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Pesticide accumulation in agricultural soils is an environmental concern, often addressed through distinct bioremediation strategies. This study has tried to analyze various soil bioremediation options viz., biostimulation, bioaugmentation, and natural attenuation in terms of efficiency and the response of autochthonous microbial flora by using atrazine as a model contaminant. Soil mesocosms were established with 100 kg of soil simulating the field conditions. The soil previously exposed to the herbicide was used for the bioaugmentation strategy undertaken in this study. We have tried to analyze how the microbial community responds to a foreign compound, both in terms of taxonomic and functional capacities? To answer this, we have analyzed metagenome of the mesocosms at a time point when 90% atrazine was degraded. Bioaugmentation for bioremediation proved to be efficient with a DT90 value of 15.48 ± 0.79 days, in comparison to the natural attenuation where the DT90 value was observed to be 41.20 ± 1.95 days. Metagenomic analysis revealed the abundance of orders Erysipelotrichales, Selemonadales, Clostridiales, and Thermoanaerobacterales exclusively in SBS mesocosm. Besides Pseudomonas, bacterial genera such as Achromobacter, Xanthomonas, Stenotrophomonas, and Cupriavidus have emerged as the dominant members in various bioremediation strategies tested in this study. Inclusive results suggest that inherent microbial flora adjust their community and metabolic machinery upon exposure to the pollutant. The site under pollutant stress showed efficient microbial communities to bio-remediate the newly polluted terrestrial ecologies in relatively less time and by economic means. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s12088-020-00877-4) contains supplementary material, which is available to authorized users.

Highlights • Antimicrobial resistance is global risk to both humans & environment health. • Aquatic system serves as hotspot for dissemination of AMR. • Metagenomics can be used for monitoring abundance of ARGs in environment. • Application of metagenomics has potential to yield novel secondary metabolites having antimicrobial potential., Antibiotic resistance is a global problem which affects human health. The imprudent use of antibiotics (medicine, agriculture, aquaculture, and food industry) has resulted in the broader dissemination of resistance. Urban wastewater & sewage treatment plants act as the hotspot for the widespread of antimicrobial resistance. Natural environment also plays an important role in the dissemination of resistance. Mapping of antibiotic resistance genes (ARGS) in environment is essential for mitigating antimicrobial resistance (AMR) widespread. Therefore, the review article emphasizes on the application of metagenomics for the surveillance of antimicrobial resistance. Metagenomics is the next generation tool which is being used for cataloging the resistome of diverse environments. We summarize the different metagenomic tools that can be used for mining of ARGs and acquired AMR present in the metagenomic data. Also, we recommend application of targeted sequencing/ capture platform for mapping of resistome with higher specificity and selectivity.

Bioremediation is an age old technology, used widely as the green route to control environmental pollutants. However, success stories from lab to land as not so common. The major challenges in taking lab-scale research into the field are the lacunae in understanding microbial processes at the polluted niche, bioavailability of the pollutant, survival of non-native species and lack of integrated multi-disciplinary approach.Most studies developed with pure culture techniques ignore the microbial population at the target niche, which dictates the efficiency of biodegradation. A Metagenomics approach harnesses the microbial community intelligence of any niche and paves the way to formulating a successful bioremediation approach, that could use bioaugmentation or biostimulation / ex-situ or in-situ treatment. Bioaugmentation will require study of survival of non-native species into any niche. In most cases, the route of bioaugmentation requires multiple inoculations depending on survival rate. Supplying nutrients and / or a microbial inocula across large areas of the polluted nice requires integration with innovative engineering tools. Remote sensing and GIS based mapping of sites require integration to help assess the extent of damage and understand the spatial and temporal variations of a contaminated site. A successful bbioremediationstrategy needs to integrate the tools of many disciplines.

The drilling, processing and transportation of oil are the main sources of pollution in water and soil. The current work analyzes the microbial diversity and aromatic compounds degradation potential in the metagenomes of communities in the wastewater treatment plant (WWTP) of a crude oil refinery. By focusing on the degradation of phenol, we observed the involvement of diverse indigenous microbial communities at different steps of the WWTP. The anaerobic bacterial and archaeal genera were replaced by aerobic and facultative anaerobic bacteria through the biological treatment processes. The phyla Proteobacteria, Bacteroidetes and Planctomycetes were dominating at different stages of the treatment. Most of the established protein sequences of the phenol degradation key enzymes belonged to bacteria from the class Alphaproteobacteria. From 35 isolated strains, 14 were able to grow on aromatic compounds, whereas several phenolic compound-degrading strains also degraded aliphatic hydrocarbons. Two strains, Acinetobacter venetianus ICP1 and Pseudomonas oleovorans ICTN13, were able to degrade various aromatic and aliphatic pollutants and were further characterized by whole genome sequencing and cultivation experiments in the presence of phenol to ascertain their metabolic capacity in phenol degradation. When grown alone, the intermediates of catechol degradation, the meta or ortho pathways, accumulated into the growth environment of these strains. In the mixed cultures of the strains ICP1 and ICTN13, phenol was degraded via cooperation, in which the strain ICP1 was responsible for the adherence of cells and ICTN13 diminished the accumulation of toxic intermediates., This study was supported by the ERA-NET project WRANA (Inno-INDIGO/0004/2014), and by the Institutional Research Funding IUT20-19 from Eesti Teadusagentuur (Estonian Research Council) to MK, by the strategic program UID/BIA/04050/2013 (POCI-01-0145-FEDER-007569) funded by national funds through the FCT I.P. and by the ERDF through the COMPETE2020-Programa Operacional Competitividade e Internacionalização (POCI) to PMS, and by Department of Biotechnology, Ministry of Science and Technology, New Delhi, BT/IN/INNO-INDIGO/29/AK/2015-16 to AK. The isolated strains are deposited in the Collection of Environmental and Laboratory Microbial Strains (CELMS; financed by the Estonian Ministry of Education and Research) (RLOMRCELMS) the public catalogue of which is available on the Estonian Electronic Microbial dataBase (EEMB) website http://eemb.ut.ee.

Pharmaceuticals and personal care products are diverse compounds used for the treatment of diseases to promote health, enhance growth and meat production in farm animals. The consumption of pharmaceuticals has increased by 36% during the year 2000–10. Pharmaceuticals are often excreted in unmetabolized form or as active metabolites into the environment. These emerging contaminants impose selection pressure on the environmental microbes leading to the development of antibiotic resistance. Microbes have now gained resistance against “the last resort of antibiotics.” Horizontal gene transfer plays the major role in the dissemination of antimicrobial resistance in diverse niches. It accounts for about 70% exchange of resistance genes between pathogens and environmental microbes. A global, multidimensional approach is required to combat antibiotic resistance. It should emphasize on the conservation of antibiotics by judicious use, adoption of hygiene and cleaner production technology, vaccine development against diseases, and the discovery of novel antimicrobials compounds using functional metagenomics and CRISPR-CAS techniques.

The extreme pursuit of economic success by over management and unreasonable development has profoundly exploited natural resources and damaged environmental ecosystems. Nature has its own ways of resolving imbalances of its environment and microorganisms often serve as drivers that work effectively to eliminate toxic pollutants. Metagenomics provides information about immense diversity and the functional ability of microorganisms inhabiting polluted samples. bioremediation has been considered as one of the potential tools to remove contaminants from the environment. Molecular ecologists are analyzing environmental deoxyribonucleic acid from diverse ecosystems such as soil, water, etc., which allows access to genomes of uncultivable microorganisms. Microbial fingerprinting methods are often employed to differentiate organisms or classes of organisms based on unique character of a universal component or section of a biomolecule. The role of microbial diversity and functions with respect to bioremediation of diesel-contaminated soils was assessed using both metagenomic analyses and enzymatic assays.

Microbial community structure of two distinct effluent treatment plants (ETPs) of pesticide and pharmaceutical industries was assessed and defined by (i) culture dependent and culture independent approaches on the basis of 16S rRNA gene sequencing, (ii) diversity index analysis - operational taxonomic units (OTUs). A total of 38 and 44 bacterial OTUs having 85-99% similarity with the closest match in the database were detected among pharmaceutical and pesticide sludge samples, respectively. Fifty percent of the OTUs were related to uncultured bacteria. These OTUs had a Shannon diversity index value of 2.09-2.33 for culturables and in the range of 3.25-3.38 for unculturables. The high species evenness values of 0.86 and 0.95 indicated the vastness of microbial diversity retrieved by these approaches. The dominant cultured bacteria indicative of microbial diversity in functional ETPs were Alcaligenes, Bacillus and Pseudomonas. Brevundimonas, Citrobacter, Pandoraea and Stenotrophomonas were specific to pesticide ETP and Agrobacterium, Brevibacterium, Micrococcus, Microbacterium, Paracoccus and Rhodococcus were specific to pharmaceutical ETP. These microbes can thus be maintained and exploited for efficient functioning and maintenance of ETPs.

Microbial capacities drive waste stabilization and resource recovery in environmental friendly processes. Depending on the composition of waste, a stress-mediated selection process ensures a scenario that generates a specific enrichment of microbial community. These communities dynamically change over a period of time while keeping the performance through the required utilization capacities. Depending on the environmental conditions, these communities select the appropriate partners so as to maintain the desired functional capacities. However, the complexities of these organizations are difficult to study. Individual member ratios and sharing of genetic intelligence collectively decide the enrichment and survival of these communities. The next-generation sequencing options with the depth of structure and function analysis have emerged as a tool that could provide the finer details of the underlying bioprocesses associated and shared in environmental niches. These tools can help in identification of the key biochemical events and monitoring of expression of associated phenotypes that will support the operation and maintenance of waste management systems. In this chapter, we link genomic tools with process optimization and/or management, which could be applied for decision making and/or upscaling. This review describes both, the aerobic and anaerobic, options of waste utilization process with the microbial community functioning as flocs, granules, or biofilms. There are a number of challenges involved in harnessing the microbial community intelligence with associated functional plasticity for efficient extension of microbial capacities for resource recycling and waste management. Mismanaged wastes could lead to undesired genotypes such as antibiotic/multidrug-resistant microbes.

This study demonstrates the diverse degradative capacity of activated biomass, when exposed to different levels of total dissolved solids (TDS) using a comparative metagenomics approach. The biomass was collected at two time points to examine seasonal variations. Four metagenomes were sequenced on Illumina Miseq platform and analysed using MG-RAST. STAMP tool was used to analyse statistically significant differences amongst different attributes of metagenomes. Metabolic pathways related to degradation of aromatics via the central and peripheral pathways were found to be dominant in low TDS metagenome, while pathways corresponding to central carbohydrate metabolism, nitrogen, organic acids were predominant in high TDS sample. Seasonal variation was seen to affect catabolic gene abundance as well as diversity of the microbial community. Degradation of model compounds using activated sludge demonstrated efficient utilisation of single aromatic ring compounds in both samples but cyclic compounds were not efficiently utilised by biomass exposed to high TDS.

Oxygenases play a key role in degradation of the aromatic compounds in the wastewater. This study explores the oxygenase coding gene sequences from the metagenome of activated biomass. Based on these results, the catabolic capacity of the activated sludge was assessed towards degradation of naphthalene, anthracene, phenol, biphenyl and o-toluidine. Oxygenases found in this study were compared with oxygenases from three other metagenome datasets. Results demonstrate that despite different geographical locations and source, many genes coding for oxygenases were common between treatment plants. 1, 2 Homogentisate dioxygenase and phenylacetate CoA oxygenases were present in all four metagenomes. Metagenomics provides a vast amount of data that needs to be mined with specific targets to harness the potential of the microbial world.

Metagenome analysis was used to understand the microbial community in activated sludge treating industrial wastewaters at a Common Effluent Treatment Plant (CETP) in South India. The taxonomic profile mapped onto National Center for Biotechnology Information (NCBI) taxonomy using MEtaGenome ANalyzer (MEGAN), demonstrated that the most abundant domain belonged to prokaryotes, dominated by bacteria. Bacteria representing nine phyla were identified from the sequence data including representatives from two new phyla, Synergistetes and Elusimicrobia. Functional analysis of the metagenome, with specific reference to the metabolism of aromatic compounds, revealed the dominance of genes of the central meta-cleavage pathway. This information was used to improve the degradative efficiency in the wastewater treatment plant. A pilot scale plant was set up with 200L of activated sludge using salicylate induced sludge and results demonstrated 52% removal in chemical oxygen demand (COD) against non-induced biomass.

Metagenomic libraries herald the era of magnifying the microbial world, tapping into the vast metabolic potential of uncultivated microbes, and enhancing the rate of discovery of novel genes and pathways. In this paper, we describe a method that facilitates the extraction of metagenomic DNA from activated sludge of an industrial wastewater treatment plant and its use in mining the metagenome via library construction. The efficiency of this method was demonstrated by the large representation of the bacterial genome in the constructed metagenomic libraries and by the functional clones obtained. The BAC library represented 95.6 times the bacterial genome, while, the pUC library represented 41.7 times the bacterial genome. Twelve clones in the BAC library demonstrated lipolytic activity, while four clones demonstrated dioxygenase activity. Four clones in pUC library tested positive for cellulase activity. This method, using FTA cards, not only can be used for library construction, but can also store the metagenome at room temperature.

Bioremediation is a process that uses microorganisms or their enzymes to remove pollutants from the environment. Generally, bioremediation technologies can be classified as in situ or ex situ. In situ bioremediation involves treating the contaminated material at the site while ex situ involves the removal of the contaminated material to be treated elsewhere. Like so much else in biology, the ease and availability of genomic data has created a new level of understanding this system. Bioremediation capabilities of the microbial population can be analyzed; not only by physiological parameters, but also by the use of genomic tools, and efficient remediation strategies can be planned. PCR and DNA- or oligonucleotide-based microarray technology is a powerful functional genomics tool that allows researchers to view the physiology of a living cell from a comprehensive and dynamic molecular perspective. This paper explores the use of such tools in bioremediation process.