halioglobus, Pseudohalioglobus and Seongchinamella. Further, various genome based delimitation parameters represented by mol % GC content, percentage of conserved proteins (POCP), and amino acid identity (AAI) along with chemotaxonomic markers (i.e. fatty acids and polar lipids) supported the inferences of genome based phylogeny and indicated that the strain SAOS 164 belongs to a novel genus. The genome was mapped to 4.8 Mb in size with 65.1 % DNA mol% G + C content. In-silico genomic investigation and phenotyping revealed diverse metabolite genes/pathways related to polymer hydrolysis, nitrogen fixation, light induced growth, carbohydrate, sulfur, phosphorus and amino acid metabolism, virulence factors, defense mechanism, and stress-responsive elements facilitating survival in the mangrove habitat. Based on polyphasic taxonomic approach including genome analyses, a novel genus Mangrovimicrobium sediminis gen. nov. sp. nov. (=SAOS 164^T = MTCC 12907^T = KCTC 52755^T = JCM 32136^T) is proposed. Additionally, the reclassification of Halioglobus pacificus (=DSM 27932^T = KCTC 23430^T = S1-72^T) to Pseudhalioglobus pacificus comb. nov. is also proposed.

Keywords: AAI; ANI; Halieaceae; Mangrove habitat; POCP; Polyphasic taxonomy; Salim Ali bird sanctuary; TYGS; WGS.

MeSH terms

Genome, Bacterial
Nitrogen Fixation*
Phylogeny*
RNA, Ribosomal, 16S / genetics
Wetlands*

Substances

RNA, Ribosomal, 16S