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.

Microorganisms can degrade petroleum hydrocarbons, providing the advantages of low cost and few side effects towards ecosystems. Here, we evaluated the mechanisms of microbial degradation of marine petroleum hydrocarbon using metagenomics and metatranscriptomics approaches in order to provide new insight into microbial degradation of petroleum hydrocarbon. Seawater samples were collected at a depth of ∼8 m from an area near a drilling platform in the Bohai Bay and metagenomic sequencing was used to evaluate the functional potential of these marine microbial communities. Metatranscriptomic sequencing, fluorescence in-situ hybridization experiments, and flow cytometry were also performed on the microbial communities of samples subjected to 12 different culture conditions. The data were also subjected to Weighted Gene Co-expression Network Analysis (WGCNA) and co-transcription data visualization to evaluate co-transcription of gene functions. Metagenomic sequencing indicated the presence of numerous genes that were related to petroleum hydrocarbon metabolism. Further, the high co-transcription of genes in multiple pathways, indicated that groups of genes were synergistically transcribed to metabolize petroleum hydrocarbons. Metatranscriptomics also showed that microbial metabolism was highly active in the enrichments and that the transcription of a large number of prokaryotic replication and repair genes were significantly up-regulated including those encoding for the type VI secretion system (T6SS) protein, DNA polymerase I, thymidine phosphorylase, mevalonate kinase, and two-component systems. Concomitantly, the transcription of ribosomal genes involved in translation and photosynthetic genes involved in energy metabolism were down-regulated. Overall, oil and oxygen presence can increase the oil-degradation rates and related genes’ transcription. Lot different metabolisms are co-regulated to exploit nutrients derived from the metabolism of petroleum hydrocarbons. Our analysis of metagenomic, metatranscriptomic and degradation data in this study show that a widespread gene spectrum involved in oil-degradation and the cooperation among genes is of great importance.

The water and sediments of urban rivers are spatially heterogeneous because of the influence of environmental and anthropogenic factors. However, the spatial and functional diversity of bacterial communities in urban river sediments are unclear. We investigated the spatial distribution of microbial compositions in sediments in Qingdao section of the Dagu River, and the effects of sediment physiochemical properties on the variation were explored. Among the seven heavy metals analyzed, only the average concentration of Cd significantly exceeded the safety limit for sediments. The detailed composition and spatial distribution of bacterial communities fluctuated substantially between sites along the river. Bacterial datasets were separated into three clusters according to the environmental characteristics of sampling areas (the urbanized, scenic, and intertidal zones). For the urbanized zone, Acidobacteria, Firmicutes, Gemmatimonadetes, Bacteroidetes, and Gammaproteobacteria were significantly enriched, implying the effects of human activity. In the intertidal zone, Alphaproteobacteria and Deltaproteobacteria were significantly enriched, which are associated with S redox processes, as in the marine environment. Variation partitioning analysis showed that the amount of variation independently explained by variables of Na, Al, total S and Zn was largest, followed by sediment nutrients, while heavy metals and pH explained independently 13% and 9% of the variance, respectively. Overall, microbial structures in the Dagu River exhibited spatial variation and functional diversity as a result of natural and anthropogenic factors. The results will enable the prediction of the changes in urban river ecosystems that maintain their ecological balance and health.

Thallium (Tl) is a highly toxic metalloid and is considered a priority pollutant by the US Environmental Protection Agency (EPA). Currently, few studies have investigated the distribution patterns of bacterial and fungal microbiomes in Tl-impacted environments. In this study, we used high-throughput sequencing to assess the bacterial and fungal profiles along a gradient of Tl contents in Tl mine waste rocks in southwestern China. Our results showed that Tl had an important, but different influence on the bacterial and fungal diversity indices. Using linear regression analysis, we furtherly divided the dominant bacterial and fungal groups into three distinct microbial sub-communities thriving at high, moderate, and low levels of Tl. Furthermore, our results also showed that Tl is also an important environmental variable that regulates the distribution patterns of ecological clusters and indicator genera. Interestingly, the microbial groups enriched in the samples with high Tl levels were mainly involved in metal and nutrient cycling. Taken together, our results have provided useful information about the responses of bacterial and fungal groups to Tl contamination.