Description and Whole-Genome Sequencing of Mariniflexile litorale sp. nov., Isolated from the Shallow Sediments of the Sea of Japan

• Published in: Microorganisms (Basel) Vol. 12; no. 7; p. 1413
• Main Authors: Romanenko, Lyudmila, Bystritskaya, Evgeniya, Savicheva, Yuliya, Eremeev, Viacheslav, Otstavnykh, Nadezhda, Kurilenko, Valeriya, Velansky, Peter, Isaeva, Marina
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 12-07-2024
• Subjects: Aquatic environment; Aquatic plants; Bacteroidota; chromosome; CRISPR; Deoxyribonucleic acid; DNA; Gene families; Gene sequencing; Genes; Genomes; Genomic analysis; Hybridization; Lipids; marine bacteria; Marine sediments; Mariniflexile litorale sp. nov; Menaquinones; Microorganisms; Motility; New species; Nucleotide sequence; Nucleotides; pan-genome analysis; Pectin; Phosphatidylethanolamine; Phospholipids; Phylogenetics; Phylogeny; Protein transport; rRNA 16S; Seawater; Sediment samplers; Sediments; shallow sediments; Strain analysis; Substrates; Whole genome sequencing; Sea of Japan; United Kingdom > UK; United States > US; Japan; Germany; Russia; shallow sediments; marine bacteria; pan-genome analysis; Bacteroidota; Mariniflexile litorale sp. nov; chromosome
• ISSN: 2076-2607; 2076-2607
• DOI: 10.3390/microorganisms12071413

A Gram-negative, aerobic, rod-shaped, non-motile, yellow-pigmented bacterium, KMM 9835
, was isolated from the sediment sample obtained from the Amur Bay of the Sea of Japan seashore, Russia. Phylogenetic analyses based on the 16S rRNA gene and whole genome sequences positioned the novel strain KMM 9835
in the genus
as a separate line sharing the highest 16S rRNA gene sequence similarities of 96.6% and 96.2% with
RSSK-9
and
SW5
, respectively, and similarity values of <96% to other recognized
species. The average nucleotide identity and digital DNA-DNA hybridization values between strain KMM 9835
and
KCTC 32427
,
KCTC 12570
,
DSM 18792
, and
M5A1M
were 83.0%, 82.5%, 83.4%, and 78.3% and 30.7%, 29.6%, 29.5%, and 24.4%, respectively. The genomic DNA GC content of strain KMM 9835
was 32.5 mol%. The dominant menaquinone was MK-6, and the major fatty acids were iso-C15:0, iso-C15:1ω10c, and C15:0. The polar lipids of strain KMM 9835
consisted of phosphatidylethanolamine, two unidentified aminolipids, an unidentified phospholipid, and six unidentified lipids. A pan-genome analysis showed that the KMM 9835
genome encoded 753 singletons. The annotated singletons were more often related to transport protein systems (SusC), transcriptional regulators (AraC, LytTR, LacI), and enzymes (glycosylases). The KMM 9835
genome was highly enriched in CAZyme-encoding genes, the proportion of which reached 7.3%. Moreover, the KMM 9835
genome was characterized by a high abundance of CAZyme gene families (GH43, GH28, PL1, PL10, CE8, and CE12), indicating its potential to catabolize pectin. This may represent part of an adaptation strategy facilitating microbial consumption of plant polymeric substrates in aquatic environments near shorelines and freshwater sources. Based on the combination of phylogenetic and phenotypic characterization, the marine sediment strain KMM 9835
(=KCTC 92792
) represents a novel species of the genus
, for which the name
sp. nov. is proposed.