Leucogemmata humicola gen. nov., sp. nov., an oligotrophic bacterium of the under-represented phylum Gemmatimonadota isolated from soil.

Abstract

A novel slow-growing bacterium, designated strain ag2_l2_5AT, was isolated from pine forest soil at Kagamiyama, Hiroshima, Japan, by using a gel microdroplet cultivation approach. The strain was characterized as a Gram-negative, non-motile bacterium with a short rod-shaped morphology. The strain formed small, circular, smooth and umbonate colonies after prolonged incubation on agar plates. Cells accumulated intracellular polyphosphate and produced membrane vesicles during the exponential growth phase. The strain grew optimally at 20-30 °C and pH 6.0-7.5, utilizing various sugars, amino acids and organic acids as carbon sources. The genomic G+C content was 62.8%. The major fatty acids were iso-C15 : 0, C16 : 1 ω7c, iso-C16 : 0, iso-C17 : 0 and C16 : 0. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain ag2_l2_5AT belongs to the class Gemmatimonadetes within the phylum Gemmatimonadota. Its closest relatives were Gemmatimonas phototrophica AP64T (91.3% gene sequence similarity), Gemmatimonas aurantiaca T-27T and Pseudogemmatithrix spongiicola 318T. Based on polyphasic characterization, the strain ag2_l2_5AT represents a novel genus and species of the class Gemmatimonadetes, for which the name Leucogemmata humicola gen. nov., sp. nov. is proposed. The type strain is ag2_l2_5AT (=NBRC 117234T=DSM120521T).