Metagenomic and Metatranscriptomic Study of Microbial Metal Resistance in an Acidic Pit Lake

Nutrient structure dynamics and microbial communities at the water-sediment interface in an extremely acidic lake in northern Patagonia

Lake Caviahue (37° 50 'S and 71° 06' W; Patagonia, Argentina) is an extreme case of a glacial, naturally acidic, aquatic environment (pH ~ 3). Knowledge of the bacterial communities in the water column of this lake, is incipient, with a basal quantification of the bacterioplankton abundance distribution in the North and South Basins of Lake Caviahue, and the described the presence of sulfur and iron oxidizing bacteria in the lake sediments. The role that bacterioplankton plays in nutrient utilization and recycling in this environment, especially in the phosphorus cycle, has not been studied. In this work, we explore this aspect in further depth by assessing the diversity of pelagic, littoral and sediment bacteria, using state of the art molecular methods and identifying the differences and commonalties in the composition of the cognate communities. Also, we investigate the interactions between the sediments of Lake Caviahue and the microbial communities present in both sediments, pore water and the water column, to comprehend the ecological relationships driving nutrient structure and fluxes, with a special focus on carbon, nitrogen, and phosphorus. Two major environmental patterns were observed: (a) one distinguishing the surface water samples due to temperature, Fe2+, and electrical conductivity, and (b) another distinguishing winter and summer samples due to the high pH and increasing concentrations of N-NH4+, DOC and SO42-, from autumn and spring samples with high soluble reactive phosphorus (SRP) and iron concentrations. The largest bacterial abundance was found in autumn, alongside higher levels of dissolved phosphorus, iron forms, and increased conductivity. The highest values of bacterial biomass were found in the bottom strata of the lake, which is also where the greatest diversity in microbial communities was found. The experiments using continuous flow column microcosms showed that microbial growth over time, in both the test and control columns, was accompanied by a decrease in the concentration of dissolved nutrients (SRP and N-NH4+), providing proof that sediment microorganisms are active and contribute significantly to nutrient utilization/mobilization.

Occurrence, fate and potential health risks of antibiotic resistomes in a constructed wetlands-reservoir ecosystem for drinking water source improvement

The development of effective and feasible engineering technologies to control the transmission of antibiotic resistance genes (ARGs) and pathogenic antibiotic-resistant bacteria (PARB) form drinking water sources is urgently needed for ensuring drinking water safety. In this study, metagenomic analysis was applied to systematically explore the full profiles, removal, and potential health risks of antibiotic resistomes in a large constructed wetlands-reservoir ecosystem (CWs-R) for drinking water source improvement. A total of 343 ARG subtypes belonging to 18 ARG types were identified from water and sediment samples in the CWs-R ecosystem, with an average abundance of 0.339 copies/cell, and bacitracin and multidrug resistance genes were the predominant ARG types in the water and sediment, respectively. The CWs-R ecosystem showed an excellent removal efficiency of ARGs and mobile genetic elements (MGEs) in water, with the total removal rate reaching 64.82 % and 77.09 %, respectively, among which the emergent plant zone and ecological storage unit played major roles. The metagenomic assembly tracked many mobile ARGs and opportunistic pathogens in the CWs-R ecosystem and identified 19 contigs as ARG-carrying pathogens, including Staphylococcus aureus, Salmonella enterica, Escherichia coli, and Klebsiella pneumonia. Overall, the CWs-R ecosystem has an important role in reducing the potential public health risks posed by antibiotic resistomes in drinking water sources but still cannot fully eliminate them. Therefore, we further classified water and sediment samples in the CWs-R ecosystem and identified potential ARGs and PARB indicators based on the metagenomic analysis results by considering the potential for horizontal transfer of ARGs to opportunistic pathogens. Taken together, this work demonstrates the CWs-R ecosystem as an economical and feasible engineering technology to reduce the dissemination of antibiotic resistomes in the drinking water source, provides useful information for monitoring and controlling antibiotic resistance in similar water sources, and ensures biosafety of drinking water.

Exploring the relationship between metal(loid) contamination rate, physicochemical conditions, and microbial community dynamics in industrially contaminated urban soils

Increasing metal(loid) contamination in urban soils and its impact on soil microbial community have attracted considerable attention. In the present study, the physicochemical parameters and the effects of twelve metal(loid) pollution on soil microbial diversity, their ecotoxic effects, and human health risk assessment in urban soils with different industrial background were studied in comparison with an unpolluted forest soil sample. Results showed that urban soils were highly contaminated, and metal(loid) contamination significantly influenced structure of the soil microbial communities. In all samples the bacterial community was dominated by Proteobacteria, and on the level of phyla characteristic differences were not possible to observe between polluted and control sampling sites. However, clear differences emerged at class and genus level, where several rare taxa disappeared from contaminated urban soils. Simper test results showed that there is 71.6 % bacterial OTU and 9.5 % bacterial diversity dissimilarity between polluted and control samples. Ratio of Patescibacteria, Armatimonadetes, Chlamydiae, Fibrobacteres, and Gemmatimonadetes indicated a significant (p < 0.05) positive correlation with soil Zn, Cr, Pb, Sn, Cu, Mn content, suggest that metal(loid)s strongly influence the structure of microbial community. In contrast, the presence of metal(loid) contamination in urban soils has been found to significantly reduce the population of Archaeal communities. This can be attributed to the depletion of organic matter caused by contamination that reached a minimum of 0.5 m/m% for nitrate and 0.9 m/m% for total organic carbon. The values of urban soil pH were close to neutral, ranging from 5.9 to 8.3. The findings of ecotoxicology test are alarming, as all the studied urban soil sites were cytotoxic to soil microorganisms, and in one site metal(loid) contamination reached genotoxic level. Moreover, all the metal(loid) contaminated sites pose severe and persistent health risk to children, highlighting the urgent need for effective measures to mitigate metal(loid) pollution in urban areas.

Effects of metal contamination with physicochemical properties on the sediment microbial communities in a tropical eutrophic-hypereutrophic urban reservoir in Brazil

We investigated the effects of metals and physicochemical variables on the microbes and their metabolisms in the sediments of Guarapiranga reservoir, a tropical eutrophic-hypereutrophic freshwater reservoir located in a highly urbanized and industrialized area in Brazil. The metals cadmium, copper, and chromium showed minor contribution to changes in the structure, composition, and richness of sediment microbial communities and functions. However, the effects of metals on the microbiota are increased when taken together with physicochemical properties, including the sediment carbon and sulfur, the bottom water electrical conductivity, and the depth of the water column. Clearly, diverse anthropic activities, such as sewage discharge, copper sulfate application to control algal growth, water transfer, urbanization, and industrialization, contribute to increase these parameters and the metals spatially in the reservoir. Microbes found especially in metal-contaminated sites encompassed Bathyarchaeia, MBG-D and DHVEG-1, Halosiccatus, Candidatus Methanoperedens, Anaeromyxobacter, Sva0485, Thermodesulfovibrionia, Acidobacteria, and SJA-15, possibly showing metal resistance or acting in metal bioremediation. Knallgas bacteria, nitrate ammonification, sulfate respiration, and methanotrophy were inferred to occur in metal-contaminated sites and may also contribute to metal removal. This knowledge about the sediment microbiota and metabolisms in a freshwater reservoir impacted by anthropic activities allows new insights about their potential for metal bioremediation in these environments.

Contrasting prokaryotic and eukaryotic community assembly and species coexistence in acid mine drainage-polluted waters

Acid mine drainage (AMD) is characterized by high acidity and high-concentration metals and sulfate, representing an extreme environment to life as well as environmental challenge worldwide. Microorganisms thriving in AMD habitats have evolved with distinct mechanisms in response to multiple stresses. Compared with microbial prokaryotes, our understanding regarding eukaryotic occurrence and role in AMD habitats remain limited. Here we examined microbial diversity and co-occurrence pattern within all domains of life in five lakes with varying degrees of AMD contamination ranging from extremely acidic to neutral. We demonstrated that AMD pollution reduced both eukaryotic and prokaryotic diversity in the lakes. In lakes with serious AMD pollution, chemoautotrophs including Ferrovum, Acidithiobacillus, and Leptospirillum showed significantly higher abundance, whereas with the macroscopic growths of photosynthetic microalgae (e.g., Coccomyxa and Chlamydomonas), heterotrophic or mixotrophic prokaryotes (e.g., Acidiphilium, Thiomonas, and Alicyclobacillus) increased in less polluted lakes. In the further improved ecosystems, Ochromonas, Rotifer, Ciliophora and other microeukaryotes appeared. Combined with a public dataset focusing on the microbes along an AMD-contaminated stream, we further demonstrated that acidity-dominated environmental selection served as the primary driver of both eukaryotic and prokaryotic community assemblies, and to a greater extent for eukaryotes. Furthermore, specific prokaryotic and eukaryotic taxa (e.g., Proteobacteria and Chlorophyta) exhibited wide taxonomic and functional associations in these AMD-polluted waters. These findings expand our knowledge on the eukaryotic diversity in AMD habitats, and provide insights into the ecological processes underlying microbial communities in response to AMD contamination.

Microbial carbon, sulfur, iron, and nitrogen cycling linked to the potential remediation of a meromictic acidic pit lake

Cueva de la Mora is a permanently stratified acidic pit lake and a model system for extreme acid mine drainage (AMD) studies. Using a combination of amplicon sequencing, metagenomics and metatranscriptomics we performed a taxonomically resolved analysis of microbial contributions to carbon, sulfur, iron, and nitrogen cycling. We found that active green alga Coccomyxa onubensis dominated the upper layer and chemocline. The chemocline had activity for iron(II) oxidation carried out by populations of Ca. Acidulodesulfobacterium, Ferrovum, Leptospirillium, and Armatimonadetes. Predicted activity for iron(III) reduction was only detected in the deep layer affiliated with Proteobacteria. Activity for dissimilatory nitrogen cycling including nitrogen fixation and nitrate reduction was primarily predicted in the chemocline. Heterotrophic archaeal populations with predicted activity for sulfide oxidation related to uncultured Thermoplasmatales dominated in the deep layer. Abundant sulfate-reducing Desulfomonile and Ca. Acidulodesulfobacterium populations were active in the chemocline. In the deep layer, uncultured populations from the bacterial phyla Actinobacteria, Chloroflexi, and Nitrospirae contributed to both sulfate reduction and sulfide oxidation. Based on this information we evaluated the potential for sulfide mineral precipitation in the deep layer as a tool for remediation. We argue that sulfide precipitation is not limited by microbial genetic potential but rather by the quantity and quality of organic carbon reaching the deep layer as well as by oxygen additions to the groundwater enabling sulfur oxidation. Addition of organic carbon and elemental sulfur should stimulate sulfate reduction and limit reoxidation of sulfide minerals.

Non-charismatic waterbodies and ecosystem disservices: Mine pit lakes are underrepresented in the literature

Pit lakes are one of the greatest legacies of open-cut mining. Despite the potential hazards of these lakes, they represent newly formed ecosystems with great scientific and ecological potential. Although thousands of pit lakes occur on every inhabited continent, with more being created, the microbial ecology of pit lakes is relatively under-researched. We evaluated the current state of microbial research in pit lakes by performing a Web of Science search and creating a literature database. Study lakes were categorized according to location and water quality (pH and conductivity) which is a key community and environmental concern. Research technology employed in the study was also categorized. We compared research effort in lakes, rivers, and streams which are the more "charismatic" inland aquatic ecosystems. Pit lake publications on microbes from 1987 to 2022 (n = 128) were underrepresented in the literature relative to rivers and streams (n = 321) and natural lakes (n = 948). Of the 128 pit lake publications, 28 were within the field of geochemistry using indirect measures of microbial activity. Most pit lake microbial research was conducted in a few acidic lakes in Germany due to social pressure for remediation and government initiative. Relatively few studies have capitalized on emerging technology. Pit lake microbial research likely lags other more charismatic ecosystems given that they are viewed as performing "ecosystem disservices," but this is socially complex and requires further research. Improving understanding of microbial dynamics in pit lakes will allow scientists to deliver safer pit lakes to communities.

Novel Microorganisms Contribute to Biosulfidogenesis in the Deep Layer of an Acidic Pit Lake

Cueva de la Mora is a permanently stratified acidic pit lake with extremely high concentrations of heavy metals at depth. In order to evaluate the potential for in situ sulfide production, we characterized the microbial community in the deep layer using metagenomics and metatranscriptomics. We retrieved 18 high quality metagenome-assembled genomes (MAGs) representing the most abundant populations. None of the MAGs were closely related to either cultured or non-cultured organisms from the Genome Taxonomy or NCBI databases (none with average nucleotide identity >95%). Despite oxygen concentrations that are consistently below detection in the deep layer, some archaeal and bacterial MAGs mapped transcripts of genes for sulfide oxidation coupled with oxygen reduction. Among these microaerophilic sulfide oxidizers, mixotrophic Thermoplasmatales archaea were the most numerous and represented 24% of the total community. Populations associated with the highest predicted in situ activity for sulfate reduction were affiliated with Actinobacteria, Chloroflexi, and Nitrospirae phyla, and together represented about 9% of the total community. These MAGs, in addition to a less abundant Proteobacteria MAG in the genus Desulfomonile, contained transcripts of genes in the Wood-Ljungdahl pathway. All MAGs had significant genetic potential for organic carbon oxidation. Our results indicate that novel acidophiles are contributing to biosulfidogenesis in the deep layer of Cueva de la Mora, and that in situ sulfide production is limited by organic carbon availability and sulfur oxidation.

Prokaryotic communities in the historic silver mine Reiche Zeche

The research and education mine “Reiche Zeche” in Freiberg (Saxony, Germany) represents one of the most famous mining facilities reminiscent to the century-long history of silver production in the Ore Mountains. The mine was set up at the end of the fourteenth century and became part of the “Bergakademie Freiberg” in 1919. Galena, pyrite, sphalerite, arsenopyrite, and chalcopyrite are the most common minerals found in the mine. As acid mine drainage is generated from the dissolution of sulfidic ores, the microbial habitats within the adits and galleries are characterized by low pH and high concentrations of metal(loid)s. The community composition was investigated at locations characterized by biofilm formation and iron-rich bottom pools. Amplicon libraries were sequenced on a MiSeq instrument. The taxonomic survey yielded an unexpected diversity of 25 bacterial phyla including ten genera of iron-oxidizing taxa. The community composition in the snottites and biofilms only slightly differed from the communities found in acidic bottom pools regarding the diversity of iron oxidizers, the key players in most investigated habitats. Sequences of the Candidate Phyla Radiation as, e.g., Dojkabacteria and Eremiobacterota were found in almost all samples. Archaea of the classes Thermoplasmata and Nitrososphaeria were detected in some biofilm communities.

Vertical environmental gradient drives prokaryotic microbial community assembly and species coexistence in a stratified acid mine drainage lake

Acid mine drainage (AMD) lakes are typical hydrologic features caused by open pit mining and represent extreme ecosystems and environmental challenges. Little is known about microbial distribution and community assembly in AMD lakes, especially in deep layers. Here, we investigated prokaryotic microbial diversity and community assembly along a depth profile in a stratified AMD lake using 16S rRNA gene sequencing combined with multivariate ecological and statistical methods. The water column in the AMD lake exhibited tight geochemical gradients, with more acidic surface water. Coupled with vertical hydrochemical variations, prokaryotic microbial community structure changed significantly, and was accompanied by increased diversity with depth. In the surface water, heterogeneous selection was the most important assembly process, whereas stochastic processes gained importance with depth. Meanwhile, microbial co-occurrences, especially positive interactions, were more frequent in the stressful surface water with reduced network modularity and keystone taxa. The pH was identified as the key driver of microbial diversity and community assembly along the vertical profile based on random forest analysis. Taken together, environmental effects dominated by acid stress drove the community assembly and species coexistence that underpinned the spatial scaling patterns of AMD microbiota in the lake. These findings demonstrate the distinct heterogeneity of local prokaryotic microbial community in AMD lake, and provide new insights into the mechanism to maintain microbial diversity in extreme acidic environments.