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.

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 wide use of antibiotics in aquaculture for prophylactic and therapeutic purposes can potentially lead to the prevalence of antibiotic resistance genes (ARGs). This study reports for the first time the profile of ARGs from effluents of coastal aquaculture located in South Jeolla province and Jeju Island, South Korea. Using quantitative PCR (qPCR), twenty-two ARGs encoding tetracycline resistance (tetA, tetB, tetD, tetE, tetG, tetH, tetM, tetQ, tetX, tetZ, tetBP), sulfonamide resistance (sul1, sul2), quinolone resistance (qnrD, qnrS, aac(6′)-Ib-cr), β-lactams resistance (blaTEM, blaCTX, blaSHV), macrolide resistance (ermC), florfenicol resistance (floR) and multidrug resistance (oqxA) and a class 1 integrons-integrase gene (intI1) were quantified. In addition, Illumina Miseq sequencing was applied to investigate microbial community differences across fish farm effluents. Results from qPCR showed that the total number of detected ARGs ranged from 4.24 × 10⁻³ to 1.46 × 10⁻² copies/16S rRNA gene. Among them, tetB and tetD were predominant, accounting for 74.8%–98.0% of the total ARGs. Furthermore, intI1 gene showed positive correlation with tetB, tetD, tetE, tetH, tetX, tetZ tetQ and sul1. Microbial community analysis revealed potential host bacteria for ARGs and intI1. Two genera, Vibrio and Marinomonas belonging to Gammaproteobacteria, showed significant correlation with tetB and tetD, the most dominant ARGs in all samples. Also, operational taxonomic units (OTUs)-based network analysis revealed that ten OTUs, classified into the phyla Proteobacteria, Cyanobacteria/Chloroplast, Bacteroidetes, Verrucomicrobia and an unclassified phylum, were potential hosts of tetracycline resistance genes (i.e., tetA, tetG, tetH, tetM, tetQ and tetZ). Further systematic monitoring of ARGs is warranted for risk assessment and management of antibacterial resistance from fish farm effluents.

The identification of airborne bacteria has traditionally been performed by retrieval in culture media, but the bacterial diversity in the air is underestimated using this method because many bacteria are not readily cultured. Advances in DNA sequencing technology have produced a broad knowledge of genomics and metagenomics, which can greatly improve our ability to identify and study the diversity of airborne bacteria. However, researchers are facing several challenges, particularly the efficient retrieval of low-density microorganisms from the air and the lack of standardized protocols for sample collection and processing. In this study, we tested three methods for sampling bioaerosols — a Durham-type spore trap (Durham), a seven-day recording volumetric spore trap (HST), and a high-throughput 'Jet' spore and particle sampler (Jet) — and recovered metagenomic DNA for 16S rDNA sequencing. Samples were simultaneously collected with the three devices during one week, and the sequencing libraries were analyzed. A simple and efficient method for collecting bioaerosols and extracting good quality DNA for high-throughput sequencing was standardized. The Durham sampler collected preferentially Cyanobacteria, the HST Actinobacteria, Proteobacteria and Firmicutes, and the Jet mainly Proteobacteria and Firmicutes. The HST sampler collected the largest amount of airborne bacterial diversity. More experiments are necessary to select the right sampler, depending on study objectives, which may require monitoring and collecting specific airborne bacteria.

Acid mine drainage (AMD),characterized by strong acidity and high metal concentrations, generates from the oxidative dissolution of metal sulfides, and acidophiles can accelerate the process significantly. Despite extensive research in microbial diversity and community composition, little is known about seasonal variations of microbial community structure (especially micro eukaryotes) in response to environmental conditions in AMD ecosystem. To this end, AMD samples were collected from Nanshan AMD lake, Anhui Province, China, over a full seasonal cycle from 2013 to 2014, and water chemistry and microbial composition were studied. pH of lake water was stable (∼3.0) across the sampling period, while the concentrations of ions varied dramatically. The highest metal concentrations in the lake were found for Mg and Al, not commonly found Fe. Unexpectedly, ultrahigh concentration of chlorophyll a was measured in the extremely acidic lake, reaching 226.43–280.95 μg/L in winter, even higher than those in most eutrophic freshwater lakes. Both prokaryotic and eukaryotic communities showed a strong seasonal variation. Among the prokaryotes, “Ferrovum”, a chemolithotrophic iron-oxidizing bacterium was predominant in most sampling seasons, although it was a minor member prior to September, 2012. Fe2+ was the initial geochemical factor that drove the variation of the prokaryotic community. The eukaryotic community was simple but varied more drastically than the prokaryotic community. Photoautotrophic algae (primary producers) formed a food web with protozoa or flagellate (top consumers) across all four seasons, and temperature appeared to be responsible for the observed seasonal variation. Ochromonas and Chlamydomonas (responsible for high algal bloom in winter) occurred in autumn/summer and winter/spring seasons, respectively, because of their distinct growth temperatures. The closest phylogenetic relationship between Chlamydomonas species in the lake and those in Arctic and Alpine suggested that the native Chlamydomonas species may have been both acidophilic and psychrophilic after a long acclimation time in this extreme environment.

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.

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.

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.