Acid Mine Drainage Ecosystem Research Articles

Genome-resolved metagenomics reveals depth-related patterns of microbial community structure and functions in a highly stratified, AMD overlaying mine tailings

Acid mine drainage (AMD) is a worldwide environmental problem, yet bioremediation is hampered by a limited knowledge of the reductive microbial processes in the AMD ecosystem. Here, we generate extensive metagenome and geochemical datasets to investigate how microbial populations and metabolic capacities driving major element cycles are structured in a highly stratified, AMD overlaying tailings environment. The results demonstrated an explicit depth-dependent differentiation of microbial community composition and function profiles between the surface and deeper tailings layers, paralleling the dramatic shifts in major physical and geochemical properties. Specifically, key genes involved in sulfur and iron oxidation were significantly enriched in the surface tailings, whereas those associated with reductive nitrogen, sulfur, and iron processes were enriched in the deeper layers. Genome-resolved metagenomics retrieved 406 intermediate or high-quality genomes spanning 26 phyla, including major new groups (e.g., Patescibacteria and DPANN). Metabolic models involving nitrogen, sulfur, iron, and carbon cycles were proposed based on the functional potentials of the abundant microbial genomes, emphasizing syntrophy and the importance of lesser-known taxa in the degradation of complex carbon compounds. These results have implications for in situ AMD bioremediation.

New Insights into Microbial Interactions with Dissolved Organic Matter in Acid Mine Drainage with the Integration of Microbial Community and Chemical Composition Analysis

Acid mine drainage (AMD) environments are one of the most extreme ecosystems on earth, and their biogeochemical cycling has been widely studied. However, the carbon cycling underlying microbial interactions with dissolved organic matter (DOM) is poorly understood in these environments. Here, we evaluated the relationships between microbial populations and DOM pools in an AMD lake by combining high-throughput microbial and chemical compositional analyses. The results demonstrated that microalgae were the predominant primary producers in the system and significantly contributed to the total DOM concentration in the water column, whereas DOM chemodiversity was correlated with bacterial community diversity. Network analyses further revealed that DOM associated with microalgae had low diversity but high relative abundance, suggesting microalgal selective organic matter contribution to the DOM pool. Conversely, diverse DOM molecules with generally low abundance were associated with heterotrophic acidophiles, including members of Alphaproteobacteria, Actinobacteria, Firmicutes, and Acidobacteria. Moreover, microalgae and bacteria exhibited predominantly positive co-occurrences with potential metabolic interactions via DOM exchange. Taken together, this study provides new insights into the microbe–DOM interactions in extreme AMD ecosystems and has significant implications for understanding the carbon cycle and microbial metabolism in extreme environments.

Thermoplasmata and Nitrososphaeria as dominant archaeal members in acid mine drainage sediment of Malanjkhand Copper Project, India.

Acid mine drainage (AMD) harbors all three life forms inspite of its toxic and hazardous nature. In comparison to bacterial diversity, an in-depth understanding of the archaeal diversity in AMD and their ecological significance remain less explored. Archaeal populations are known to play significant roles in various biogeochemical cycles within the AMD ecosystem, and it is imperative to have a deeper understanding of archaeal diversity and their functional potential in AMD system. The present study is aimed to understand the archaeal diversity of an AMD sediment of Malanjkhand Copper Project, India through archaea specific V6 region of 16S rRNA gene amplicon sequencing. Geochemical data confirmed the acidic, toxic, heavy metal-rich nature of the sample. Archaea specific V6-16S rRNA gene amplicon data showed a predominance of Thermoplasmata (BSLdp215, uncultured Thermoplasmata, and Thermoplasmataceae) and Nitrososphaeria (Nitrosotaleaceae) members constituting ~ 95% of the archaeal community. Uncultured members of Bathyarchaeia, Group 1.1c, Hydrothermarchaeota, and Methanomassiliicoccales along with Methanobacteriaceae, Methanocellaceae, Haloferaceae, Methanosaetaceae, and Methanoregulaceae constituted the part of rare taxa. Analysis of sequence reads indicated that apart from their close ecological relevance, members of the Thermoplasmata present in Malanjkhand AMD were mostly involved in chemoheterotrophy, Fe/S redox cycling, and with heavy metal resistance, while the Nitrososphaeria members were responsible for ammonia oxidation and fixation of HCO3- through 3-hydroxypropionate/4-hydroxybutyrate cycle at low pH and oligotrophic environment which subsequently played an important role in nitrification process in AMD sediment. Overall, the present study elucidated the biogeochemical significance of archaeal populations inhabiting the toxic AMD environment.

Contrasting seasonal variations of geochemistry and microbial community in two adjacent acid mine drainage lakes in Anhui Province, China.

Acid mine drainage (AMD) is generated by the bio-oxidation of sulfide minerals. To understand the AMD formation and evolution, it is necessary to determine the composition and variation of acidophilic community, and their role in AMD ecosystem. In this study, we compared seasonal variations of geochemistry and microbial composition of two adjacent AMD lakes with different formation histories in Anhui Province, China. Lake Paitu (PT) formed in 1970s near a mine dump and the pH was in the range of 3.01-3.16, with the lowest in spring and summer while the highest in winter. The main ions in PT were Al and SO42-, whereas Fe concentration was relatively low. The concentrations of these ions were the lowest in summer and the highest in winter. Lake Tafang (TF) formed in around 2013 in a pit was more acidic (pH 2.43-2.75), but the seasonal variation of pH was the same as PT. Compared with Lake PT, TF had higher Fe, lower Al and SO42- concentrations, and showed no significant seasonal changes. Despite salient seasonal variations of prokaryotic composition in Lake PT, Ferrovum was the major iron-oxidizing bacterium in most seasons. Furthermore, Lake PT was also rich in heterotrophic bacteria (48.6±15.9%). Both prokaryotic diversity and evenness of Lake TF were lower than PT, and chemolithotrophic iron-oxidizing bacteria (71.7±25.4%) were dominant in almost all samples. Besides Ferrovum, more acid tolerant iron-oxidizer Leptospirillum and Acidithiobacillus were also abundant in Lake TF. Chlamydomonas was the major eukaryote in Lake PT and it flourished repeatedly at the end of December, causing an extremely high chlorophyll a concentration (587μg/L) at one sampling site in 2016, which provided rich nutrients for heterotrophic bacteria. The main alga in Lake TF was Chrysonebula, but its concentration was low, apparently because of the strong acidity and dark red color of lake water.

Ferric Uptake Regulator Provides a New Strategy for Acidophile Adaptation to Acidic Ecosystems.

Acidophiles play a dominant role in driving elemental cycling in natural acid mine drainage (AMD) habitats and exhibit important application value in bioleaching and bioremediation. Acidity is an inevitable environmental stress and a key factor that affects the survival of acidophiles in their acidified natural habitats; however, the regulatory strategies applied by acidophilic bacteria to withstand low pH are unclear. We identified the significance of the ferric uptake regulator (Fur) in acidophiles adapting to acidic environments and discovered that Fur is ubiquitous as well as highly conserved in acidophilic bacteria. Mutagenesis of the fur gene of Acidithiobacillus caldus, a prototypical acidophilic sulfur-oxidizing bacterium found in AMD, revealed that Fur is required for the acid resistance of this acidophilic bacterium. Phenotypic characterization, transcriptome sequencing (RNA-seq), mutagenesis, and biochemical assays indicated that the Acidithiobacillus caldus ferric uptake regulator (AcFur) is involved in extreme acid resistance by regulating the expression of several key genes of certain cellular activities, such as iron transport, biofilm formation, sulfur metabolism, chemotaxis, and flagellar biosynthesis. Finally, a Fur-dependent acid resistance regulatory strategy in A. caldus was proposed to illustrate the ecological behavior of acidophilic bacteria under low pH. This study provides new insights into the adaptation strategies of acidophiles to AMD ecosystems and will promote the design and development of engineered biological systems for the environmental adaptation of acidophiles.IMPORTANCE This study advances our understanding of the acid tolerance mechanism of A. caldus, identifies the key fur gene responsible for acid resistance, and elucidates the correlation between fur and acid resistance, thus contributing to an understanding of the ecological behavior of acidophilic bacteria. These findings provide new insights into the acid resistance process in Acidithiobacillus species, thereby promoting the study of the environmental adaptation of acidophilic bacteria and the design of engineered biological systems.

Microbial Diversity and Community Assembly across Environmental Gradients in Acid Mine Drainage

Microorganisms play an important role in weathering sulfide minerals worldwide and thrive in metal-rich and extremely acidic environments in acid mine drainage (AMD). Advanced molecular methods provide in-depth information on the microbial diversity and community dynamics in the AMD-generating environment. Although the diversity is relatively low and in general inversely correlated with the acidity, a considerable number of microbial species have been detected and described in AMD ecosystems. The acidophilic microbial communities dominated by iron/sulfur-oxidizing microbes vary widely in their composition and structure across diverse environmental gradients. Environmental conditions affect the microbial community assembly via direct and indirect interactions with microbes, resulting in an environmentally dependent biogeographic pattern. This article summarizes the latest studies to provide a better understanding of the microbial biodiversity and community assembly in AMD environments.

Significant seasonal variations of microbial community in an acid mine drainage lake in Anhui Province, China

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.

Microbial Community Composition in Acid Mine Drainage Lake of Xiang Mountain Sulfide Mine in Anhui Province, China

Acid mine drainage (AMD) lake of Xiang Mountain in Anhui Province, China, was characterized by acidic waters (pH around 2.8) containing high concentrations of soluble metals and sulfate. To investigate the function and dynamics of this extreme ecosystem, four water samples were collected from the lake in the fall of 2010. The acidophilic community structure was analyzed by molecular approaches, and bacterial and archaeal clone libraries of 16S rRNA genes were constructed. In contrast to dominance of chemolithotrophic acidophiles in typical AMD environments, autotrophic iron/sulfur-oxidizing bacteria were detected in only one sample with low abundance. Unexpectedly, the Cyanobacteria group was the predominant in all four samples (54.9%−77%). Chemoheterotrophs Acidiphilium and Acidisphaera were also abundant. These two heterotrophic groups contain bacteriochlorophyll that can perform photosynthesis, an advantage to grow and survive in such oligotrophic acidic environments. Only two clone sequences related to Legionella (2.8% of the total clones) were recovered from one sample in sharp contrast to its higher abundance (12.7%) in the summer of 2009. All archaeal sequences were affiliated to the phylum Crenarchaeota. The results of statistical analysis suggested that the water chemistry of the AMD lake controlled microbial composition of the AMD ecosystem.

Cultivation-dependent and cultivation-independent characterization of the microbial community in acid mine drainage associated with acidic Pb/Zn mine tailings at Lechang, Guangdong, China

Cultivation-based and molecular approaches were used to characterize the phylogenetic composition and structure of the microbial community in an extremely acidic (pH 2.0) acid mine drainage (AMD) associated with Pb/Zn mine tailings that were undergoing vigorous acid generation. Acidophilic bacteria were isolated and enumerated on solid media, and were found to be restricted to isolates related to Acidithiobacillus ferrooxidans and Acidiphilium cryptum. By contrast, cloning and phylogenetic analysis of 16S rRNA genes revealed that, although low in total taxonomically distinct groups, the tailings AMD ecosystem harbored a wide range of phylogenetically diverse microbes. Of the 141 clones examined, 104 were phylogenetically affiliated with the recently discovered, iron-oxidizing Leptospirillum group III within the Nitrospira. It thus appears that iron serves as the major electron donor in this habitat. Thirty clones were affiliated with the Proteobacteria, half of which belonged to organisms related to Alphaproteobacteria species capable of ferric iron reduction. Other clones were grouped with Betaproteobacteria and Gammaproteobacteria (six clones each), and even with Deltaproteobacteria (three clones), a subdivision with anaerobic sulfate or metal (iron) reduction as the predominant physiological trait of its members. Finally, four clones were clustered within the Firmicutes and the Acidobacteria. Approximately half of the sequence types representing the majority of the total clones fell into lineages that are poorly represented by cultured organisms or have thus far been represented by only a few environmental sequences. Thus, the present study extends our knowledge of the biodiversity of microorganisms populating highly acidic AMD environments.