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.


Plant growth promoting potential of a bacterial isolate from Tea garden in Assam

Tea is an economically important crop cultivated under warm and humid conditions. Assam is one of the largest tea-producing states in India. The tropical climatic condition gives the tea its unique malty taste but it also makes tea more prone to fungal diseases, which ultimately results in economic loss. Factors like insect/pathogen attack, drought, and heavy metals contribute to significant loss in tea production. Fungal diseases are significant contributors in reduced productivity of tea crops. Specifically, in the tea sector, estimated crop loss due to disease, pest, and weeds is reported to be around 85 million kg. Traditionally, chemical fertilizers, pesticides and insecticides are routinely used in tea gardens to tackle biotic stress factors. These chemicals are harmful for the ecosystem. The presence of pesticide residues in Assam Tea is a cause of great concern.

Plant Growth Promoting Rhizobacteria (PGPR) contributes in plant growth promotion activities, which eventually contributes to better farming. PGPRs colonize plant roots and benefit the plant system by solubilizing minerals such as phosphate, fixing Nitrogen in roots, producing phytohormones such as auxin; producing siderophore, iron scavenging molecules. They are also known to induce systemic resistance thereby developing robust mechanisms to resist biotic and abiotic stress.

Although PGPR associated with crops such as wheat, maize, rice, etc. have been widely studied, it is important to note that, despite Assam representing the largest tea producing states, the rhizosphere of tea has been poorly explored. Even in comparison with other crops, this commercial crop is highly ignored. Thus, it is important to characterize bacteria isolated from the tea rhizosphere and understand their functional potential for PGP traits, including biocontrol activity against pathogenic fungi.

Researchers from Assam University, NCMR-NCCS Pune and SPPU Pune conducted a study in which 23 distinct bacterial morphotypes were isolated from the tea garden of Assam, India. The isolates were screened for their plant growth promotion (PGP) and antifungal traits against three pathogenic fungi, namely Rhizoctonia solani, Corticium rolfsii, and Fomes lamaensis. Out of 23 isolates, 7 isolates showed potential in antifungal activities, amongt which, isolate A6 was found to have promising PGP and antifungal traits. Isolate A6 also exhibited biosurfactant production abilities. Biochemical and molecular characterization revealed its identity as Brevibacterium sediminis.

Biofilm – forming ability of fresh A6 culture was also assessed. Biofilm formation is considered as a prerequisite to colonize plant roots. Only after root colonization, the bacterium can perform the PGP activities. The finding of the study revealed that the isolate A6 forms moderately adherent biofilm. Biosurfactants now addressed as ‘green surfactants’ are well documented in the literature for plant growth promotion by their detrimental effect on pathogens. Hence, these biosurfactants and/or biosurfactant producing microbes are potential substitutes for the harsh chemical pesticides and insecticides being currently used in agriculture.

The study indicated isolate A6’s ability to exhibit PGP properties including the biocontrol activity and biosurfactant production and also to withstand the environmental stress such as its ability to grow and remain metabolically active in acidic pH. Also, the current findings need validation of reproducibility in tea plants. However, this study suggest and indicate that the bacterial isolate Brevibacterium sediminis A6 can be a potential PGPR candidate to be used in combination with other PGPR isolates for improving crop health and eventually the overall crop productivity.