Complete Genome Sequence of Pseudomonas balearica DSM 6083T

Biocontrol Effect of Bacillus velezensis D7-8 on Potato Common Scab and Its Complete Genome Sequence Analysis

Potato common scab, caused by Streptomyces species, is a widespread soil-borne disease that poses a significant threat to potato cultivation globally. In this study, a Bacillus velezensis D7-8 strain was isolated from a potato. This endophytic bacterium exhibited broad-spectrum antifungal activity, and pot trials demonstrated that the D7-8 strain effectively controlled potato common scab with an efficacy of 42.07%. The complete genome sequence of the D7-8 strain was sequenced and subsequently identified as B. velezensis through multiple bioinformatic methods, primarily through structural variation analysis of whole-genome sequences. The machine learning method predicted that the expression profiles of colinear genes among closely related Bacillus species were highly consistent. Metabolite analysis of crude extracts using ultra-high-performance liquid chromatography coupled with quadrupole-Orbitrap high-resolution mass spectrometry (UPLC-Q-Exactive HRMS) revealed that D7-8 produces bioactive compounds, including surfactin and fengycin, both known for their antimicrobial properties. This study elucidates the antagonistic effect of B. velezensis D7-8 against Streptomyces acidiscabies and provides a valuable reference for future research on accurate microbial identification.

Use of Taguchi design for optimization of diesel-oil biodegradation using consortium of Pseudomonas stutzeri, Cellulosimicrobium cellulans, Acinetobacter baumannii and Pseudomonas balearica isolated from tarball in Terengganu Beach, Malaysia

A consortium of bacteria capable of decomposing oily hydrocarbons was isolated from tarballs on the beaches of Terengganu, Malaysia, and classified as Pseudomonas stutzeri, Cellulosimicrobium cellulans, Acinetobacter baumannii and Pseudomonas balearica. The Taguchi design was used to optimize the biodegradation of diesel using these bacteria as a consortium. The highest biodegradation of diesel-oil in the experimental tests was 93.6%, and the individual n-alkanes decomposed 87.6-97.6% over 30 days. Optimal settings were inoculum size of 2.5 mL (1.248 OD_600nm); 12% (v/v) the initial diesel-oil in a minimal salt medium of pH 7.0, 30.0 gL^-1 NaCl and 2.0 gL^-1 NH₄NO₃ concentration, incubated at 42 °C temperature and 150 rpm agitation speed. Parameters significantly improved diesel-oil removal by consortium as shown by the model determination coefficient (R² = 90.89%; P < 0.001) with a synergistic effect of agitation speed significantly contributing 81.03%. Taguchi design determined the optimal settings for the parameters under study, which significantly improved diesel-oil removal by consortium. This can be used to design a novel bioremediation strategy that can achieve optimal decontamination of oil pollution in a shorter time.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s40201-022-00812-3.

Evaluation of a novel, multi-functional inhibitor compound for prevention of biofilm formation on carbon steel in marine environments

Chemical biocides remain the most effective mitigation strategy against microbiologically influenced corrosion (MIC), one of the costliest and most pervasive forms of corrosion in industry. However, toxicity and environmental concerns associated with these compounds are encouraging the development of more environmentally friendly MIC inhibitors. In this study, we evaluated the antimicrobial effect of a novel, multi-functional organic corrosion inhibitor (OCI) compound, cetrimonium trans-4-hydroxy-cinnamate (CTA-4OHcinn). Attachment of three bacterial strains, Shewanella chilikensis, Pseudomonas balearica and Klebsiella pneumoniae was evaluated on wet-ground (120 grit finish) and pre-oxidised carbon steel surfaces (AISI 1030), in the presence and absence of the new OCI compound. Our study revealed that all strains preferentially attached to pre-oxidised surfaces as indicated by confocal laser scanning microscopy, scanning electron microscopy and standard colony forming unit (CFU) quantification assays. The inhibitor compound at 10 mM demonstrated 100% reduction in S. chilikensis attachment independent of initial surface condition, while the other two strains were reduced by at least 99.7% of the original viable cell number. Our results demonstrate that CTA-4OHcinn is biocidal active and has promise as a multifunctional, environmentally sound MIC inhibitor for industrial applications.

Heterotrophic nitrifying/aerobic denitrifying bacteria: Ammonium removal under different physical-chemical conditions and molecular characterization

Biological ammonium removal via heterotrophic nitrification/aerobic denitrification (HN/AD) was characterized for two isolates from a wastewater treatment station (WWTS). They were identified as Pseudomonas balearica UFV3 and Gordonia amicalis UFV4. Their ability to remove ammonium via NH/DA was validated by chromatography, and the influence of different physical-chemical factors on removal was evaluated. The presence of genes involved in conventional nitrification and denitrification processes was investigated via PCR and comparative genomics. Both isolates removed 100% of the ammonium in a medium containing citrate as its carbon source with a C/N ratio of 8, 3% salt, pH 7 and 30 °C. Nitrogen balance showed that approximately 55% of the ammonium removed was lost as N_2(g), and 45% was assimilated. Molecular characterization revealed the absence of genes involved in autotrophic nitrification in the genome of the two isolates and the presence of genes involved in anaerobic denitrification only in P. balearica UFV3, suggesting the involvement of other genes in the HN/AD process. This was the first report of G. amicalis and P. balearica with the capability for HN/AD.

Genomic Analysis of Pseudomonas sp. Strain SCT, an Iodate-Reducing Bacterium Isolated from Marine Sediment, Reveals a Possible Use for Bioremediation

Strain SCT is an iodate-reducing bacterium isolated from marine sediment in Kanagawa Prefecture, Japan. In this study, we determined the draft genome sequence of strain SCT and compared it to complete genome sequences of other closely related bacteria, including Pseudomonas stutzeri. A phylogeny inferred from concatenation of core genes revealed that strain SCT was closely related to marine isolates of P. stutzeri. Genes present in the SCT genome but absent from the other analyzed P. stutzeri genomes comprised clusters corresponding to putative prophage regions and possible operons. They included pil genes, which encode type IV pili for natural transformation; the mer operon, which encodes resistance systems for mercury; and the pst operon, which encodes a Pi-specific transport system for phosphate uptake. We found that strain SCT had more prophage-like genes than the other P. stutzeri strains and that the majority (70%) of them were SCT strain-specific. These genes, encoded on distinct prophage regions, may have been acquired after branching from a common ancestor following independent phage transfer events. Thus, the genome sequence of Pseudomonas sp. strain SCT can provide detailed insights into its metabolic potential and the evolution of genetic elements associated with its unique phenotype.

Genome Sequences of Two Naphthalene-Degrading Strains of Pseudomonas balearica, Isolated from Polluted Marine Sediment and from an Oil Refinery Site

The genome sequences of Pseudomonas balearica strains LS401 (CCUG 66666) and st101 (CCUG 66667) have been determined. The strains were isolated as naphthalene degraders from polluted marine sediment and from a sample from an oil refinery site, respectively. These genomes provide essential data about the biodegradation capabilities and the ecological implications of P. balearica.