Bacterial response to sharp geochemical gradients caused by acid mine drainage intrusion in a terrace: Relevance of C, N, and S cycling and metal resistance

Soil rehabilitation shaped different patterns of bacterial and archaeal community in AMD-irrigated paddy soil

Microorganisms are essential for soil rehabilitation and long-term sustainability of established plants. However, the recovery process of microorganisms in AMD-irrigated paddy soil is poorly understood at present. To verify this, we sampled AMD-irrigated paddy soils before at different rehabilitation stages by characterizing bacteria and archaea community from a chronosequence of AMD-irrigated rehabilitation to pre-disturbance levels from references sites. Next-generation sequencing is used to describe shifts in diversity and taxonomic composition of bacterial and archaeal. Co-occurrence networks are constructed to reveal potential microbial interaction patterns. The result showed bacterial community followed an observable taxonomic transition overtimes, with community structure becoming more similar to that of unmined reference sites. But the archaeal community only showed a seasonal change, which may hint that the archaeal community needs more time in rehabilitation. Both bacterial and archaeal community composition changes were apparent at high taxonomic levels, bacterial communities become dominated by Proteobacteria phylum, and archaeal community was dominated by Crenarchaeota, we proposed the possible reason is bacterial community were mainly derived by soil pH while the archaeal community was impacted by heavy metal. The bacterial co-occurrence networks increased in complexity during succession, improving the community's resistance to environmental disturbance, while the archaeal did not change monotonically with time. This study highlights the distinct recovery pattern of the bacterial and archaeal community during AMD-irrigated paddy soil rehabilitation, which provides a deep understanding of their role in paddy soil, and subsequent harnessing of their potential to pave the way in future rehabilitation strategies for mined sites.

Microbiome-environment interactions in antimony-contaminated rice paddies and the correlation of core microbiome with arsenic and antimony contamination

Mining activities of antimony (Sb) and arsenic (As) typically result in severe environmental contamination. These contaminants accumulate in rice and thus threaten the health of local residents, who consume Sb- and As-enriched rice grains. Microorganisms play a critical role in the transformation and transportation of Sb and As in paddy soil. Thus, an understanding of the microbiology of contaminated sites would promote the production of safe agricultural products. In this study, six Sb- and As-contaminated rice fields near an active Sb-mining area were investigated. The Sb and As concentrations of all samples were elevated compared to the background level in China. Nitrate, total As, total Sb, and Fe(III) were the major determinants of the microbial community structure. Seven bacterial taxa (i.e. Bradyrhizobium, Bryobacter, Candidatus Solibacter, Geobacter, Gemmatimonas, Halingium, and Sphingomonas) were identified as the core microbiome. These taxa were strongly correlated with the As and Sb contaminant fractions and likely to metabolize As and Sb. Results imply that many soil microbes can survival in the Sb/As contaminated sites.

Sulfate-reducing bacterial community shifts in response to acid mine drainage in the sediment of the Hengshi watershed, South China

Sulfate-reducing bacteria (SRB) are an attractive option for treating acid mine drainage (AMD) and are considered to be of great significance in the natural attenuation of AMD, but the available information regarding the highly diverse SRB community in AMD sites is not comprehensive. The Hengshi River, which is continually contaminated by AMD from upstream mining areas, was selected as a study site for investigation of the distribution, diversity, and abundance of SRB. Overall, high-throughput sequencing of the 16S rRNA and dsrB genes revealed the high diversity, richness, and OTU numbers of SRB communities, suggesting the existence of active sulfate reduction in the study area. Further analysis demonstrated that AMD contamination decreased the richness and diversity of the microbial community and SRB community, and led to spatiotemporal shifts in the overall composition and structure of sediment microbial and SRB communities along the Hengshi watershed. However, the sulfate reduction activity was high in the midstream, even though AMD pollution remained heavy in this area. Spatial distributions of SRB community indicated that species of Clostridia may be more tolerant of AMD contamination than other species, because of their predominance in the SRB communities. In addition, the results of CCA revealed that environmental parameters, such as pH, TS content, and Fe content, can significantly influence total microbial and SRB community structure, and dissolved organic carbon was another important factor structuring the SRB community. This study extends our knowledge of the distribution of indigenous SRB communities and their potential roles in natural AMD attenuation.

Metagenomic exploration of multi-resistance genes linked to microbial attributes in active nonferrous metal(loid) tailings

Mine tailings sites are considered as a continuous source of discharged metal(loid)s and residual organic flotation reagents. They are extremely toxic environments representing unique ecological niches for microbial communities. Mine tailings as a source of multi-resistance genes have been poorly investigated. Metagenomic analysis for four active nonferrous metal(loid) tailings sites with different environmental parameters was conducted. The abundance of Thiobacillus, able to tolerate acidity and showing iron- and sulfur/sulfide oxidation capacities, was significantly different (p < 0.05) between acid and neutral tailings sites. Correlation analyses showed that Zn, Pb, TP, Cd, and Cu were the main drivers influencing the bacterial compositions. Multi-metal resistance genes (MRGs) and antibiotic resistance genes (ARGs), such as baca and copA, were found to be co-selected by high concentrations of metal(loid)s tailings. The main contributors to different distributions of MRGs were Thiobacillus and Nocardioides genus, while genera with low abundance (<0.1%) were the main contributors for ARGs. Functional metabolic pathways related to Fe-S metabolism, polycyclic aromatic hydrocarbons (PAHs) degradation and acid stress were largely from Altererythrobacter, Lysobacter, and Thiobacillus, respectively. Such information provides new insights on active tailings with highly toxic contaminants. Short-term metal(loid) exposure of microorganism in active nonferrous metal(loid) tailings contribute to the co-occurrence of ARGs and MRGs, and aggravation of tailings acidification. Our results recommend that the management of microorganisms involved in acid tolerance and metal/antibiotic resistance is of key importance for in-suit treatment of the continuous discharge of tailings with multiple metal(loid) contaminants into impoundments.

Energy and environmental impact assessment of a passive remediation bioreactor for antimony-rich mine drainage

Industrial processes, such as smelting and mining, lead to antimony (Sb) contamination, which poses an environmental and human health risk. In this study, the energy consumption and environmental impacts of a passive biological treatment system were quantitatively evaluated using life cycle assessment (LCA), and the results were compared with that of an adsorption purification system. The results showed that the biosystem had a lower energy consumption compared with the adsorption system, with an energy savings of 27.39%. The environmental impacts of the bioreactor were also lower regarding acidification, ecotoxicity, carcinogens, climate change, resource depletion, and respiratory effects. The construction resulted in the most energy consumption (99%) for the passive bioreactor. Therefore, adopting environmentally friendly construction materials could make the biosystem a more energy-efficient option. Results demonstrated that the bioreactor in this research can have great potential for Sb mine drainage applications in terms of energy savings and environmental remediation without diminishing performance. The study findings can be useful for deciding the most energy effective process for mine drainage remediation. In addition, the identification of the energy and environmental impacts of the processes provide valuable information for the design of future systems that consume less materials and utilize new construction materials.

Microbial adaptation in vertical soil profiles contaminated by an antimony smelting plant

Antimony mining has resulted in considerable pollution to the soil environment. Although studies on antinomy contamination have been conducted, its effects on vertical soil profiles and depth-resolved microbial communities remain unknown. The current study selected three vertical soil profiles (0–2 m) from the world's largest antimony mining area to characterize the depth-resolved soil microbiota and investigate the effects of mining contamination on microbial adaptation. Results demonstrated that contaminated soil profiles showed distinct depth-resolved effects when compared to uncontaminated soil profiles. As soil depth increased, the concentrations of antimony and arsenic gradually declined in the contaminated soil profiles. Acidobacteria, Chloroflexi, Proteobacteria and Thaumarchaeota were the most variable phyla from surface to deep soil. The co-occurrence networks were loosely connected in surface soil, but obviously recovered and were well-connected in deep soil. The metagenomic results indicated that microbial metabolic potential also changed with soil depth. Genes encoding C metabolism pathways were negatively correlated with antimony and arsenic concentrations. Abundances of arsenic-related genes were enriched by severe contamination, but reduced with soil depth. Overall, soil depth-resolved characteristics are often many meters deep and such effects affected the indigenous microbial communities, as well as their metabolic potential due to different contaminants along vertical depths.

Investigation of the Ecological Roles of Putative Keystone Taxa during Tailing Revegetation

Metal contamination released from tailings is a global environmental concern. Although phytoremediation is a promising remediation method, its practice is often impeded by the adverse tailing geochemical conditions, which suppress biological activities. The ecosystem services provided by indigenous microorganisms could alter environmental conditions and facilitate revegetation in tailings. During the process, the keystone taxa of the microbial community are assumed an essential role in regulating the community composition and functions. The identity and the environmental functions of the keystone taxa during tailing revegetation, however, remain unelucidated. The current study compared the microbial community composition and interactions of two contrasting stibnite (Sb₂S₃) tailings, one revegetated and one unvegetated. The microbial interaction networks and keystone taxa were significantly different in the two tailings. Similar keystone taxa were also identified in other revegetated tailings, but not in their corresponding unvegetated tailings. Metagenome-assembled genomes (MAGs) indicated that the keystone taxa in the revegetated tailing may use both organic and inorganic energy sources (e.g., sulfur, arsenic, and antimony). They could also facilitate plant growth since a number of plant-growth-promoting genes, including phosphorus solubilization and siderophore production genes, were encoded. The current study suggests that keystone taxa may play important roles in tailing revegetation by providing nutrients, such as P and Fe, and promoting plant growth.

Characterization of Nitrate-Dependent As(III)-Oxidizing Communities in Arsenic-Contaminated Soil and Investigation of Their Metabolic Potentials by the Combination of DNA-Stable Isotope Probing and Metagenomics

Arsenite (As(III)) oxidation has important environmental implications by decreasing both the mobility and toxicity of As in the environment. Microbe-mediated nitrate-dependent As(III) oxidation (NDAO) may be an important process for As(III) oxidation in anoxic environments. Our current knowledge of nitrate-dependent As(III)-oxidizing bacteria (NDAB), however, is largely based on isolates, and thus, the diversity of NDAB may be underestimated. In this study, DNA-stable isotope probing (SIP) with ¹³C-labeled NaHCO₃ as the sole carbon source, amplicon sequencing, and shotgun metagenomics were combined to identify NDAB and investigate their NDAO metabolism. As(III) oxidation was observed in the treatment amended with nitrate, while no obvious As(III) oxidation was observed without nitrate addition. The increase in the gene copies of aioA in the nitrate-amended treatment suggested that As(III) oxidation was mediated by microorganisms containing the aioA genes. Furthermore, diverse putative NDAB were identified in the As-contaminated soil cultures, such as Azoarcus, Rhodanobacter, Pseudomonas, and Burkholderiales-related bacteria. Metagenomic analysis further indicated that most of these putative NDAB contained genes for As(III) oxidation and nitrate reduction, confirming their roles in NDAO. The identification of novel putative NDAB expands current knowledge regarding the diversity of NDAB. The current study also suggests the proof of concept of using DNA-SIP to identify the slow-growing NDAB.