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.

Metagenomics has provided the discovery of genes and metabolic pathways involved in the degradation of xenobiotics. Some microorganisms can metabolize these compounds, potentiating phytoremediation in association with plant. This study aimed to study the metagenome and the occurrence of atrazine degradation genes in rhizospheric soils of the phytoremediation species Inga striata and Caesalphinea ferrea. The genera of microorganisms predominant in the rhizospheric soils of I. striata and C. ferrea were Mycobacterium, Conexibacter, Bradyrhizobium, Solirubrobacter, Rhodoplanes, Streptomyces, Geothrix, Gaiella, Nitrospira, and Haliangium. The atzD, atzE, and atzF genes were detected in the rhizospheric soils of I. striata and atzE and atzF in the rhizospheric soils of C. ferrea. The rhizodegradation by both tree species accelerates the degradation of atrazine residues, eliminating toxic effects on plants highly sensitive to this herbicide. This is the first report for the species Agrobacterium rhizogenes and Candidatus Muproteobacteria bacterium and Micromonospora genera as atrazine degraders.

Most bioremediation studies on volatile organic compounds (VOCs) have focused on a single contaminant or its derived compounds and degraders have been identified under single contaminant conditions. Bioremediation of multiple contaminants remains a challenging issue. To identify a bacterial consortium that degrades multiple VOCs (dichloromethane (DCM), benzene, and toluene), we applied DNA-stable isotope probing. For individual tests, we combined a ¹³C-labeled VOC with other two unlabeled VOCs, and prepared three unlabeled VOCs as a reference. Over 11 days, DNA was periodically extracted from the consortia, and the bacterial community was evaluated by next-generation sequencing of bacterial 16S rRNA gene amplicons. Density gradient fractions of the DNA extracts were amplified by universal bacterial primers for the 16S rRNA gene sequences, and the amplicons were analyzed by terminal restriction fragment length polymorphism (T-RFLP) using restriction enzymes: HhaI and MspI. The T-RFLP fragments were identified by 16S rRNA gene cloning and sequencing. Under all test conditions, the consortia were dominated by Rhodanobacter, Bradyrhizobium/Afipia, Rhizobium, and Hyphomicrobium. DNA derived from Hyphomicrobium and Propioniferax shifted toward heavier fractions under the condition added with ¹³C-DCM and ¹³C-benzene, respectively, compared with the reference, but no shifts were induced by ¹³C-toluene addition. This implies that Hyphomicrobium and Propioniferax were the main DCM and benzene degraders, respectively, under the coexisting condition. The known benzene degrader Pseudomonas sp. was present but not actively involved in the degradation.

The interaction between different volatile organic compounds (VOCs) is a critical issue associated with bioremediation of co-contaminated sites. Contradictory results have been reported on the effects of co-existence of VOCs on biodegradation of each VOC. These contradictions are thought to be caused by inter-study variability in microbial diversity. To examine the effects of co-existing VOCs on biodegradation of each VOC, a series of biodegradation tests were carried out with a microcosm capable of degrading all three VOCs: dichloromethane (DCM), benzene, and toluene. We added different combinations of the VOCs to the microcosm while monitoring VOC concentration and microbial community diversity. Degradation of DCM and benzene was minimally influenced by co-existence of other VOCs; however, degradation of toluene was dramatically enhanced by the co-existence of benzene. Propioniferax was identified in cultures exposed to benzene alone and cultures simultaneously exposed to benzene, toluene, and DCM. Propioniferax was dominant, but prior to this study, it was not known to degrade benzene, toluene, and DCM. In the cultures exposed to only toluene, Rhodanobacter, Mycobacterium, Bradyrhizobium, and Intrasporangium increased during the biodegradation. The former three bacteria increased more rapidly when benzene and DCM were also included. These results suggest that co-existence of benzene and DCM can enhance the activity of Rhodanobacter, Mycobacterium, and Bradyrhizobium and consequently accelerate the degradation of toluene.

The chiral herbicide imazethapyr (IM) is frequently used to control weeds in soybean fields in northeast China. However, the impact of IM enantiomers on microbial communities in soil is still unknown. Genetic markers (16S rRNA V3-V4 regions) were used to characterize and evaluate the variation of the bacterial communities potentially effected by IM enantiomers. Globally, the bacterial community structure based on the OTU profiles in (−)-R-IM-treated soils was significantly different from those in (+)-S-IM-treated soils, and the differences were enlarged with the treatment dose increasing. Interestingly, the Rhizobiaceae family and several other beneficial bacteria, including Bradyrhizobium, Methylobacterium, and Paenibacillus, were strongly enriched in (−)-R-IM treatment compared to (+)-S-IM treatment. In contrast, the pathogenic bacteria, including Erwinia, Pseudomonas, Burkholderia, Streptomyces, and Agrobacterium, were suppressed in the presence of (−)-R-IM compared to (+)-S-IM. Furthermore, we also observed that the bacterial community structure in (−)-R-IM-treated soils was more quickly restored to its original state compared with those in (+)-S-IM-treated soils. These findings unveil a new role of chiral herbicide in the development of soil microbial ecology and provide theoretical support for the application of low-persistence, high-efficiency, and eco-friendly optical rotatory (−)-R-IM.

Two prominent polybrominated diphenyl ether (PBDE) congeners have been included in the persistent organic pollutant list, 2,2′,4,4′,5-tetrabromodiphenyl ether (BDE-99) and 2,2,4,4′-tetrabromodiphenyl ether (BDE-47), which have been detected in treated municipal wastewater, river water, and sediments in China. A lab-scale column experiment was established to investigate the effects of the competitive sorption of BDE-47 on BDE-99 biodegradation and migration in two types of river-based aquifer soils during groundwater recharge with reclaimed water. Two types of recharge columns were used, filled with either silty clay (SC) or black carbon-amended silty clay (BCA). The decay rate constants of BDE-99 in the BCA and SC systems were 0.186 and 0.13 m⁻¹ in the single-solute system and 0.128 and 0.071 m⁻¹ in the binary-solute system, respectively, showing that the decay of BDE-99 was inhibited by the coexistence of BDE-47. This was particularly evident in the SC system because the higher hydrophobicity of BDE-99 determined the higher affinity and competition for sorption sites onto black carbon. The biodegradation of BDE-99 was suppressed by the coexistence of BDE-47, especially in the SC system. Lesser-brominated congeners (BDE-47 and BDE-28) and higher-brominated congeners (BDE-100, BDE-153, BDE-154, and BDE-183) were generated in the four recharge systems, albeit at different ratios. Bacterial biodiversity was influenced by the presence of BDE-47 in the SC system, while it had no significant effect on the BCA system, because the high sorption capacity of black carbon on the hydrophobic PBDEs effectively reduced their toxicity. The ranking order of the most abundant classes changed markedly due to the coexistence of BDE-47 in both the SC and BCA systems. The ranking order of the most abundant genera changed from Azospira, Methylotenera, Desulfovibrio, Methylibium, and Bradyrhizobium to Halomonas, Hyphomicrobium, Pseudomonas, Methylophaga, and Shewanella, which could be involved in PBDE degradation.

In this study, a bacterial strain able to use sulcotrione, a β-triketone herbicide, as sole source of carbon and energy was isolated from soil samples previously treated with this herbicide. Phylogenetic study based on16S rRNA gene sequence showed that the isolate has 100 % of similarity with several Bradyrhizobium and was accordingly designated as Bradyrhizobium sp. SR1. Plasmid profiling revealed the presence of a large plasmid (>50 kb) in SR1 not cured under nonselective conditions. Its transfer to Escherichia coli by electroporation failed to induce β-triketone degrading capacity, suggesting that degrading genes possibly located on this plasmid cannot be expressed in E. coli or that they are not plasmid borne. The evaluation of the SR1 ability to degrade various synthetic (mesotrione and tembotrione) and natural (leptospermone) triketones showed that this strain was also able to degrade mesotrione. Although SR1 was able to entirely dissipate both herbicides, degradation rate of sulcotrione was ten times higher than that of mesotrione, showing a greater affinity of degrading-enzyme system to sulcotrione. Degradation pathway of sulcotrione involved the formation of 2-chloro-4-mesylbenzoic acid (CMBA), previously identified in sulcotrione degradation, and of a new metabolite identified as hydroxy-sulcotrione. Mesotrione degradation pathway leads to the accumulation of 4-methylsulfonyl-2-nitrobenzoic acid (MNBA) and 2-amino-4 methylsulfonylbenzoic acid (AMBA), two well-known metabolites of this herbicide. Along with the dissipation of β-triketones, one could observe the decrease in 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibition, indicating that toxicity was due to parent molecules, and not to the formed metabolites. This is the first report of the isolation of bacterial strain able to transform two β-triketones.

Mine activities leaked heavy metals into surrounding soil and may affected indigenous microbial communities. In the present study, the diversity and composition of the bacterial community in soil collected from three regions which have different pollution degree, heavy pollution, moderate pollution, and non-pollution, within the catchment of Chao River in Beijing City, were compared using the Illumina MiSeq sequencing technique. Rarefaction results showed that the polluted area had significant higher bacterial alpha diversity than those from unpolluted area. Principal component analysis (PCA) showed that microbial communities in the polluted areas had significant differences compared with the unpolluted area. Moreover, PCA at phylum level and Matastats results demonstrated that communities in locations shared similar phyla diversity, indicating that the bacterial community changes under metal pollution were not reflected on phyla structure. At genus level, the relative abundance of dominant genera changed in sites with degrees of pollution. Genera Bradyrhizobium, Rhodanobacter, Reyranella, and Rhizomicrobium significantly decreased with increasing pollution degree, and their dominance decreased, whereas several genera (e.g., Steroidobacter, Massilia, Arthrobacter, Flavisolibacter, and Roseiflexus) increased and became new dominant genera in the heavily metal-polluted area. The potential resistant bacteria, found within the genera of Thiobacillus, Pseudomonas, Arthrobacter, Microcoleus, Leptolyngbya, and Rhodobacter, are less than 2.0 % in the indigenous bacterial communities, which play an important role in soil ecosystem. This effort to profile the background diversity may set the first stage for better understanding the mechanism underlying the community structure changes under in situ mild heavy metal pollution.

Previous researches have confirmed that modified nanoscale carbon black (MCB) can decrease the bioavailability of heavy metals in soil and accumulation in plant tissues, resulting in the increase of biomass of plant. However, as a nanoparticle, the effects of MCB on plant cell morphology and microbial communities in Cd-contaminated soil are poorly understood. This study, through greenhouse experiments, investigated the effects of MCB as an amendment for 5 mg·kg⁻¹ Cd-contaminated soil on plant growth, plant cellular morphogenesis, and microbial communities. Two types of plants, metal-tolerant plant ryegrass (Lolium multiflorum), and hyperaccumulator plant chard (Beta vulgaris L. var. cicla) were selected. The results indicated that adding MCB to Cd-contaminated soil, the dry biomass of shoot ryegrass and chard increased by 1.07 and 1.05 times, respectively, comparing with control group (the treatment without MCB). Meanwhile, the physiological characteristics of plant root denoted that adding MCB reduced the damage caused by Cd to plants. The acid phosphatase activity of soils treated with MBC was higher and the dehydrogenase activity was lower than control group during whole 50 days of incubation, while the urease and catalase activity of soils treated with MBC were higher than control group after 25 days of incubation. When compared with the treatment without MCB, the abundances of nitrogen-functional bacteria (Rhodospirillum and Nitrospira) and phosphorus-functional bacteria (Bradyrhizobium and Flavobacterium) increased but that of nitrogen-functional bacteria, Nitrososphaera, declined. The presence of MCB resulted in increased microbial community abundance by reducing the bioavailability of heavy metals in soil, while increasing the abundance of plants by increasing the amount of available nitrogen in soil. The result of this study suggests that MCB could be applied to the in-situ immobilization of heavy metal in contaminated soils because of its beneficial effects on plants growth, root cellular morphogenesis, and microbial community.

This comparative field study examined the responses of bacterial community structure and diversity to the revegetation of zinc (Zn) smelting waste slag with eight plant species after 5 years. The microbial community structure of waste slag with and without vegetation was evaluated using high-throughput sequencing. The physiochemical properties of Zn smelting slag after revegetation with eight plant rhizospheres for 5 years were improved compared to those of bulk slag. Revegetation significantly increased the microbial community diversity in plant rhizospheres, and at the phylum level, Proteobacteria, Acidobacteria, and Bacteroidetes were notably more abundant in rhizosphere slags than those in bulk waste slag. Additionally, revegetation increased the relative abundance of plant growth-promoting rhizobacteria such as Flavobacterium, Streptomyces, and Arthrobacter as well as symbiotic N₂ fixers such as Bradyrhizobium. Three dominant native plant species (Arundo donax, Broussonetia papyrifera, and Robinia pseudoacacia) greatly increased the quality of the rhizosphere slags. Canonical correspondence analysis showed that the differences in bacterial community structure between the bulk and rhizosphere slags were explained by slag properties, i.e., pH, available copper (Cu) and lead (Pb), moisture, available nitrogen (N), phosphorus (P), and potassium (K), and organic matter (OM); however, available Zn and cadmium (Cd) contents were the slag parameters that best explained the differences between the rhizosphere communities of the eight plant species. The results suggested that revegetation plays an important role in enhancing bacterial community abundance and diversity in rhizosphere slags and that revegetation may also regulate microbiological properties and diversity mainly through changes in heavy metal bioavailability and physiochemical slag characteristics.