A stable home for an equine pathogen: valid publication of the binomial Prescottella equi gen. nov., comb. nov., and reclassification of four rhodococcal species into the genus Prescottella

Opinion 106 of the Judicial Commission has clarified the nomenclature of the taxon variously named Rhodococcus equi , ‘Prescottella equi’ and Rhodococcus hoagii . As a consequence, we present here the genus name Prescottella and that of its nomenclatural type species, Prescottella equi comb. nov., for valid publication and propose the reclassification of four rhodococcal species as novel combinations in the genus, namely Prescottella agglutinans Guo et al. 2015 comb. nov., Prescottella defluvii Kämpfer et al. 2014 comb. nov., Prescottella soli Li et al. 2015 comb. nov. and Prescottella subtropica Lee et al. 2019 comb. nov. In addition, we note that a clinical isolate, strain 86–07 (=W8901), likely represents an additional species within the genus Prescottella . Nearly a century after the original description of the type strain of the type species as Corynebacterium equi , we provide a stable home for Prescottella equi and its relatives.

Isolation, Characterization, and Antibiofilm Activity of Pigments Synthesized by Rhodococcus sp. SC1

Infections from multi-drug resistant bacteria and biofilms constitute a serious problem worldwide. There is a need for new antibacterial and antibiofilm compounds in the fight against infectious diseases. In recent years, pigment-producing microorganisms have drawn a great deal of attention as a promising source for antibacterial and antibiofilm compounds. Here, we report the antibacterial and antibiofilm activity of pigments synthesized by bacteria isolated from soil. This study aimed to perform an evaluation of the antibacterial, antibiofilm, and characteristic of crude pigments from Rhodococcus sp. SC1 isolates. The total pigment extract exhibited antibacterial activity against Gram-positive and Gram-negative reference bacteria with required minimum inhibitory concentration (MIC) values ranging from 64 to 256 µg/ml. Moreover, it reduced biofilm formation of Gram-negative reference bacteria at sub-MIC concentration. For characterization of the pigments, UV-absorbance, thin layer chromatography, fourier transform infrared spectroscopy, and QTOF-LC/MS analyses were performed. The results of this study showed that pigments of Rhodococcus sp. SC1 isolates can be a candidate for medical applications.

Rhodococcus spelaei sp. nov., isolated from a cave, and proposals that Rhodococcus biphenylivorans is a later synonym of Rhodococcus pyridinivorans, Rhodococcus qingshengii and Rhodococcus baikonurensis are later synonyms of Rhodococcus erythropolis, and Rhodococcus percolatus and Rhodococcus imtechensis are later synonyms of Rhodococcus opacus

Two novel actinobacterial strains, designated C9-5^T and C3-43, were isolated from soil samples of a cave in Jeju Island, Republic of Korea, and subjected to taxonomic study by a polyphasic approach. The organisms exhibited a typical rod-coccus developmental cycle during growth and grew at 10-30 °C, pH 5-9 and 0-3 % (w/v) NaCl. In 92 single-copy core gene sequence analysis, strain C9-5^T was loosely associated with Rhodococcus tukisamuensis, albeit sharing low 16S rRNA gene sequence similarity (97.4 %). A combination of morphological and chemotaxonomic characteristics supported assignment with the genus Rhodococcus. With respect to 16S rRNA gene sequence similarity, the novel isolates showed the highest identity to the type strain of Rhodococcus subtropicus (98.7 % sequence similarity), followed by Rhodococcus olei (98.5 %) and Rhodococcus pedocola (98.4 %).The average nucleotide identity and digital DNA-DNA hybridization values between strain C9-5^T and members of the genus Rhodococcus were ≤81.5 and ≤37.1 %, respectively. A set of physiological and chemotaxonomic properties together with overall genomic relatedness differentiated the novel isolates from members of the genus Rhodococcus, for which the name Rhodococcus spelaei sp. nov. is proposed. The type strain is C9-5^T (=KACC 19822^T=DSM 107558^T). Based on genome analysis performed here, it is also proposed that Rhodococcus biphenylivorans Su et al. 2015 is a later heterotypic synonym of Rhodococcus pyridinivorans Yoon et al. 2000, Rhodococcus qingshengii Xu et al. 2007 and Rhodococcus baikonurensis Li et al. 2004 are later heterotypic synonyms of Rhodococcus erythropolis (Gray and Thornton 1928) Goodfellow and Alderson 1979 (Approved Lists 1980), and Rhodococcus percolatus Briglia et al. 1996 and Rhodococcus imtechensis Ghosh et al. 2006 are later heterotypic synonyms of Rhodococcus opacus Klatte et al. 1995.

Enhanced polyhydroxybutyrate (PHB) production by newly isolated rare actinomycetes Rhodococcus sp. strain BSRT1-1 using response surface methodology

Poly-β-hydroxybutyrate (PHB) is a biodegradable polymer, synthesized as carbon and energy reserve by bacteria and archaea. To the best of our knowledge, this is the first report on PHB production by a rare actinomycete species, Rhodococcus pyridinivorans BSRT1-1. Response surface methodology (RSM) employing central composite design, was applied to enhance PHB production in a flask scale. A maximum yield of 3.6 ± 0.5 g/L in biomass and 43.1 ± 0.5 wt% of dry cell weight (DCW) of PHB were obtained when using RSM optimized medium, which was improved the production of biomass and PHB content by 2.5 and 2.3-fold, respectively. The optimized medium was applied to upscale PHB production in a 10 L stirred-tank bioreactor, maximum biomass of 5.2 ± 0.5 g/L, and PHB content of 46.8 ± 2 wt% DCW were achieved. Furthermore, the FTIR and ¹H NMR results confirmed the polymer as PHB. DSC and TGA analysis results revealed the melting, glass transition, and thermal decomposition temperature of 171.8, 4.03, and 288 °C, respectively. In conclusion, RSM can be a promising technique to improve PHB production by a newly isolated strain of R. pyridinivorans BSRT1-1 and the properties of produced PHB possessed similar properties compared to commercial PHB.

Rhodococcus oryzae sp. nov., a novel actinobacterium isolated from rhizosphere soil of rice (Oryza sativa L.)

A Gram-stain-positive, non-motile, creamy-white actinobacterium, which has an elementary branching rod-coccus life cycle was isolated from the rhizosphere soil of rice (Oryza sativa L.) collected from Northeast Agricultural University in Harbin, Heilongjiang province, north-east PR China, and its taxonomic status was examined by using a polyphasic approach. Results from the 16S rRNA gene sequence study showed that the isolate, designated strain NEAU-CX67^T, belonged to the genus Rhodococcus and formed a cluster with Rhodococcus maanshanensis DSM 44675^T, Rhodococcus kronopolitis NEAU-ML12^T and Rhodococcus tukisamuensis JCM 11308^T (98.3, 98.1 and 97.7% gene sequence similarity, respectively). The major fatty acids were C_16 : 0, 10-methyl C_18 : 0, C_18 : 1 ω9c and C_16 : 1 ω7c. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The major isoprenoid quinone was MK-8(H₂). Whole-cell hydrolysates contained meso-diaminopimelic acid. Arabinose, galactose and ribose were detected as diagnostic sugars from whole-cell hydrolysates. Mycolic acids were detected. The genomic DNA G+C content of strain NEAU-CX67^T was 64.6 mol%. Strain NEAU-CX67^T exhibited low average nucleotide identity and digital DNA-DNA hybridization values with R. maanshanensis DSM 44675^T (92.1 and 45.4 %) and R. tukisamuensis JCM 11308^T (81.9 and 24.4 %). On the basis of results of phylogenetic, genotypic, physiological and chemotaxonomic analysis, strain NEAU-CX67^T is considered to represent a novel species of the genus Rhodococcus for which the name Rhodococcus oryzae sp. nov. is proposed. The type strain is NEAU-CX67^T (=DSM 107701^T=CCTCC AB 2018233^T).

Fungicides enhanced the abundance of antibiotic resistance genes in greenhouse soil

Long-term substantial application of fungicides in greenhouse cultivation led to residual pollution in soils and then altered soil microbial community. However, it is unclear whether residual fungicides could affect the diversity and abundance of antibiotic resistance genes (ARGs) in greenhouse soils. Here, the dissipation of fungicides and its impact on the abundance of ARGs were determined using shotgun metagenomic sequencing in the greenhouse and mountain soils under laboratory conditions. Our results showed the greenhouse soils harbored more diverse and abundant ARGs than the mountain soils. The application of carbendazim, azoxystrobin, and chlorothalonil could increase the abundance of total ARGs in the greenhouse soils, especially for those dominant ARG subtypes including sul2, sul1, aadA, tet(L), tetA(G), and tetX2. The abundant ARGs were significantly correlated with mobile genetic elements (MGEs, e.g. intI1and R485) in the greenhouse soils but no significant relationship in the mountain soils. Meanwhile, the co-occurrence patterns of ARGs and MGEs, e.g., sul2 and R485, sul1 and transposase, were further verified via the genetic arrangement of genes on the metagenome-assembled contigs in the greenhouse soils. Additionally, host tracking analysis indicated that ARGs were mainly carried by enterobacteria in the greenhouse soils but actinomyces in the mountain soils. These findings confirmed that some fungicides might serve as the co-selectors of ARGs and elevated their abundance via MGEs-mediated horizontal gene transfer in the greenhouse soils.

Sphingobium aromaticivastans sp. nov., a novel aniline- and benzene-degrading, and antimicrobial compound producing bacterium

A strictly aerobic, orange-pigmented strain was isolated and designated as UCM-25^T. This strain is capable of degrading aniline and benzene, while is also producing antimicrobial compounds which inhibit the growth of some common pathogenic microbes. A near full-length 16S rRNA gene sequence revealed similarity to Sphingobium chlorophenolicum NBRC 16172^T (98.6%). The level of DNA-DNA hybridization between the new isolate and the related species suggests UCM-25^T to be a new species belonging to the genus Sphingobium. The bacterial cells contained phosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid, phosphatidylcholine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, three unidentified polar lipids, and an unidentified aminophospholipid. Ubiquinone Q-10 was the major quinone and spermidine was the major polyamine. The G+C content in the DNA of strain UCM-25^T was 62.9 mol%. Cells contained summed feature 8 (C_18:1ω7c and/or C_18:1ω6c), summed feature 3 (C_16:1ω7c and/or C_16:1ω6c), C_16:0, and C_14:0 2-OH as major fatty acids. Based on the comparison of phenotypic, genotypic, and chemotaxonomic characteristics, strain UCM-25^T represents a new member of the genus Sphingobium, for which the name S. aromaticivastans sp. nov. is proposed. The type strain is UCM-25^T (=KACC 19288^T =DSM 105181^T).

Current taxonomy of Rhodococcus species and their role in infections

Rhodococcus is a genus of obligate aerobic, Gram-positive, partially acid-fast, catalase-positive, non-motile, and none-endospore bacteria. The genus Rhodococcus was first introduced by Zopf. This bacterium can be isolated from various sources of the environment and can grow well in non-selective medium. A large number of phenotypic characterizations are used to compare different species of the genus Rhodococcus, and these tests are not suitable for accurate identification at the genus and species level. Among nucleic acid-based methods, the most powerful target gene for revealing reliable phylogenetic relationships is 16S ribosomal RNA gene (16S rRNA gene) sequence analysis, but this gene is unable to differentiation some of Rhodococcus species. To date, whole genome sequencing analysis has solved taxonomic complexities in this genus. Rhodococcus equi is the major cause of foal pneumonia, and its implication in human health is related to cases in immunocompromised patients. Macrolide family together with rifampicin is one of the most effective antibiotic agents for treatment rhodococcal infections.