Jain, K. R. | bioRxiv Science

bioRxiv2026

Niche-based selection and metabolic plasticity in the microbiome: Chronic press disturbances reconfigure the taxo-phenomic landscape of an industrialized riverine ecosystem

Riverine ecosystems particularly in industrialized environment are subjected to chronic press disturbances, resulting from the decadal release of synthetic organic compounds and other xenobiotics. While indigenous microbial communities are highly sensitive to such stressors, the resulting metabolic restructuring and functional reshaping of the microbiome, driven by these long-term anthropogenic pressures remains poorly characterized. In this study, a microbial ecology of Bhadar River flowing across the Jetpur Industrial Estate, (Jetpur) were studied. Using a cross-sectional comparative approach, soil/sediment samples were collected from the diverse polluted and non-polluted sites from the estate. The taxonomic profiling using 16S rRNA gene amplicon sequencing, taxo-phenomic shifts (through metaphenomics) was studied, while the functional potential of metabolic pathways was validated using high-resolution shot-gun metagenomic study. Due to prolong pollution, the samples were rich in sulphur (9809 to 12391 mg/L), where polluted samples were having elevated COD (2432 to 4150 mg/L) as well as BOD (1000 to 1420 mg/L) values, along with the presence of heavy metals (e.g., Fe, Mg). Results revealed a distinct taxonomic shift at both the bacterial and archaeal levels. In non-polluted sites Proteobacteria (33 to 57%) dominated along with Acidobacteria and Actinobacteria, with diverse genera like Alcaligenes and Serratia. Whereas, polluted sites exhibited marked increase in Bacteroidetes (13 to 29%), Firmicutes, and Synergistetes and genera like Alkalitalea, Mesotoga and Desulfomicrobium, reflecting anaerobic, fermentative, and sulfate-reducing phenotypes. The archaeal communities at polluted sites were dominated by Euryarchaeota (78 to 99%), specifically methanogenic genera of Methanosaeta and Methanocalculus, contrasting with the Methanomassiliicoccus dominance in non-polluted areas. The alpha-diversity was marginally higher in polluted sites (Shannon: 4.11 to 4.81 vs. 3.81 to 5.39 (non-polluted)), but beta-diversity underscored clear separation (94% variance explained by pollution). The shot-gun metagenomic analysis indicated a substantial enhancement in anaerobic metabolic capacities within the polluted microbiome, primarily in sulphur respiration (dissimilatory sulfate reduction), methanogenesis (elucidating biogenic pathways), along with nitrogen cycling (identifying key denitrification and ammonification genes). The polluted microbiome have developed the potential to metabolise/degrade complex aromatic compounds (pcaK for benzoate/protocatechuate transport) and heavy metal resistance. The strong positive co-occurrences among anaerobic phyla (Thermotogae, Synergistetes, Bacteroidetes) in polluted sites was established, indicating syntrophic interactions for xenobiotic metabolism. These findings provide a theoretical ecological model for perturbed industrial ecosystems, emphasizing the role of habitat selection in shaping microbial functional diversity and demonstrate the remarkable adaptation of autochthonous communities to persistent press disturbances.

microbiology↗

bioRxiv2023

Bacterial mixed cultures followed mixed-order kinetics during mono-azo dye decolourization and degradation in batch studies

Over the years little has been focused on kinetic and thermodynamic aspect of bioremediation studies on dyes. In this study, detailed kinetic and thermodynamic analyses of results obtained during a primary study on a mono-azo dye: Reactive violet 5R (RV5), decolourization and degradation by bacterial mixed cultures SB4 were performed. Various kinetic models (zero-, first- and second-order behaviour and Monod model) were applied to understand the decolourization mechanism in batch process. Similarly, steady-state kinetics for determination of Michaelis-constant and maximal dye removal rate was derived. With increasing RV5 concentration, the specific decolourization rate had increased from 0.61mg/L/h to 1.38mg/L/h. The apparent kinetics of RV5 decolourization reaction followed mixed-order behaviour. The process was endothermic. The enthalpy and entropy values calculated to 45.6kJ/mol and 146J/mol/K, respectively, with an activation energy of 87kJ/mol. The Gibbs free energy change suggests that, decolourization reaction under experimental conditions was non-spontaneous below 20{degrees}C but was spontaneous at higher temperatures.

microbiology↗

bioRxiv2023

Chronic industrial perturbation and seasonal change induces shift in the bacterial community from gammaproteobacteria to betaproteobacteria at Amlakhadi canal

Escalating proportions of industrially contaminated sites are one of the major catastrophes faced at the present time due to the industrial revolution. In the outlook of the obstacles associated with culturing the microbes, the direct metagenomic analysis of various complex niches is rapidly gaining attention. In this study, metagenomic approach using next generation sequencing technologies was applied to exemplify the taxonomic abundance and metabolic potential of the microbial community residing in Amlakhadi canal, Ankleshwar at two different seasons. All the metagenomes revealed a predominance of Proteobacteria phylum. However, difference was observed within class level where Gammaproteobacteria was relatively high in polluted metagenome in Summer while in Monsoon the abundance shifted to Betaproteobacteria. Similarly, significant statistical differences were obtained while comparing the genera amongst contaminated sites where Serratia, Achromobacter, Stenotrophomonas and Pseudomonas were abundant at one season and the dominance changed to Thiobacillus, Thauera, Acidovorax, Nitrosomonas, Sulfuricurvum, Novosphingobium, Hyphomonas and Geobacter at the next season. Further upon functional characterization, the microbiomes demonstrated diverse survival mechanisms adapted by the inherent microbial community such as degradation of aromatic compounds, heavy metal resistance, oxidative stress responses and multidrug resistance efflux pumps. The results have important implications in understanding and predicting the impacts of human-induced activities on microbial communities inhabiting natural niche and their responses in coping with the fluctuating pollution load.

microbiology↗