Complete Genome Sequence of Rhodococcus opacus Strain MoAcy1 (DSM 44186), an Aerobic Acetylenotroph Isolated from Soil

We report the genome of Rhodococcus opacus strain MoAcy1 ( DSM 44186 ), an aerobic soil isolate capable of using acetylene as its primary carbon and energy source (acetylenotrophy). The genome is composed of a single circular chromosome of ∼8 Mbp and two closed plasmids, with a G+C content of 67.3%.

Exploring the Nature of the Antimicrobial Metabolites Produced by Paenibacillus ehimensis Soil Isolate MZ921932 Using a Metagenomic Nanopore Sequencing Coupled with LC-Mass Analysis

The continuous emergence of multidrug-resistant (MDR) pathogens poses a global threat to public health. Accordingly, global efforts are continuously conducted to find new approaches to infection control by rapidly discovering antibiotics, particularly those that retain activities against MDR pathogens. In this study, metagenomic nanopore sequence analysis coupled with spectroscopic methods has been conducted for rapid exploring of the various active metabolites produced by Paenibacillus ehimensis soil isolate. Preliminary soil screening resulted in selection of a Gram-positive isolate identified via 16S ribosomal RNA gene sequencing as Paenibacillus ehimensis MZ921932. The isolate showed a broad range of activity against MDR Gram-positive, Gram-negative, and Candida spp. A metagenomics sequence analysis of the soil sample harboring Paenibacillus ehimensis isolate MZ921932 (NCBI GenBank accession PRJNA785410) revealed the presence of conserved biosynthetic gene clusters of petrobactin, tridecaptin, locillomycin (β-lactone), polymyxin, and macrobrevin (polyketides). The liquid chromatography/mass (LC/MS) analysis of the Paenibacillus ehimensis metabolites confirmed the presence of petrobactin, locillomycin, and macrobrevin. In conclusion, Paenibacillus ehimensis isolate MZ921932 is a promising rich source for broad spectrum antimicrobial metabolites. The metagenomic nanopore sequence analysis was a rapid, easy, and efficient method for the preliminary detection of the nature of the expected active metabolites. LC/MS spectral analysis was employed for further confirmation of the nature of the respective active metabolites.

A Metagenomic Nanopore Sequence Analysis Combined with Conventional Screening and Spectroscopic Methods for Deciphering the Antimicrobial Metabolites Produced by Alcaligenes faecalis Soil Isolate MZ921504

The continuous development of multidrug resistance pathogens with limited therapeutic options has become a great problem globally that impose sever health hazards. Accordingly, searching for of new antimicrobials became an urgent demand and great challenge. Soil significantly have been associated with several species that are antibiotic producers. In this study, combination of conventional screening methods with Liquid chromatography- Mass spectroscopy (LC/MS) and metagenomic nanopore sequence analysis have been conducted for the deciphering the active metabolites produced by soil isolate(s). Preliminary soil screening resulted in a Gram-negative isolate identified via 16S ribosomal RNA as Alcaligenes faecalis isolate MZ921504 with promising antimicrobial activities against wide range of MDR gram-positive and gram-negative pathogens. The LC/MS analysis of the metabolites of A. faecalis isolate MZ921504 confirmed the presence of ectoine, bacillibactin, quinolobactin and burkholderic acid. Metagenomics sequence analysis of the soil sample (NCBI GenBank accession PRJNA771993) revealed the presence of conserved biosynthetic gene clusters of ectoine, bacteriocin, bacillibactin, quinolobactin, terpene and burkholderic acid of A. faecalis. In conclusion, A. faecalis isolate MZ921504 is a promising source for antimicrobial metabolites. LC/MS spectral analysis and third generation sequencing tools followed by secondary metabolite gene clusters analysis are useful methods to predict the nature of the antimicrobial metabolites.

Flavobacterium hydrocarbonoxydans sp. nov., isolated from polluted soil

This paper presents a polyphasic taxonomic study of a Gram-stain-negative bacterium designated GA093T, a soil isolate capable of benzo(α)pyrene degradation. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain GA093T is a member of the genus Flavobacterium , and formed an independent phylogenetic line while clustering with the type strains of Flavobacterium hibernum , Flavobacterium branchiarum and Flavobacterium hydatis . Strain GA093T was facultatively anaerobic, and could grow at 4–33 °C (optimum, 30 °C), at pH 6–11 (optimum, pH 7) and in the presence of 0–2 % (w/v) NaCl (optimum, 0 %). Strain GA093T was capable of producing acid from various carbon sources, which was comparable to other related species of Flavobacterium . The strain contained MK-6 as the only isoprenoid quinone, iso-C15 : 0 as the major cellular fatty acid, phosphatidylethanolamine and phosphatidylinositol as diagnostic polar lipids, and sym-homospermidine as the major polyamine. The chemotaxonomic properties of strain GA093T were consistent with the general properties of Flavobacterium except the presence of phosphatidylinositol, which distinguished it from other related species. The total stretch of the obtained genome of GA093T was 5.05 Mbp, and the DNA G+C content was 34.79 mol%. The genome contained genes potentially related to the degradation of aromatic hydrocarbons. On the basis of the present polyphasic analysis, strain GA093T was found to have properties that distunguished it as representing a novel species of the genus Flavobacterium , for which the name Flavobacterium hydrocarbonoxydans sp. nov. is proposed. The type strain is GA093T (=KCTC 72594T=LMG 31760T).

Isolation and Extraction of PHB from Soil Isolate: Determining its Physio- Chemical characteristics with an application study in Biomedical

Biopolymer Poly Hydroxy Butyrate (PHB) is gaining importance based on its physiochemical and biological characteristics. Hence, the characteristics of the PHB extracted from soil bacterial isolate as studied with an aim of developing a 2D films for biomedical applications. The isolates from soil samples were screened for the ability to produce PHB and confirmed using Sudan black staining methods. The physio-chemical characteristics were studied using FTIR, FESEM and GCMS analysis. FTIR spectrum obtained for the extracted polymer shows peaks at 1723.51 cm-1and 1287.63 cm-1 which confirms that the extracted polymer is PHB. FESEM image reveals the presence of pores of different size throughout the sample. The surface consists of multiple pores with different sizes. GC-MS analysis revealed the presence of various compounds attributing for the PHB production from the isolate. As a biological characteristic, a novel wound dressing 2D laminate bio composite films were developed using PHB extracts. The antibacterial activity of the developed film showed significant inhibitory zones against Escherichia coli and Klebsiella pneumoniae. The present research work showed promising results and proved that the PHB obtained from bacterial sp. can be used as an alternative to non-degradable plastics with a wide range of applications in biomedical industries.

Screening and Isolation of a Novel Polyene-Producing Streptomyces Strain Inhibiting Phytopathogenic Fungi in the Soil Environment

Microbial-based eco-friendly biological substances are needed to protect crops from phytopathogenic fungi and replace toxic chemical fungicides that cause serious environmental issues. This study screened for soil antifungal Streptomyces strains, which produce rich, diverse, and valuable bioactive metabolites in the soil environment. Bioassay-based antifungal screening of approximately 2,400 Streptomyces strains led to the isolation of 149 strains as tentative antifungal producers. One Streptomyces strain showing the most potent antifungal activities against Candida albicans and Fusarium oxysporum was identified as a putative anti-phytopathogenic soil isolate that is highly homologous to Streptomyces rubrisoli (named S. rubrisoli Inha 501). An in vitro antifungal assay, pot-test, and field-test against various phytopathogenic fungi confirmed that S. rubrisoli Inha 501 is a potential novel phytopathogenic fungicide producer to protect various crops in the soil environment. Whole-genome sequencing of S. rubrisoli Inha 501 and an anti-SMASH genome mining approach revealed an approximately 150-kb polyene biosynthetic gene cluster (BGC) in the chromosome. The target compound isolation and its BGC analysis confirmed that the giant linear polyene compound exhibiting the anti-phytopathogenic activity in S. rubrisoli Inha 501 was highly homologous to the previously reported compound, neotetrafibricin A. These results suggest that a bioassay-based screening of a novel antifungal Streptomyces strain followed by its genome mining for target compound BGC characterization would be an efficient approach to isolating a novel candidate phytopathogenic fungicide that can protect crops in the soil environment.

Complete genome resources for Ralstonia bacterial wilt strains UW763 (phylotype I); Rs5, UW700 (phylotype II); UW386, RUN2474, RUN2279 (phylotype III)

We share whole genome sequences of six strains from the Ralstonia solanacearum species complex, a diverse group of beta-Proteobacteria that cause plant vascular wilt diseases. Using single-molecule real-time (SMRT) technology, we sequenced and assembled full genomes of Rs5 and UW700, two phylotype IA-sequevar 7 (IIA-7) strains from the southeastern US that are closely related to the R. solanacearum species type strain, K60, but were isolated >50 years later. Four sequenced strains from Africa include a soil isolate from Nigeria (UW386, III-23), a tomato isolate from Senegal (UW763, I-14), and two potato isolates from the Madagascar highlands (RUN2474, III-19 and RUN2279, III-60). This resource will support studies of the genetic diversity, ecology, virulence, and microevolution of this globally distributed group of high-impact plant pathogens.

Phenotype and Virulence Assessment of a Burkholderia pseudomallei Soil Isolate from Malaysia

Burkholderia pseudomallei, a Gram-negative soil saprophyte, is the causative agent of life-threatening melioidosis. B. pseudomallei from soil and water remains a common source of human and animal infection via skin abrasions, ingestion or inhalation. Despite the reported sero-prevalence in healthy individuals among Malaysian rice farmers, there are limited reports on B. pseudomallei isolated from water or soil around the country. In this study, we characterized a B. pseudomallei soil isolate and compared it to local clinical isolates. 16s rRNA sequencing was adopted to confirm the identity of the soil isolate, NC20. B. pseudomallei NC20 colony morphology, in vitro growth rate and antibiotic sensitivity were examined and compared to two B. pseudomallei clinical isolates, UM6 and D286. Virulence properties such as biofilm formation and infection in a nematode host were also examined. The soil isolate NC20 exhibited distinguishable features of B. pseudomallei, comparable growth rate and similar antibiotic resistance profile to UM6 and D286. Additionally, NC20 is a medium-level biofilm producer with levels similar to D286, where the amount of biofilm produced was much less relative to UM6. Interestingly, NC20 exhibited weaker killing of the Caenorhabditis elegans infection model relative to the clinical isolates. The comparison between soil-derived and clinical isolates of B. pseudomallei demonstrated that both soil and clinical isolates shared certain phenotypic properties but the soil isolate was somewhat less virulent than the clinical isolates used in this study.