Petroleum hydrocarbon pollution is a global problem. However, the effects of different petroleum pollution levels on soil microbial communities and ecological functions are still not clear. In this study, we analyzed the changes in microbial community structures and carbon and nitrogen transformation functions in oil-contaminated soils at different concentrations by chemical analysis, high-throughput sequencing techniques, cooccurrence networks, and KEGG database comparison functional gene annotation. The results showed that heavy petroleum concentrations (petroleum concentrations greater than 20,000 mg kg⁻¹) significantly decreased soil microbial diversity (p = 0.01), soil microbiome network complexity, species coexistence patterns, and prokaryotic carbon and nitrogen fixation genes. In medium petroleum contamination (petroleum concentrations of between 4000 mg kg⁻¹ and 20,000 mg kg⁻¹), microbial diversity (p > 0.05) and carbon and nitrogen transformation genes showed no evident change but promoted species coexistence patterns. Heavy petroleum contamination increased the Proteobacteria phylum abundance by 3.91%–57.01%, while medium petroleum contamination increased the Actinobacteria phylum abundance by 1.69%–0.26%. The results suggested that petroleum concentrations played a significant role in shifting soil microbial community structures, ecological functions, and species diversities.

An increase in polycyclic aromatic hydrocarbon (PAH) pollution poses significant challenges to human and ecosystem health in the Three Gorges Reservoir (TGR) of the Yangtze River. Based on the combination of PAH analysis with qPCR and high-throughput sequencing of bacteria, 32 topsoil samples collected from 16 sites along the TGR were used to investigate the distribution and biodegradation pathways of PAHs in the water-level-fluctuation zone (WLFZ). The results indicated that the concentrations of PAHs were 43.8–228.2 and 30.8–206.3 ng/g soil (dry weight) under the high- and low-water-level (HWL and LWL) conditions, respectively. The PAH concentration in urban areas was higher than that in rural areas. Under both the HWL and LWL conditions, the abundance of the bamA gene, a biomarker of anaerobic PAH biodegradation, was significantly higher than that of the ring-hydroxylating-dioxygenase (RHD) gene, a biomarker of aerobic PAH biodegradation. The abundance of the bamA gene was significantly positively correlated with PAHs (R² = 0.8), and the biodegradation percentage of PAHs incubated anaerobically was greater than that in the aerobically incubated microcosm experiments. These data implicated a key role of the anaerobic pathway in PAH biodegradation. Co-occurrence network analysis suggested that anaerobic Anaerolineaceae, Dechloromonas, Bacteroidetes_vadin HA17 and Geobacter were key participants in the biodegradation of PAHs. The diversity analysis of functional bacteria based on the bamA gene and microcosm experiments further demonstrated that nitrate was the primary electron acceptor for PAH biodegradation. These findings provide a new perspective on the mechanism of PAH biodegradation in the TGR and knowledge that can be used to develop strategies for environmental management.

Nutrient loading is a major threat to estuaries and coastal environments worldwide, therefore, it is critical that we have good monitoring tools to detect early signs of degradation in these ecologically important and vulnerable ecosystems. Traditionally, bottom-dwelling macroinvertebrates have been used for ecological health assessment but recent advances in environmental genomics mean we can now characterize less visible forms of biodiversity, offering a more holistic view of the ecosystem and potentially providing early warning signals of disturbance. We carried out a manipulative nutrient enrichment experiment (0, 150 and 600 g N fertilizer m⁻²) in two estuaries in New Zealand to assess the effects of nutrient loading on benthic communities. After seven months of enrichment, environmental DNA (eDNA) metabarcoding was used to examine the response of eukaryotic (18S rRNA), diatom only (rbcL) and bacterial (16S rRNA) communities. Multivariate analyses demonstrated changes in eukaryotic, diatom and bacterial communities in response to nutrient enrichment at both sites, despite differing environmental conditions. These patterns aligned with changes in macrofaunal communities identified using traditional morphological techniques, confirming concordance between disturbance indicators detected by eDNA and current monitoring approaches. Clear shifts in eukaryotic and bacterial indicator taxa were seen in response to nutrient loading while changes in diatom only communities were more subtle. Community changes were discernible between 0 and 150 g N m⁻² treatments, suggesting that estuary health assessment tools could be developed to detect early signs of degradation. Increasing variation in community structure associated with nutrient loading could also be used as an indicator of stress or approaching tipping points. This work represents a first step towards the development of molecular-based estuary monitoring tools, which could provide a more holistic and standardized approach to ecosystem health assessment with faster turn-around times and lower costs.

The microbial characteristics and bacterial communities of sediment sludge upon different concentrations of exposure to uranium were investigated by high solution transmission electron microscopy (HRTEM), energy dispersive X-ray spectroscopy (EDS), X-ray photoelectron spectroscopy (XPS) and high-throughput sequencing. After exposure to initial uranium concentrations of 10–50 μM for 24 h in synthetic wastewater, the removal efficiencies of uranium reached 80.7%–96.5%. The spherical and short rod bacteria were dominant in the sludge exposed to uranium. HRTEM-EDS and XPS analyses indicated that reduction and adsorption were the main mechanisms for uranium removal. Short-term exposure to low concentrations of uranium resulted in a decrease in bacterial richness but an increase in diversity. A dramatic change in the composition and abundances of the bacterial community were present in the sediment sludge exposed to uranium. The highest removal efficiency was identified in the sediment sludge exposed to 30 μM uranium, and the dominant bacteria included Acinetobacter (44.9%), Klebsiella (20.0%), Proteiniclasticum (6.7%), Enterobacteriaceae (6.6%), Desulfovibrio (4.4%), Porphyromonadaceae (4.1%), Comamonas (2.4%) and Sedimentibacter (2.3%). By comparison to the inoculum sediment sludge, exposure to uranium caused a substantial difference in the majority of bacterial abundance.

The distribution pattern of root-associated bacteria in native plant growth in tailing dumps with extreme conditions remains poorly understood and largely unexplored. Herein we chose a native plant, Bidens bipinnata, growing on both an Sb tailing dump (WKA) and adjacent normal soils (WKC) to in-depth understand the distribution pattern of root-associated bacteria and their responses on environmental factors. We found that the rhizosphere microbial diversity indices in the tailing dump were significantly different from that in the adjacent soil, and that such variation was significantly related with soil nutrients (TC, TOC, TN) and metal(loid) concentrations (Sb and As). Some dominant genera were significant enriched in WKA, suggesting their adaption to harsh environments. Notably, these genera are proposed to be involved in nutrient and metal(liod) cycling, such as nitrogen fixing (Devosia, Cellvibrio, Lysobacter, and Cohnella), P solubilizing (Flavobacterium), and Sb and As oxidation (Paenibacillus, Bacillus, Pseudomonas, and Thiobacillus). Our results suggest that certain root-associated bacteria in tailing dump were governed by soil edaphic factors and play important ecological roles in nutrient amendments and metal cycling for the successful colonization of Bidens bipinnata in this tailing dump.

Applying an electric field to stimulate the microbial reductive dechlorination of polychlorinated biphenyls (PCBs) represents a promising approach for bioremediation of PCB-contaminated sites. This study aimed to demonstrate the biocathodic film-facilitated reduction of PCB 61 in a sediment-based bioelectrochemical reactor (BER) and, more importantly, the characterizations of electrode-microbe interaction from microbial and electrochemical perspectives particularly in a time-dependent manner. The application of a cathodic potential (−0.45 V vs. SHE) significantly improved the rate and extent of PCB 61 dechlorination compared to the open-circuit scenario (without electrical stimulation), and the addition of an external surfactant further increased the dechlorination, with Tween 80 exerting more pronounced effects than rhamnolipid. The bacterial composition of the biofilms and the bioelectrochemical kinetics of the BERs were found to be time-dependent and to vary considerably with the incubation time and slightly with the coexistence of an external surfactant. Excellent correlations were observed between the dechlorination rate and the relative abundance of Dehalogenimonas, Dechloromonas, and Geobacter, the dechlorination rate and the cathodic current density recorded from the chronoamperometry tests, and the dechlorination rate and the charge transfer resistance derived from the electrochemical impedance tests, with respect to the 120 day-operation. After day 120, PCB 61 was resistant to further appreciable reduction, but substantial hydrogen production was detected, and the bacterial community and electrochemical parameters observed on day 180 were not distinctly different from those on day 120.

Mining activities have introduced various pollutants to surrounding aquatic and terrestrial environments, causing adverse impacts to the environment. Indigenous microbial communities are responsible for the biogeochemical cycling of pollutants in diverse environments, indicating the potential for bioremediation of such pollutants. Antimony (Sb) has been extensively mined in China and Sb contamination in mining areas has been frequently encountered. To date, however, the microbial composition and structure in response to Sb contamination has remained overlooked. Sb and As frequently co-occur in sulfide-rich ores, and co-contamination of Sb and As is observed in some mining areas. We characterized, for the first time, the microbial community profiles and their responses to Sb and As pollution from a watershed heavily contaminated by Sb tailing pond in Southwest China. The indigenous microbial communities were profiled by high-throughput sequencing from 16 sediment samples (535,390 valid reads). The comprehensive geochemical data (specifically, physical-chemical properties and different Sb and As extraction fractions) were obtained from river water and sediments at different depths as well. Canonical correspondence analysis (CCA) demonstrated that a suite of in situ geochemical and physical factors significantly structured the overall microbial community compositions. Further, we found significant correlations between individual phylotypes (bacterial genera) and the geochemical fractions of Sb and As by Spearman rank correlation. A number of taxonomic groups were positively correlated with the Sb and As extractable fractions and various Sb and As species in sediment, suggesting potential roles of these phylotypes in Sb biogeochemical cycling.

Miscanthus has good tolerance to heavy metals (HMs) and has received increasing attention in studies of HM-contaminated soil remediation. In this study, four Miscanthus cultivars (M. lutarioriparius Xiangnadi NO4, M. sinensis Xiangmang NO1, M. lutarioriparius × M. sinensis hybrid Xiangzamang NO1, and M. floridulus Wujiemang NO1) that grow in China were studied. Their tolerance and enrichment abilities in soils containing 50 mg kg⁻¹ cadmium (Cd) and the structure and function of their rhizosphere bacterial communities during the remediation process were analyzed. The results exhibiting a tolerance index (TI) higher than 75 in roots and the aboveground parts (TI > 60, indicating highly tolerant plants) indicated that all four Miscanthus cultivars were tolerant to high Cd concentrations. Moreover, Cd was mainly enriched in roots, the translocation ability from roots to aboveground parts was weak, and the four cultivars exhibited phytostabilization ability in Cd-contaminated soils. High-throughput sequencing (HTS) analysis showed that the Miscanthus rhizosphere bacterial community comprised 33 phyla and 446 genera, including plant growth-promoting rhizobacteria (PGPRs), such as Bacillus, Sphingomonas, and Mesorhizobium. The addition of Cd affected the Miscanthus rhizosphere bacterial community and reduced community diversity. Phylogenetic molecular ecological networks (pMENs) indicated that Cd addition reduced interactions between Miscanthus rhizosphere bacteria and thereby led to a simpler network structure, increased the number of negative-correlation links, enhanced the competition between rhizosphere bacterial species, reduced the number of key bacteria, and changed the composition of those bacteria. PICRUSt functional predictive analysis indicated that Cd stress reduced soil bacterial functions in the Miscanthus rhizosphere. The results of this study provide a basis for the remediation of Cd-contaminated soils by Miscanthus and provide a reference for the subsequent regulation of Miscanthus remediation efficiency by PGPRs or key bacteria.

Microbial communities in activated sludge (AS) have a significant influence on the functions and stability of aeration tanks in wastewater treatment plants (WWTPs). The microbial community structure is affected by various factors, among which operational parameters outcompeted as the key factors in shaping its structure. However, as an important operational parameter of aeration tank, the mechanisms by which sludge retention time (SRT) affect community properties remain unclear. In this study, 144 AS samples from aeration tanks of 48 full-scale WWTPs operating under different SRT conditions were examined via high-throughput Illumina-MiSeq sequencing technology. The results indicated that SRT significantly affected the diversity, composition, assembly, and co-occurrence patterns of the microbial community in aeration tanks. Moreover, our results provided clear evidence that the microbial communities in aeration tanks operating under SRT of 10–20 days have the highest biodiversity, the lowest stochastic processes influence, the more stable molecular ecological network structure, the lowest risks of filamentous sludge bulking and enhanced nitrogen removal potential. The microbial communities could be more stable and resilient to disturbance when aeration tanks were operated under this SRT condition. The findings of this study provided a reference for the optimization of aeration tanks from an of microbial community perspective.

The increasing release of engineered nanoparticles (NPs) from consumer products has raised great concerns about their impacts on biological wastewater treatment. In this study, the widely-used ZnO NP was selected as a model NP to investigate its impact on high-rate denitrifying granular sludge in terms of sludge properties and community structure. A hormesis effect was observed during short-term exposure, in which the specific denitrification activity (SDA) was stimulated by 10% at 1 mg L⁻¹ ZnO NPs, but inhibited by 23% at 5.0 mg L⁻¹ ZnO NPs. When continuously exposed to 2.5 mg L⁻¹ ZnO NPs, the nitrogen removal capacity of the denitrification reactor was nearly deprived within 15 days, and the relative abundance of the dominant denitrifying bacterium (Castellaniella) was decreased from 51.0 to 8.0%. Meanwhile, the dehydrogenase activity (DHA) and the content of extracellular polymeric substance (EPS) significantly decreased to 22.3 and 61.1%, respectively. Nevertheless, the presence of phosphate substantially weakened the adverse effects of ZnO NPs on the SDA, EPS, DHA and the relative abundance of functional genes even exposed to 6.25 mg L⁻¹ ZnO NPs, which was associated with the fact that the level of Zn(II) released from ZnO NPs was significantly reduced in the presence of phosphate. Therefore, the toxicity of ZnO NPs may be mainly attributed to the release of toxic Zn(II) and could be attenuated in the presence of phosphate. Overall, this study provided further reference and meaningful insights into the impact of engineered NPs on biological wastewater treatment.