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Multilocus sequence based identification and adaptational strategies of Pseudomonas sp. from the supraglacial site of Sikkim Himalaya.

ABSTRACT: Microorganisms inhabiting the supraglacial ice are biotechnologically significant as they are equipped with unique adaptive features in response to extreme environmental conditions of high ultraviolet radiations and frequent freeze-thaw. In the current study, we obtained eleven strains of Pseudomonas from the East Rathong supraglacial site in Sikkim Himalaya that showed taxonomic ambiguity in terms of species affiliation. Being one of the most complex and diverse genera, deciphering the correct taxonomy of Pseudomonas species has always been challenging. So, we conducted multilocus sequence analysis (MLSA) using five housekeeping genes, which concluded the taxonomic assignment of these strains to Pseudomonas antarctica. This was further supported by the lesser mean genetic distances with P. antarctica (0.73%) compared to P. fluorescens (3.65%), and highest ANI value of ~99 and dDDH value of 91.2 of the representative strains with P. antarctica PAMC 27494. We examined the multi-tolerance abilities of these eleven Pseudomonas strains. Indeed the studied strains displayed significant tolerance to freezing for 96 hours compared to the mesophilic control strain, while except for four strains, seven strains exhibited noteworthy tolerance to UV-C radiations. The genome-based findings revealed many cold and radiation resistance-associated genes that supported the physiological findings. Further, the bacterial strains produced two or more cold-active enzymes in plate-based assays. Owing to the polyadaptational attributes, the strains ERGC3:01 and ERGC3:05 could be most promising for bioprospection.

SUBMITTER: Mukhia S

PROVIDER: S-EPMC8786180 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Pseudomonas aeruginosa is a ubiquitous microorganism and an important opportunistic pathogen responsible for a broad spectrum of infections mainly in immunosuppressed and critically ill patients. Molecular investigations traditionally rely on pulsed field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). In this work we propose a core genome multilocus sequence typing (cgMLST) scheme for P. aeruginosa, a methodology that combines traditional MLST principles with whole genome sequencing data. All publicly available complete P. aeruginosa genomes, representing the diversity of this species, were used to establish a cgMLST scheme targeting 2,653 genes. The scheme was then tested using genomes available at contig, chromosome and scaffold levels. The proposed cgMLST scheme for P. aeruginosa typed over 99% (2,314/2,325) of the genomes available for this study considering at least 95% of the cgMLST target genes present. The absence of a certain number gene targets at the threshold considered for both the creation and validation steps due to low genome sequence quality is possibly the main reason for this result. The cgMLST scheme was compared with previously published whole genome single nucleotide polymorphism analysis for the characterization of the population structure of the epidemic clone ST235 and results were highly similar. In order to evaluate the typing resolution of the proposed scheme, collections of isolates belonging to two important STs associated with cystic fibrosis, ST146 and ST274, were typed using this scheme, and ST235 isolates associated with an outbreak were evaluated. Besides confirming the relatedness of all the isolates, earlier determined by MLST, the higher resolution of cgMLST denotes that it may be suitable for surveillance programs, overcoming possible shortcomings of classical MLST. The proposed scheme is publicly available at: https://github.com/BioinformaticsHIAEMolecularMicrobiology/cgMLST-Pseudomonas-aeruginosa.

Project description:BACKGROUND:Himalaya is an ecologically pristine environment. The geo-tectonic activities have shaped various environmental niches with diverse microbial populations throughout the Himalayan biosphere region. Albeit, limited information is available in terms of molecular insights into the microbiome, including the uncultured microbes, of the Himalayan habitat. Hence, a vast majority of genomic resources are still under-explored from this region. Metagenome analysis has simplified the extensive in-depth exploration of diverse habitats. In the present study, the culture-independent whole metagenome sequencing methodology was employed for microbial diversity exploration and identification of genes involved in various metabolic pathways in two geothermal springs located at different altitudes in the Sikkim Himalaya. RESULTS:The two hot springs, Polok and Reshi, have distinct abiotic conditions. The average temperature of Polok and Reshi was recorded to be 62?°C and 43?°C, respectively. Both the aquatic habitats have alkaline geochemistry with pH in the range of 7-8. Community profile analysis revealed genomic evidence of plentiful bacteria, with a minute fraction of the archaeal population in hot water reservoirs of Polok and Reshi hot spring. Mesophilic microbes belonging to Proteobacteria and Firmicutes phyla were predominant at both the sites. Polok exhibited an extravagant representation of Chloroflexi, Deinococcus-Thermus, Aquificae, and Thermotogae. Metabolic potential analysis depicted orthologous genes associated with sulfur, nitrogen, and methane metabolism, contributed by the microflora in the hydrothermal system. The genomic information of many novel carbohydrate-transforming enzymes was deciphered in the metagenomic description. Further, the genomic capacity of antimicrobial biomolecules and antibiotic resistance were discerned. CONCLUSION:The study provided comprehensive molecular information about the microbial treasury as well as the metabolic features of the two geothermal sites. The thermal aquatic niches were found a potential bioresource of biocatalyst systems for biomass-processing. Overall, this study provides the whole metagenome based insights into the taxonomic and functional profiles of Polok and Reshi hot springs of the Sikkim Himalaya. The study generated a wealth of genomic data that can be explored for the discovery and characterization of novel genes encoding proteins of industrial importance.

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Multilocus sequence based identification and adaptational strategies of Pseudomonas sp. from the supraglacial site of Sikkim Himalaya.

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