Rhodococcus soli sp. nov., an actinobacterium isolated from soil using a resuscitative technique

Abstract

A Gram-positive, aerobic, non-motile, non-spore forming strain, designated DSD51W(T), was isolated using a resuscitative technique from a soil sample collected from Kyoto park, Japan, and characterized by using a polyphasic approach. The morphological and chemotaxonomic properties of the isolate were typical of those of members of the genus Rhodococcus. Strain DSD51W(T) was found to form a coherent cluster with Rhodococcus hoagii ATCC 7005(T), Rhodococcus equi NBRC 101255(T), Rhodococcus defluvii Call(T) and Rhodococcus kunmingensis YIM 45607(T) as its closest phylogenetic neighbours in 16S rRNA gene sequence analysis. However, the DNA-DNA hybridization values with the above strains were 58.2 ± 2.2, 58.4 ± 1.9, 45.1 ± 1.4 and 40.3 ± 4.7 %, respectively. In combination with differences in physiological and biochemical properties, strain DSD51W(T) can be concluded to represent a novel species of the genus Rhodococcus, for which the name Rhodococcus soli sp. nov. is proposed, with the type strain DSD51W(T) (=KCTC 29259(T) = JCM 19627(T) = DSM 46662(T) = KACC 17838(T)).

Genomic Characteristics and Pan-Genome Analysis of Rhodococcus equi

“…In our study, the genome of plasmid type-B R. equi isolated from HIV patients was determined for the first time, the average genome size of the four clinical isolates sequenced was 5.16M, average GC content was 68.57%, it is consistent with the general characteristics of R. equi genome. Previous studies have pointed out that the phylogenetic position of the species based on equivocal 16S rDNA and numerical phenetic studies has been repeatedly questioned, meanwhile, the ANI value of species well above the consensus 95-96% threshold for prokaryotic species demarcation (mean ANI value was 99.13%) ( Guo et al., 2015 ; Li et al., 2015 ; Anastasi et al., 2016 ; Sangal et al., 2016 ). To more clearly identify the strains in this study, we collected the genomes of all Rhodococcus in the public database for ANI analysis.…”

Alcaligenes endophyticus sp. nov., isolated from roots of Ammodendron bifolium

“…The G+C content of the genomic DNA was determined by HPLC [19] using Escherichia coli DH5a as the reference strain. DNA-DNA relatedness was carried out by the fluorometric micro-well method [20,21] at the optimal hybridization temperature (50 C).…”

Challenges of unculturable bacteria: environmental perspectives

“…Since the natural milieu usually contains every nutrient required for bacterial growth, isolation techniques that stimulate the environment in the laboratory and in situ cultivation have been attracting attention during the last decade (Table 3). The main focus, however, has been on the resuscitation of VBNC bacteria (Table 4) in response to the addition of recombinant Rpf or extracellular organic matter (EOM) from M. luteus (also called supernatant Rpf or SRpf) (Su et al 2012(Su et al , 2015aLi et al 2014bLi et al , 2015Zou et al 2014;Jin et al 2017). EOM is the sterile filtered culture supernatant of M. luteus grown on LMM and composed mainly of proteins and polysaccharides with concentrations of 25.1 and 405.7 mg L -1 , respectively.…”

“…Aiming to map the importance of VBNC bacteria in industrial wastewater and improve sewage treatment systems, Gordonia jinhuaensis ZYR51 T (as a novel species of the genus Gordonia) was isolated, along with other strains, from pharmaceutical wastewater, using Rpf (Fu et al 2014;Li et al 2014b;Zou et al 2014). The novel strains Rhodococcus soli DSD51W T (Li et al 2015) and Arthrobacter liuii DSXY973 T (Yu et al 2015) belonging to the genus Rhodococcus and Arthrobacter, respectively, were resuscitated from soil samples. Use of recombinant Rpf protein promoted the isolation of unique bacterial species from waste composting sample and enhanced the cellulase activity of enrichment cultures.…”