Pedomonas mirosovicensis gen. nov., sp. nov., a bacterium isolated from soil with the aid of Micrococcus luteus culture supernatant containing resuscitation-promoting factor

Abstract

An orange-golden iridescent culture, designated A1X5R2T, was isolated from a compost soil suspension which was amended with Micrococcus luteus NCTC 2665T culture supernatant. The cells were non-motile, Gram-stain-negative, 0.4–0.5 µm wide and 0.7–1.4 µm long. The 16S rRNA-based phylogenetic and whole-genome analyses revealed that strain A1X5R2T forms a distinct lineage within the family Sphingosinicellaceae and is closely related to members of the genus Sphingoaurantiacus ( S. capsulatus , 93.04 % similarity, and S. polygranulatus , 92.77 %). The organism grew at 22–47 °C (optimal at 37 °C), salinity <3 % (optimal at 1.5 %) and at pH 7. The major respiratory quinone was ubiquinone-10, but a small quantity of ubiquinone-9 was also detected The major polyamine was homospermidine, but a small quantity of putrescine was also detected. The strain contained C18 : 1ω7c, C16 : 0, C16 : 1 ω7c and C18 : 0 as the major fatty acids. The main polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphatidylinositol, sphingoglycolipid, diphosphatidylglycerol, two unidentified phospholipids and three unidentified amino lipids. The DNA G+C content was 64.9 mol%. According to the results of phylogenetic and phylogenomic analyses, as well as its physiological characteristics, strain A2X5R2T represents the type species of a novel genus within the family Sphingosinicellaceae . The name Pedomonas mirosovicensis gen. nov., sp. nov. is proposed, with the type strain being A1X5R2T (=NCCB 100839T=DSM 112829T).

Reaching unreachables: Obstacles and successes of microbial cultivation and their reasons

“…Lopez Marin ( Lopez Marin et al, 2021 ) isolated 51 novel bacterial species belonging mainly to the phyla Actinomycetota , Pseudomonadota , and Bacteroidota on reasoner’s 2A (R2A) agar and an agar made from the soil’s water-soluble fraction after supplementing Micrococcus luteus Rpf-containing supernatant to soils. Some of these species were members of novel genera, such as Pedomonas mirosovicensis of the family Sphingosinicellaceae , or Solicola gregarius of the family Nocardioidaceae ( Lopez Marin et al, 2022 , 2023 ). Spent supernatants containing growth factors have also aided the cultivation of Chloroflexota strains ( Xian et al, 2020 ) or Leucobacter , the growth of which was supported through the action of zincmethylphyrins and coproporphyrins produced by Sphingopyxis sp.…”

Solicola gregarius gen. nov., sp. nov., a soil actinobacterium isolated after enhanced cultivation with Micrococcus luteus culture supernatant

“…The culture was recovered after 3 days of growth on 1/10 R2A, along with other colonies [4]. This technique has enabled several other novel bacteria to be cultured, especially from the phyla Pseudomonadota and Actinomycetota ; one such isolate, Pedomonas mirosovicensis strain A1X5R2 T , has been described recently [10]. After its initial isolation from 1/10 R2A plates, plate count agar (PCA; Oxoid) was also used to cultivate A5X3R13 T .…”