Rhizospheric microbes play important roles in plant growth and heavy metals (HMs) transformation, possessing great potential for the successful phytoremediation of environmental pollutants. In the present study, the rhizosphere of Elsholtzia haichowensis Sun was comprehensively studied to uncover the influence of environmental factors (EFs) on the whole microbial communities including bacteria, fungi and archaea, via quantitative polymerase chain reaction (qPCR) and high-throughput sequencing. By analyzing molecular ecological network and multivariate regression trees (MRT), we evaluated the distinct impacts of 37 EFs on soil microbial community. Of them, soil pH, HMs, soil texture and nitrogen were identified as the most influencing factors, and their roles varied across different domains. Soil pH was the main environmental variable on archaeal and bacterial community but not fungi, explaining 25.7%, 46.5% and 40.7% variation of bacterial taxonomic composition, archaeal taxonomic composition and a-diversity, respectively. HMs showed important roles in driving the whole microbial community and explained the major variation in different domains. Nitrogen (NH4-N, NO3-N, NO2-N and TN) explained 47.3% variation of microbial population composition and 15.9% of archaeal taxonomic composition, demonstrating its influence in structuring the rhizospheric microbiome, particularly archaeal and bacterial community. Soil texture accounted for 10.2% variation of population composition, 28.9% of fungal taxonomic composition, 19.2% of fungal a-diversity and 7.8% of archaeal a-diversity. Rhizosphere only showed strong impacts on fungi and bacteria, accounting for 14.7% and 4.9% variation of fungal taxonomic composition and bacterial a-diversity. Spatial distance had stronger influence on bacteria and archaea than fungi, but not as significant as other EFs. For the first time, our study provides a complete insight into key influential EFs on rhizospheric microbes and how their roles vary across microbial domains, giving a hand for understanding the construction of microbial communities in rhizosphere.

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.

Pollutants discharged from wastewater are the main cause of the spread of antibiotic resistance in river biofilms. There is controversy regarding the primary contribution of environmental selectors such as antibiotics and heavy metals to the development of antibiotic resistance in bacterial communities. Here, this study compared the effect of environmental safety concentration Cu²⁺ and enrofloxacin (ENR) on the evolution of antibiotic resistance by examining phenotypic characteristics and genotypic profiles of bacterial communities in a river biofilm, and then distinguished the major determinants from a comprehensive perspective. The pollution induced community tolerance in ENR-treated group was significantly higher than that in Cu²⁺-treated group (at concentration levels of 100 and 1000 μg/L). Metagenomic sequencing results showed that ENR significantly increased the number and total abundance of antibiotic resistance genes (ARGs), but there was no significant change in the Cu²⁺- treated group. Compared with Cu²⁺, ENR was the major selective agent in driving the change of taxonomic composition because the taxonomic composition in ENR was the most different from the original biofilm. Comparing and analyzing the prokaryotic composition, the phylum of Proteobacteria was enriched in both ENR and Cu²⁺ treated groups. Among them, Acidovorax and Bosea showed resistance to both pollutants. Linking taxonomic composition to ARGs revealed that the main potential hosts of fluoroquinolone resistance genes were Comamonas, Sphingopyxis, Bradyrhizobium, Afipia, Rhodopseudomonas, Luteimonas and Hoeflea. The co-occurrence of ARGs and metal resistance genes (MRGs) showed that the multidrug efflux pump was the key mechanism connecting MRGs and ARGs. Network analysis also revealed that the reason of Cu²⁺ selected for fluoroquinolones resistant bacterial communities was the coexistence of multidrug efflux gene and MRGs. Our research emphasizes the importance of antibiotics in promoting the development of antibiotic resistant bacterial communities from the perspective of changes in community structure and resistome in river biofilms.

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.

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.

To detect effects of pesticides on non-target freshwater organisms the Species at risk (SPEARpesticides) bioindicator based on biological traits was previously developed and successfully validated over different biogeographical regions of Europe using species-level data on stream invertebrates. Since many freshwater biomonitoring programmes have family-level taxonomic resolution we tested the applicability of SPEARpesticides with family-level biomonitoring data to indicate pesticide effects in streams (i.e. insecticide toxicity of pesticides). The study showed that the explanatory power of the family-level SPEAR(fm)pesticides is not significantly lower than the species-level index. The results suggest that the family-level SPEAR(fm)pesticides is a sensitive, cost-effective, and potentially European-wide bioindicator of pesticide contamination in flowing waters. Class boundaries for SPEARpesticides according to EU Water Framework Directive are defined to contribute to the assessment of ecological status of water bodies. We show that SPEARpesticides can be based on family-level biomonitoring data and is applicable for large-scale monitoring programmes to detect and quantify pesticide contamination.

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.

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.