Chitinophaga extrema sp. nov., isolated from subsurface soil and leaf litter in a tropical peat swamp forest

Abstract

A Gram-negative, filamentous aerobic bacterium designated as strain Mgbs1T was isolated on 12 April 2017 from the subsurface soil and leaf litter substrate at the base of a Koompassia malaccensis tree in a tropical peat swamp forest in the northern regions of the state of Selangor, Malaysia (3° 39′ 04.7′ N 101° 17′ 43.7′′ E). Phylogenetic analyses based on the full 16S rRNA sequence revealed that strain Mgbs1T belongs to the genus Chitinophaga with the greatest sequence similarity to Chitinophaga terrae KP01T (97.65 %), Chitinophaga jiangningensis DSM27406T (97.58 %), and Chitinophaga dinghuensis DHOC24T (97.17 %). The major fatty acids of strain Mgbs1T (>10 %) are iso-C15 : 0, C16 : 1 ω5c and iso-C17 : 0 3-OH while the predominant respiratory quinone is menaquinone-7. Strain Mgbs1T has a complete genome size of 8.03 Mb, with a G+C content of 48.5 mol%. The DNA–DNA hybridization (DDH) score between strain Mgbs1T and C. jiangningensis DSM27406T was 15.9 %, while in silico DDH values of strain Mgbs1T against C. dinghuensis DHOC24T and C. terrae KP01T were 20.0 and 19.10% respectively. Concurrently, Average Nucleotide Identity (ANI) scores between strain Mgbs1T against all three reference strains are 73.2 %. Based on the phenotypic, chemotaxonomic, and phylogenetic consensus, strain Mgbs1T represents a novel species of the genus Chitinophaga , for which the name Chitinophaga extrema sp. nov. is proposed (=DSM 108835T=JCM 33276T).

Chitinophaga silvatica sp. nov., isolated from forest soil, and reclassification of Chitinophaga extrema as a later heterotypic synonym of Chitinophaga solisilvae

“…These results also supported that strain K2CV101002-2 T represented a novel species within the genus Chtinophaga. According to the species descriptions [2,3], both C. extrema Mgbs1 T and C. solisilvae O9 T took iso-C 15 : 0 , C 16 : 1 ω5c and iso-C 17 : 0 3-OH as the major fatty acids with a relatively high content (7.2 and 7.8 %) of summed feature 3 (C 16 : 1 ω7c and/or C 16 : 1 ω6c) and MK-7 as the predominant respiratory quinone, which supported the conclusion of genomic and phenotypic comparisons.…”

“…Now, it belongs to the family Chitinophagaceae in the phylum Bacteroidetes while myxobacteria only refer to the group of Myxococcales in Proteobacteria. More than 41 species in the genus Chitinophaga had been validly published, including the recently described Chitinophaga extrema [2], Chitinophaga solisilvae [3], Chitinophaga fulva [4], etc., and most of them were obtained from soil, especially forest soil, such as Chitinophaga tropicalis , Chitinophaga varians , Chitinophaga silvisoli , Chitinophaga caseinilytica , Chitinophaga flava and Chitinophaga dinghuensis [5–10]. This is probably due to their roles in such environments and some Chitinophaga species have shown plant growth promoting (PGP) abilities by altering the carbon source use of their fungal hosts as endosymbiotic bacteria and decomposing both dead fungal and plants in substance recycling [11, 12].…”

“…The phenotypic characterization results supported that strain K2CV101002-2 T represented a novel distinct species of the genus Chtinophaga. Moreover, we also compared C. extrema Mgbs1 T and C. solisilvae O9 T according to the original species descriptions [2,3] and the two strains showed the same results in most phenotypic characteristics including growth media (R2A agar, NA, TSA and MacConkey agar), production of flexirubin-type pigments, enzyme activities (oxidase, catalase, acid phosphatase, alkaline phosphatase, trypsin, naphthol-AS-BI-hosphohydrolase, βgalactosidase, α-glucosidase, N-acetyl-β-glucosaminidase, leucine arylamidase, valine arylamidase and cystine arylamidase), hydrolysis of gelatin and chitin, and substrates assimilation (d-glucose, d-mannose, maltose, lactose, l-arabinose, raffinose and trehalose), which suggested that they should belong to the same species.…”

“…These results also supported that strain K2CV101002-2 T represented a novel species within the genus Chtinophaga . According to the species descriptions [2, 3], both C. extrema Mgbs1 T and C.…”

Chitinophaga rhizophila sp. nov., isolated from rhizosphere soil of banana

“…Currently, the genus Chitinophaga includes 43 validly published species as listed in the LPSN (https://lpsn.dsmz.de/genus/chitinophaga). Most members of Chitinophaga were isolated from soil environments [2–6]. In addition, some species originated from endophyte of different plants [7, 8], rock surface [9], infected humans [10], activated sludge and sediment [11, 12].…”