A novel species isolated from a bacterial consortia of contaminated soil enriched for the remediation of e-waste

The genus Pseudomonas is widespread and has been reported to occur in diverse ecological niches. Members of the genus Pseudomonas are metabolically versatile and harbor various biotechnologically important properties. Pseudomonas sesami is reported to have plant growth-promoting activity. Strains of Pseudomonas produce thermotolerant proteolytic and lipolytic enzymes which result in food spoilage. Pseudomonas putida, Pseudomonas furukawaii, Pseudomonas knackmussii and many other pseudomonads have been reported for the remediation of xenobiotic compounds. In the present study, researchers at NCMR-NCCS Pune report the detailed characterization of a Pseudomonas strain, which was isolated from soil samples from Lalkuan, Nainital, Uttarakhand, India. The strain was found to be part of the bacterial consortia obtained for developing remediation of e-waste.

The strain was Gram-stain-negative, rod-shaped, aerobic, oxidase-positive and catalase-positive. Colonies are L-form with entire margins, creamy color, umbonate elevation and non-mucoid. Cell can tolerate up to 3% salinity. Based on 16S rRNA gene sequence the strain belongs to the genus Pseudomonas and showed highest sequence similarity to Pseudomonas furukawaii followed by Pseudomonas aeruginosa and Pseudomonas resinovorans. The G+C content in the genome was 64.24mol%. The phylogenetic analysis revealed that the strain forms a distinct clade in the family Pseudomonadaceae. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The phenotypic, chemotaxonomic and genetic analysis, including overall genome relatedness index values, indicated that the strain represents a novel species of the genus Pseudomonas, for which the name Pseudomonas lalkuanensis sp. nov. is proposed.

The cells of the strain were motile as observed by using the hanging drop method. The oxidase and catalase activities were investigated using an oxidase disc and observing bubble production. The phylogenetic analysis showed that strain formed a separate clade with P. resinovorans keeping P. furukawaii and P. aeruginosa in an outer clade with strong bootstrap support. This phylogenetic analysis reveals that the strain is phylogenetically distinct from P. furukawaii and P. resinovorans. The orthoANI and dDDH values of the strain were clearly below the thresholds for the proposal of novel prokaryotic species indicating that the strain belongs to a novel species of the genus Pseudomonas.

Reference: https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.004559

Bacterial communities associated with the biofilm formation in Pangong Tso Lake

Pangong Tso Lake is situated in the Himalayan Plateau on both sides of India/China border. This high-altitude lake has an oligotrophic environment with extremes of temperature and exposure to UV radiation. The water of the Pangong Tso is generally very clear. The sediments, including the pebbles and small rocks, did not show any biofilm or microbial mats formation in the past.  However, human activities have increased tremendously near this lake, which might lead to disturbance of this lake ecosystem.  The presence of biofilms in a small area near the shore of the Pangong Tso next to the Maan village was observed by researchers.

Pangong Tso lake

Researchers at NCMR-NCCS Pune were curious to understand the bacterial communities associated with the Pangong Tso lake sediment, water and biofilms. Researchers also studied the metabolic potential of the bacterial community. They used amplicon sequencing of the particular region of 16S rRNA gene and other different tools for this study.  Based on the previous findings on biofilm bacterial communities, researchers hypothesized that the biofilm bacterial communities at Pangong Tso Lake consist of phototrophs and chemotrophs. They also hypothesized that the diversity of the biofilms community is different from suspended water and sediments, where biofilm formation was not observed.

Researchers collected sediment and microbial biofilms sample from the Pangong Tso Lake. Analysis of physio-chemical parameters of water was done. The Calcium and Magnesium chloride contents of water were analyzed .The dissolved Chloride content of water, Sulphate concentration, Nitrate nitrogen and Ammonium nitrogen estimation was done using different techniques. DNA extraction was done from water, sediment and microbial biofilm samples. Different bioinformatics and statistic tools were used in the study. The metabolic potential of the microbial community was predicted using functional prediction tool Tax4Fun and the relative abundance of highly abundant genes involved in different functions were compared across the biofilm, sediment and the water sample.

Overall a total of 6,682,012 raw sequences were generated in the study. Proteobacteria was the most dominant and diverse phylum followed by Bacteroidetes, Acidobacteria, Planctomycetes, Actinobacteria, Firmicutes, Verrucomicrobia, Chlorofexi and Gemmatimonadetes. Significant differences were observed in the microbial diversity of water with sediment and microbial biofilm samples. The water sample was least diverse in comparison to the microbial biofilm and sediment samples. Among the top 50 bacterial genera, which constitutes about 50% of the entire microbiome, Loktanella was highly abundant in the water sample, Rhizobium in sediment samples, and Planktosalinus and Aliidomarina were in biofilm samples. The relative abundance of Proteobacteria was the highest in the water. A sharp decline was observed in the relative abundance of Proteobacteria in sediment and biofilm samples.

Loktanella constitutes nearly half of the total bacterial communities in the water sample, while Loktanella represented less than 1% in the biofilm and sediment samples. Differences were observed in the relative abundance of bacterial taxa across the biofilm and the sediment samples at the phylum and genus based on the Welch t test. Bacterial phyla Verrucomicrobia, Deinococcus-Thermus and Cyanobacteria were explicitly enriched in the biofilm samples. The abundance of Planktosalinus, Aliidiomarina, Halomonas, Predibacter, Paracoccus, and Hyphomonas was significantly high in the microbial mat, whereas Enterobacter and Mesorhizobium were highly abundant in the sediment samples. In addition to this higher abundance of Flavobacterium, Pseudomonas, Luteolibacter, Dyadobacter, Chryseobacterium, Halomonas, Stenotrophomonas, Hyphomonas, Enterobacter, Peredibacter, Acinetobacter, Arenibacter and Exiguobacterium was also recorded across the samples.

A total of 49 pathways were highly abundant, with more than 0.5% mean relative abundance. The pathways related to different functions like peptidases, porphyrin and chlorophyll metabolism, glycoxylate and dicarboxylate metabolism, chaperones and folding catalysts, DNA repair and recombination proteins, pyruvate metabolism, nitrogen metabolism, propanoate metabolism, cysteine and methionine metabolism, butanoate metabolism, transcription machinery, prokaryotic defense system, alanine, aspartate and glutamate metabolism, and homologous recombination were highly abundant in the biofilm samples.

The less diverse bacterial communities in microbial biofilm in comparison to sediments indicated the enrichment of a specific group of bacteria. Stratification of Cyanobacteria (primary producer), sulfate-reducing/ oxidizing bacteria and anoxygenic phototrophic bacteria in the hypersaline microbial mat, took place according to the micro-gradient of oxygen, sulfide, and light which selectively allows the specific bacteria to colonize. The higher abundance of Cyanobacteria in the biofilm samples in comparison to sediment and water sample supported the hypothesis on the establishment of primary producers in the biofilm samples. Sediment samples were the most diverse in comparison to water and microbial biofilm samples, which represents both rare and abundant taxa in the sample. The less diverse bacterial communities in microbial biofilm in comparison to sediments indicated the enrichment of a specific group of bacteria.

To conclude, significant differences were observed in the bacterial diversity in the lake water, sediment, and microbial biofilm samples. Enrichment of specific phyla like Verrucomicrobia, Deinococcus-Thermus, and Cyanobacteria in the microbial biofilm samples indicated the development of saprophytic and photosynthetic communities, which is an important succession event in this high-altitude lake. The predictive analysis of potential functions of these communities also supported the observation as the genes involved in porphyrin and chlorophyll metabolism, glyoxylate and dicarboxylate metabolism, DNA repair and recombination proteins were enriched in the microbial biofilm samples.

Reference: https://link.springer.com/article/10.1007/s00284-020-02244-4