Rhabdothermincola sediminis gen. nov., sp. nov., a new actinobacterium isolated from hot spring sediment, and emended description of the family Iamiaceae

Abstract

One thermophilic bacterium, designated strain SYSU G02662T, was isolated from hot spring sediment sampled in Tibet, PR China. Polyphasic taxonomic analyses and whole-genome sequencing were used to determine the taxonomy position of the strain. Phylogenetic analysis using 16S rRNA gene sequences indicated that strain SYSU G02662T showed the highest sequence similarity to Actinomarinicola tropica SCSIO 58843T (95.1 %). The strain could be differentiated from other species of the family Iamiaceae by its distinct phenotypic and genotypic characteristics. Cells of strain SYSU G02662T were aerobic, Gram-staining-positive and short rodshaped. Growth occurred optimally at 45 °C and pH 7.0. In addition, meso-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. The respiratory quinone was MK-9 (H8), while the major fatty acids (>10 %) were C16 : 0, C17 : 0, C18 : 0 and iso-C16 : 0. The detected polar lipids included diphosphatidylglycerol, phosphatidylinositol mannoside and phosphatidylinositol. The G+C content of the genomic DNA was 70.5 % based on the draft genomic sequence. On the basis of phenotypic, genotypic and phylogenetic data, strain SYSU G02662T represents a novel species of a novel genus in the family Iamiaceae , for which the name Rhabdothermincola sediminis gen. nov., sp. nov. is proposed. The type strain of the proposed novel species is SYSU G02662T (=CGMCC 4.7688T=KCTC 49500T).

Cultivation of Dominant Freshwater Bacterioplankton Lineages Using a High-Throughput Dilution-to-Extinction Culturing Approach Over a 1-Year Period

“…Among the 19 strains assigned to Acidimicrobiales , 17 strains belonged to the acIV lineage ( Figure 1C ), which is another typical and abundant freshwater bacterial group that was first discovered in samples obtained from Adirondack Mountain Lake ( Hiorns et al, 1997 ), named by Warnecke et al (2004) , and subdivided into four subclades (acIV-A to D) ( Humbert et al, 2009 ; Philosof et al, 2009 ; Newton et al, 2011 ; Martinez-Garcia et al, 2012b ; Okazaki et al, 2021 ). The families Ilumatobacteriaceae ( Matsumoto et al, 2009 ) and Iamiaceae ( Kurahashi et al, 2009 ; Liu et al, 2021 ) and the genus “ Candidatus Limnosphaera” ( Kim et al, 2017 ) are considered the nearest taxa to the acIV lineage. Moreover, although the acIV lineage has been widely identified in many freshwater lakes ( Humbert et al, 2009 ; Philosof et al, 2009 ; Martinez-Garcia et al, 2012b ; Okazaki et al, 2021 ), no cultured representatives have been reported to date.…”

Thermomonas flagellata sp. nov. and Thermomonas alba sp. nov., two novel members of the phylum Pseudomonadota isolated from hot spring sediments

“…Bootstrap analysis was performed with 1000 replications [24]. Arenimonas donghaensis HO3-R19 T (DQ411038) was used as an outgroup [25]. The genomes of strains SYSU G04041 T and SYSU G04536 T were sequenced by Novogene Biotech (Beijing, PR China) using the Illumina platform.…”

Rhabdothermincola salaria sp. nov., a novel actinobacterium isolated from a saline lake sediment

“…majanohamensis and R. sediminis [5, 7–14]. To date, only a few studies have briefly described the potential ecological functions of the acidimicrobial species by metagenomic analysis [15].…”

“…Colony size, shape and colour of strain EGI L10124 T were also observed and recorded after 30 days of incubation at 30 °C on marine agar 2216. Catalase activity was detected by bubbles production with the 3 % (v/v) H 2 O 2 [7]. Oxidase activity and Gram-staining were determined with testing kits according to the manufacturer's instructions.…”

“…The family Iamiaceae, belonging to the order Iamiales, class Acidimicrobiia, was first described by Kurahashi et al and recommended by Salam et al with the type strain Iamia majanohamensis [5,6]. The genus Rhabdothermincola was first proposed as a new genus within this family by Liu et al with Rhabdothermincola sediminis SYSU G02662 T as the type species isolated from hot spring sediments [7]. However, due to the existing difficulties and challenges in isolating Acidimicrobiia members under normal culture conditions, so far only 10 species of this class have been successfully isolated, cultured and validly published, namely Desertimonas flava, Ilumatobacter fluminis, Acidiferrimicrobium australe, Acidimicrobium ferrooxidans, Ferrimicrobium acidiphilum, Ferrithrix thermotolerans, Actinomarinicola tropica, Aquihabitans daechungensis, I. majanohamensis and R. sediminis [5,[7][8][9][10][11][12][13][14].…”