Functional Analysis of a Polluted River Microbiome Reveals a Metabolic Potential for Bioremediation

Deciphering Indigenous Bacterial Diversity of Co-Polluted Sites to Unravel Its Bioremediation Potential: A Metagenomic Approach

Polluted drains across the globe are affected due to reckless disposal of untreated industrial effluents resulting in significant water pollution affecting microbial community structure/dynamics. To elucidate this, polluted samples were collected from Budha Nala (BN) drain, Tung Dhab (TD) drain, and wastewater treatment plant (WWTP) receiving an inflow of organic pollutants as well as heavy metals due to anthropogenic activities. The sample of unpolluted pristine soil (PS) was used as control, as there is no history of usage of organic chemicals at this site. The bacterial diversity of these samples was sequenced using the Illumina MiSeq platform by amplifying the V3/V4 region of 16S rRNA. The majority of operational taxonomic unit (OTUs) at polluted sites belonged to phyla Proteobacteria specifically Gammaproteobacteria class, followed by Actinobacteria, Bacteriodetes, Chloroflexi, Firmicutes, Planctomycetes, WS6, and TM7, whereas unpolluted site revealed the prevalence of Proteobacteria followed by Actinobacteria, Planctomycetes, Firmicutes, Acidobacteria, Chloroflexi, Bacteroidetes, Verrucomicrobia, and Nitrospirae. The data sets decode unclassified species of the phyla Proteobacteria, Bacteriodetes, Chloroflexi, Firmicutes, and WS6, along with some unclassified bacterial species. The study provided a comparative study of changed microbial community structure, their possible functions across diverse geographical locations, and identifying specific bacterial genera as pollution bio-indicators of aged polluted drains.

Simulatenous evaluation of composting experiments and metagenome analyses to illuminate the effect of Streptomyces spp. on organic matter degradation

The effect of Streptomyces spp. on organic matter degradation was investigated in the present study. Streptomyces spp. isolated from compost systems were eliminated based on the results of cellulose, starch, xylan degradation tests, morphological inspection, and 16S rRNA analysis. The eliminated strains were re-given to compost systems to determine their effect on organic matter degradation and maturation. Sample analyses indicated that 15 days of composting had been adequate to maintain maturation. The amounts of strains added to the system were high enough to create a detectable change such as inhibition of other microbiota members. Results also indicated a variant change in organic matter degradation due to the added strain. The difference in organic matter degradation between strains depended partially on the segregation of secondary metabolites. On the other hand, strains also inhibited each other in the case of their binary and triple utilization in compost. Another explanation for variant activity was provided based on the enzymatic activity of the strains validated by metagenomic counts evaluation. Metagenome count numbers revealed the tendency of compost microbiota toward degradation products of cellulose. Findings obtained from composting experiments and metagenome analyses indicated the presence of a different degradation route based on xylan activity. Results also implied a decrease in competition between the dominant strain and microbiota members in the case of sequential xylan and cellulose degradation. Meticulous evaluation of results obtained from metagenome analysis also provided some insights on certain conditions regarding the progress of composting along with storage conditions of manure before use.

Microplastics can selectively enrich intracellular and extracellular antibiotic resistant genes and shape different microbial communities in aquatic systems

Microplastics (MPs), as emerging contaminants, are posing potential risks to environment, and animal and human health. The ubiquitous presence of MPs in natural ecosystems provides favorable platform to selectively adsorb antibiotic resistant genes (ARGs) and bacteria (ARB) and bacterial assemblages, especially in wastewater which is hotspot for MPs, ARGs and ARB. In this study, the selective capture of intracellular ARGs (iARGs), extracellular ARGs (eARGs), and bacterial assemblages by MPs with different materials (i.e. polyethylene, polyvinylchloride, and polyethylene terephthalate) and sizes (200 μm and 100 μm) was investigated. The results showed that iARGs (i.e. i-TetA, i-TetC, i-TetO, i-sul1), integron-integrase gene (intI1), and eARGs (i.e. e-TetA and e-bla_TEM) were selectively enriched on MPs. Relative abundances of i-sul1, i-TetA, and intI1 were generally higher than that of i-TetC and i-TetO on all MPs. Moreover, MPs also have strong effects on the formation of microflora in wastewater, which resulted in different bacterial communities and functions in the wastewater and on the MPs. These findings suggested that MPs could affect the selective enrichment of ARB and ARGs in water environment.

Draft Genome Sequence of Methanobacterium paludis IBT-C12, Recovered from Sediments of the Apatlaco River, Mexico

Methanobacterium paludis is a hydrogenotrophic archaea first described in 2014 and isolated from a peatland area. So far, there is only one sequenced genome of this taxon. Here, we report the draft genome sequence of M. paludis IBT-C12, a metagenome-assembled genome (MAG) from sediments in the Apatlaco River, Mexico.

Hi-C deconvolution of a textile dye-related microbiome reveals novel taxonomic landscapes and links phenotypic potential to individual genomes

Microbial biodiversity is represented by a variety of genomic landscapes adapted to dissimilar environments on Earth. These genomic landscapes contain functional signatures connected with the community phenotypes. Here, we assess the genomic microbial diversity landscape at a high-resolution level of a polluted river-associated microbiome (Morelos, México), cultured in a medium enriched with anthraquinone Deep Blue 35 dye. We explore the resultant textile dye microbiome to infer links between predicted biodegradative functions, and metagenomic and metabolic potential, especially using the information obtained from individual reconstructed genomes. By using Hi-C proximity-ligation deconvolution method, we deconvoluted 97 genome composites (80% potentially novel species). The main taxonomic determinants were Methanobacterium, Clostridium, and Cupriavidus genera constituting 50, 22, and 11% of the total community profile. Also, we observed a rare biosphere of novel taxa without clear taxonomic standing. Removal of 50% chemical oxygen demand with 23% decolorization was observed after 30 days of dye enrichment. Genes related to catalase-peroxidase, polyphenol oxidase, and laccase enzymes were predicted as associated with textile dye biodegradation phenotype under our study conditions, highlighting the potential of metagenome-wide analysis to predict biodegradative determinants. This study prompts high-resolution screening of individual genomes within textile dye river sediment microbiomes or complex communities under environmental pressures.

Colonization characteristics of bacterial communities on plastic debris: The localization of immigrant bacterial communities

The unique characteristics of bacterial communities on plastic debris and microplastics in the environment have been widely studied in recent years. However, due to the randomness of sampling, it is hard to identify whether the unique characteristics of bacterial communities on plastic debris is due to the plastics as substrate itself, or the accumulation and transportation by plastics. Therefore, the ecological effects of bacterial communities on plastic debris, including the species invasion, are still not clear. To investigate such issue, we took the Haihe Estuary (Tianjin, China) as an example, and designed a strategy to sample and redeploy randomly collected environmental plastic debris for 6 weeks, thus the variation of bacterial communities on plastic debris could be assessed. At the same time, commercial experimental plastic debris was used as the control group to monitor the growth of local bacterial communities on plastics in the cultivation environment. Our study discussed the bacterial communities on the environmental plastic debris from three aspects, including colonization characteristics, taxonomic analysis and molecular metabolism estimation. We found that the bacterial communities on environmental plastic debris tended to show local characteristics, which were less affected by their original characteristics. Therefore, the results reminded us that the ecological risks of bacterial communities on plastics, which were brought by the transportation of plastic debris in the environment, may not be as serious as it was expected previously.