The overuse of pesticides for augmenting agriculture productivity always comes at the cost of environment, biodiversity, and human health and has put the land, water, and environmental footprints under severe threat throughout the globe. Underpinning and maximizing the microbiome functions in pesticide-contaminated environments has become a prerequisite for a sustainable environment and resilient agriculture. It is imperative to elucidate the metabolic network of the microbial communities and environmental variables at the contaminated site to predict the best strategy for remediation and soil microbe-pesticide interactions. High throughput next-generation sequencing and in silico analysis allow us to identify and discern the members and characteristics of core microbiomes at the contaminated site. Integration of modern high throughput multi-omics investigations and informatics pipelines provide novel approaches and pathways to capitalize on the core microbiomes for enhancing environmental functioning and mitigation. The role of eco-genomics tools in visualising the microbial network, taxonomy, functional potential, and environmental variables in contaminated habitats is discussed in this review. The integrated role of the potential microbe identification as individual or consortia, mechanistic approach for pesticide degradation, identification of responsible enzymes/genes, and in silico approach is emphasized for the prospects of the area.

A paradoxical impact of high rates of production and consumption of antibiotics is their widespread release in the environment. Consequently, low concentrations of antibiotics and their byproducts have been routinely identified from various environmental settings especially from aquatic environments. However, the impact of such low concentrations of antibiotics on the exposed host especially in early life remains poorly understood. We exposed zebrafish to two different environmental concentrations of oxytetracycline and sulfamethoxazole, from larval stage to adulthood (∼120 days) and characterized their impact on the taxonomic diversity, antibiotic resistance genes, and metabolic pathways of the gut microbiome using metagenomic shotgun sequencing and analysis. Long term exposure of environmental concentrations of oxytetracycline and sulfamethoxazole significantly impacted the taxonomic composition and metabolic pathways of zebrafish gut microbiome. The antibiotic exposed samples exhibited significant enrichment of multiple flavobacterial species, including Flavobacterium sp. F52, Flavobacterium johnsoniae and Flavobacterium sp. Fl, which are well known pathogenic bacteria. The relative abundance of antibiotic resistance genes, especially several tetratcycline and sulfonamide resistance genes were significantly higher in the exposed samples and showed a linear correlation with the antibiotic concentrations. Furthermore, several metabolic pathways, including folate biosynthesis, oxidative phosphorylation, and biotin metabolism pathways, showed significant enrichment in the antibiotic exposed samples. Collectively, our results suggest that early life exposure of the environmental concentrations of antibiotics can increase the abundance of unfavorable bacteria, antibiotic resistance genes and associated pathways in the gut microbiome of zebrafish.

The majority of experimental studies carried out to date, regarding the effects of pollutants on meiofauna have been conducted by means of closed systems, and rarely using open ones. The current work explored the impact of three Polycyclic Aromatic Hydrocarbons (PAHs), anthracene, pyrene and benzo[a]pyrene, applied alone or combined, on meiobenthic nematodes using both systems. The results revealed that single PAHs impacted the nematofauna similarly in closed or open systems with a higher toxicity observed for benzo[a]pyrene. However, the closed microcosms contaminated with PAHs became organically enriched, resulting in more non-selective deposit feeders and omnivores-carnivores. Taxonomic and functional effects related to combinations of PAHs were close to those of individual treatments in closed systems, however, for open ones, the outcomes were different. The caudal morphology influenced the response of taxa during their avoidance/endurance of hydrocarbons in open systems where the effects of PAHs mixtures appeared not only additive but also synergetic. Based on the results of the study, the use of open systems is preferred to closed ones as the research outcomes were more accurate and representing better conditions prevailing in nature.

Urban wastewater effluents bring large amounts of nutrients, organic matter and organic microcontaminants into freshwater ecosystems. The effects of this complex mixture of pollutants on freshwater invertebrates have been studied mainly in temperate rivers and streams with high dilution capacities. In contrast, Mediterranean streams and rivers have lower dilution capacities especially during the seasonal drought, and are therefore exposed to high concentrations of pollutants. Here, we assess the effects of urban wastewater pollution on invertebrate communities from Mediterranean streams under different hydrological conditions. Specifically, we assessed the invertebrates taxonomic composition and functional biological traits in 12 streams, differing in stream and substrate size (sand or cobbles), under low (2 surveys) and baseflow (1 survey) conditions. In each stream, we selected reaches both upstream and downstream of the wastewater discharge point. Our results indicate that urban wastewater pollution favours the most tolerant invertebrate taxa and homogenises functional trait composition over time. Changes in functional traits were more evident during the seasonal drought, when the low flow conditions at the upstream and downstream sites were more severe and, pollutant concentrations downstream were at their highest. However, the effects of urban wastewater pollution were not uniform in the downstream sites; as local invertebrate communities differed in according to the river substrate and stream size (i.e., width and discharge). Overall, urban pollution caused by wastewater enhanced both, taxonomic and functional differences between the invertebrate communities. Such an absence of homogenisation among wastewater pollution impacted sites was probably related to the relevant role of stream substrate-size as well flow conditions in the rivers receiving the impact. These are attributes that need to be considered when setting the pollutant discharge limits in rivers and streams receiving effluents.

Concerns regarding microplastic contamination have spread from aquatic environments to terrestrial systems with a growing number of studies have been reported. Notwithstanding, the potential effects on soil ecosystems remain largely unexplored. In this study, the effects of polyethylene microplastics on soil enzymatic activities and the bacterial community were evaluated, and the microbiota colonizing on microplastics were also investigated. Microplastic amendment (2000 fragments per kg soil) significantly increased the urease and catalase activities in soil after 15 days, and no discernible alteration of invertase activities was detected. Results from high-throughput sequencing of 16S rRNA revealed that the alpha diversities (richness, evenness, and diversity) of the microbiota in soil were not obviously changed by the PE amendment, whereas the diversity indexes of microbiota on plastic fragments were significantly lower than those in the control and amended soils. Different taxonomic composition was observed in between the control and amended soils after 90 days of incubation. Bacterial assemblages with distinct community structure colonized the PE microplastics. Additionally, several taxa including plastic-degrading bacteria and pathogens were more abundant on microplastics. Simultaneously, the predicted functional profiles showed that the pathways of amino acid metabolism and xenobiotics biodegradation and metabolism were higher on the microplastics. These results indicated that microplastics in soil, compared with those in aquatic environments, can also act as a distinct microbial habitat, potentially altering the ecological functions of soil ecosystems.

As zoned areas of industries, industrial parks have great impacts on the environment. Several studies have demonstrated that chemical compounds and heavy metals released from industrial parks can contaminate soil, water, and air. However, as an emerging pollutant, antimicrobial resistance genes (ARGs) in industrial parks have not yet been investigated. Here, we collected soil samples from 35 sites in an industrial park in China and applied a metagenomics strategy to profile the ARGs and virulence factors (VFs). We further compared the relative abundance of ARGs between the sites (TZ_31–35) located in a beta-lactam antimicrobial-producing factory and other sites (TZ_1–30) in this industrial park. Metagenomic sequencing and assembly generated 14, 383, 065 contigs and 17, 631, 051 open reading frames (ORFs). Taxonomy annotation revealed Proteobacteria and Actinobacteria as the most abundant phylum and class, respectively. The 32 pathogenic bacterial genera listed in the virulence factor database (VFDB) were all identified from the soil metagenomes in this industrial park. In total, 685,354 ARGs (3.89% of the ORFs) and 272,694 virulence factors (VFs) (1.55% of the ORFs) were annotated. These ARGs exhibited resistance to several critically important antimicrobials, such as rifampins, fluroquinolones, and beta-lactams. In addition, no significant difference in the relative abundance of ARGs was observed between sites TZ_31–35 and TZ_1–30, indicating that ARGs have already disseminated widely in this industrial park. The present study gave us a better understanding of the whole picture of the resistome and virulome in the soil of the industrial park and suggested that we should treat the industrial park as a whole in the surveillance and maintenance of ARGs.

A microcosm experiment was carried out to study the ecotoxicity and interactions between heavy metals and polyvinyl chloride microplastics. Fifteen treatments were tested and results were examined after one month. In details, this work aims to study the ecotoxicological effects of cadmium (10 and 20 mg kg⁻¹ Dry Weight DW), polyvinyl chloride (PVC) and its modified forms; PVC-DETA (PD) and PVC-TETA (PT) (20 and 40 mg kg⁻¹ DW), separately and in mixtures, on meiofauna from Bizerte lagoon (NE Tunisia) with focus on nematode features. The results obtained showed that individual treatments were toxic for meiofauna and particularly for free-living nematodes. No clear trends characterized the numerical responses but significant reductions were observed for diversity indices. Moreover, the binary combinations of contaminants have a lesser toxic effect compared to their individual effects. This effect could be related to the high-capacity chelating ability of PVC and its polymers against cadmium.

Volatile Petroleum Hydrocarbon (VPH) class effects on soil microbial composition were investigated using two next-generation sequencing (NGS) techniques – 454 pyrosequencing and ion torrent sequencing. Microbial activity was stimulated by adding different VPH compound classes to the sandy soil in comparison with live controls without VPH addition. Microbial community structure was significantly affected by the various VPH classes. At the genus level, Rhodococcus, Desulfosporosinus, Polaromonas, Mesorhizobium and Methylibium had the highest relative abundances in the straight-chain alkane (str-alk) treated soil as compared to the control (p < 0.05, 2 sample t-tests) while Pseudomonas was more dominant in the cyclic alkane (cyc-alk) contaminated soil. Pseudonocardia was significantly higher in relative abundance in the aromatic hydrocarbon (aro-H) treated batches as compared to the control (p < 0.05, 2 sample t-tests). A non-metric multidimensional scaling (NMDS) of the Bray Curtis similarity between microbial communities in the batches revealed at least 60% similarity for each treatment and also showed that VPH class was a statistically significant factor in shaping the bacterial communities in the soil treatments (Global R = 0.861, p < 0.01). The NGS platforms (454 GS Junior and Ion torrent) compared in this study did not appear to affect the outcomes of the microbial community structure and composition analysis.