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

New insights into efficient iron sulfide oxidation for arsenic immobilization by microaerophilic and acidophilic Fe(II)-oxidizing bacteria under micro-oxygen and acidic conditions

Microbial-mediated FeS oxidation to Fe(Ⅲ) minerals via chemolithoautotrophic Fe(Ⅱ) oxidizers under pH/O₂ limitations engages As immobilization. However, this process is constrained under the dual stress of micro-oxygen and acidic conditions due to the critically diminished Fe(Ⅱ) oxidation capacity. Therefore, the interplay between Fe(Ⅱ) oxidation, carbon metabolism, and As immobilization in Fe(Ⅱ)-oxidizing bacteria under micro-oxygen and acidic conditions remains unclear. This study presents the first successful enrichment of microaerophilic and acidophilic Fe(II)-oxidizing bacteria (MAFeOB). These bacteria are capable of oxidizing FeS to Fe(III) minerals and immobilizing up to 27,835 mg/kg of As(Ⅴ) under micro-oxygen content (below 3.2 mg/L) and acidic pH (4.5-6.2). Through comprehensive metagenomic analysis, it was speculated that MAFeOB harbor a suite of genes potentially participating in critical processes, including carbon fixation, Fe(II) oxidation, and arsenic detoxification. Notably, a potential electron transfer pathway from Cyc2_repCluster2 to Cytochrome cbb3-type oxidases facilitates Fe(II) oxidation. Furthermore, As(Ⅲ) efflux pump (arsA, arsB, acr3) and As(Ⅲ) oxidase (aioA) genes indicate MAFeOB's potential for As immobilization. Our findings underscore the pivotal role of MAFeOB in overcoming limitations associated with Fe(III) mineral formation, thereby enhancing arsenic immobilization under micro-oxygen and acidic water.

Enhanced nitrogen removal from low C/N ratio wastewater by coordination of ternary electron donors of Fe0, carbon source and sulfur: Focus on oxic/anoxic/oxic process

Insufficient organics was the major obstacle for total nitrogen (TN) removal in conventional pre-anoxic denitrification when treating low carbon to nitrogen (C/N) ratio wastewater. This study constructed a novel ternary-electron donors (Fe0, organics and S0) enhanced oxic/anoxic/oxic (O/A/O) process, integrating simultaneous nitrification and denitrification and autotrophic denitrification (ADN), and evaluated its feasibility to achieve efficient nutrient removal under organics-deficient condition. Long-term operation results showed that TN removal was lower (9.9 %) when Fe0 added individually, then raised to 27.3 %∼46.0 % in simultaneous presence of Fe0 and organics. And the highest TN removal (82.0 %) was obtained by coordination of ternary-electron donors, with 8.46 ± 0.43 mg/L TN in effluent. Meanwhile, the O/A/O process exhibited excellent total phosphorous (TP) removal (84.8 %∼98.4 %) derived from chemical precipitation by Fe0, of which the effluent was <0.76 ± 0.04 mg/L TP. Metabolic characteristics indicated that the coordination of multi-electron donors improved microbial metabolism and denitrifying enzymatic activities, thereby promoting ammonia assimilation and enhancing TN removal. And the secretion of EPS was also stimulated, which favored the bio-utilization of Fe0 and S0 and alleviated organics dependence. Besides, the notable increase in abundances of aerobic denitrifiers (23.95 %∼27.37 %), autotrophic denitrifiers (9.31 %) and denitrifying genes further verified the synergy effect of multi-electron donors on TN removal. This study revealed the enhancement mechanism of O/A/O process by coordination of ternary-electron donors, verified its cost-effectiveness and provided innovative insights on low C/N ratio wastewater remediation.

Seasonal variation drives species coexistence and community succession in microbial communities of stratified acidic pit lakes

Acidic pit lakes (APLs) are a special type of ecosystem and represent a significant environmental issue worldwide. While previous studies have explored the structure and function of microbial communities in APLs stratification, natural attenuation, and remediation processes, little is known about the succession patterns of microbial association networks and the underlying assembly mechanisms during seasonal succession. In this study, the distribution characteristics and succession patterns of prokaryotic and eukaryotic microorganisms in APLs across different seasons were investigated using 16S rRNA and 18S rRNA high-throughput sequencing technologies, combined with ecological and multivariate statistical methods. The diversity, composition and structure of prokaryotic and eukaryotic microbial communities showed obvious seasonal differences, and the surface waters were more susceptible to seasonal disturbances. Temperature is the most critical factor influencing the seasonal succession of microbial communities. During the year-round succession, variable selection (40.86 %) dominated in the prokaryotic community and homogeneous selection (69.64 %) dominated in the eukaryotic community. Moreover, the proportion of deterministic processes increased with increasing water temperature differences. Co-occurrence networks were more complex and inter-kingdom exchanges were more frequent during the warm seasons (summer and autumn), and microbial communities were more stable during the cool seasons (spring and winter). Meanwhile, the inter-kingdom interactions between eukaryotes and prokaryotes are predominantly positive in all seasons except autumn, which may serve as a strategy to resist environmental stress. These findings indicate that there is a significant seasonal heterogeneity between eukaryotes and prokaryotes in APLs, providing valuable insights into the ecological processes of microbial community succession in extreme environments.

The Effect of Cysteine on the Removal of Cadmium in Paddy Soil by Combination with Bioremediation and the Response of the Soil Microbial Community

Bioremediation is widely recognized as a promising and efficient approach for the elimination of Cd from contaminated paddy soils. However, the Cd removal efficacy achieved through this method remains unsatisfactory and is accompanied by a marginally higher cost. Cysteine has the potential to improve the bioleaching efficiency of Cd from soils and decrease the use cost since it is green, acidic and has a high Cd affinity. In this study, different combination modes of cysteine and microbial inoculant were designed to analyze their effects on Cd removal and the soil microbial community through the sequence extraction of Cd fraction and high-throughput sequencing. The results demonstrate that the mixture of cysteine and the microbial inoculant was the best mode for increasing the Cd removal efficiency. And a ratio of cysteine to microbial inoculant of 5 mg:2 mL in a 300 mL volume was the most economically efficient matching. The Cd removal rate increased by 7.7-15.1% in comparison with the microbial inoculant treatment. This could be ascribed to the enhanced removal rate of the exchangeable and carbonate-bound Cd, which achieved 94.6% and 96.1%, respectively. After the treatment, the contents of ammonium nitrogen (NH3-N), total phosphorus (TP), available potassium (AK), and available phosphorus (AP) in the paddy soils were increased. The treatment of combinations of cysteine and microbial inoculant had an impact on the soil microbial diversity. The relative abundances of Alicyclobacillus, Metallibacterium, and Bacillus were increased in the paddy soils. The microbial metabolic functions, such as replication and repair and amino acid metabolism, were also increased after treatment, which benefitted the microbial survival and adaptation to the environment. The removal of Cd was attributed to the solubilizing, complexing, and ion-exchanging effects of the cysteine, the intra- and extracellular adsorption, and the production of organic acids of functional microorganisms. Moreover, cysteine, as a carbon, nitrogen, and sulfur source, promoted the growth and metabolism of microorganisms to achieve the effect of the synergistic promotion of microbial Cd removal. Therefore, this study underscored the potential of cysteine to enhance the bioremediation performance in Cd-contaminated paddy soils, offering valuable theoretical and technical insights for this field.

Impact of steel slag, gypsum, and coal gangue on microbial immobilization of metal(loid)s in non-ferrous mine waste dumps

Non-ferrous mine waste dumps globally generate soil pollution characterized by low pH and high metal(loid)s content. In this study, the steel slag (SS), gypsum (G), and coal gangue (CG) combined with functional bacteria consortium (FB23) were used for immobilizing metal(loid)s in the soil. The result shown that FB23 can effectively decrease As, Pb, and Zn concentrations within 10 d in an aqueous medium experiment. In a 310-day field column experiment, solid waste including SS, G, and CG combined with FB23 decreased As, Cd, Cu, and Pb concentrations in the aqueous phase. Optimized treatment was obtained by combining FB23 with 1% SS, 1% G, and 1.5% CG. Furthermore, the application of solid waste (SS, G, and CG) increased the top 20 functional bacterial consortium (FB23) abundance at the genus level from 1% to 21% over 50 days in the soil waste dump. Moreover, dissolved organic carbon (DOC) and pH were identified as the main factors influencing the reduction in bioavailable As, Cd, Cu, and Pb in the combination remediation. Additionally, the reduction of Fe and sulfur S was crucial for decreasing the mobilization of the metal(loid)s. This study provides valuable insights into the remediation of metal contamination on a larger scale.

Intimate microbe-water-mineral interactions mediate alkalization in the pyroxene-rich iron ore mines in Panxi area, Southwest China

In contrast to acid mine drainage, the microbial assembly and (bio)geochemical processes in alkaline mine conditions remain under-investigated. Here, microbe-water-mineral interactions were systematically investigated in two representative iron mines with alkaline conditions in the Panxi mining area, Southwest China. Compared to reference riverine samples less interfered by mining activities, the iron ore samples, composed of vanadium-titanium magnetite and pyroxene-rich bedrocks, exhibited elevated levels of Fe, HCl-extractable Fe(II), total sulfur, nitrate and sulfate, but lower total carbon (TC). Meanwhile, the mine drainage showed significantly higher sulfate, but lower TC concentrations than the riverine samples. Intriguingly, the Serpentinimonas spp., typically reported in serpentinites, prevailed in the microbial communities from the mine samples exhibiting higher pH. This suggests that the alkaline environments in Panxi mines result from serpentinization-like reactions. Enrichment of Thiobacillus spp. was observed in the mine-dwelling microbial communities, positively correlated with total sulfur, sulfate, nitrate, and Fe(II). Genome-resolved metagenomics suggested a chemoautotrophic lifestyle for the Thiobacillus species (e.g., carbon fixation, sulfur oxidation, and oxygen respiration), which may generate H+ and mitigate alkalization. This study provides valuable insights into progressive development of alkaline mine ecosystems and offers guidance for developing appropriate engineering strategies to restore the abandoned alkaline mines.

Taxonomic and functional partitioning of Chloroflexota populations under ferruginous conditions at and below the sediment-water interface

The adaptation of the phylum Chloroflexota to various geochemical conditions is thought to have originated in primitive microbial ecosystems, involving hydrogenotrophic energy conservation under ferruginous anoxia. Oligotrophic deep waters displaying anoxic ferruginous conditions, such as those of Lake Towuti, and their sediments may thus constitute a preferential ecological niche for investigating metabolic versatility in modern Chloroflexota. Combining pore water geochemistry, cell counts, sulfate reduction rates, and 16S rRNA genes with in-depth analysis of metagenome-assembled genomes, we show that Chloroflexota benefit from cross-feeding on metabolites derived from canonical respiration chains and fermentation. Detailing their genetic contents, we provide molecular evidence that Anaerolineae have metabolic potential to use unconventional electron acceptors, different cytochromes, and multiple redox metalloproteins to cope with oxygen fluctuations, and thereby effectively colonizing the ferruginous sediment-water interface. In sediments, Dehalococcoidia evolved to be acetogens, scavenging fatty acids, haloacids, and aromatic acids, apparently bypassing specific steps in carbon assimilation pathways to perform energy-conserving secondary fermentations combined with CO2 fixation via the Wood-Ljungdahl pathway. Our study highlights the partitioning of Chloroflexota populations according to alternative electron acceptors and donors available at the sediment-water interface and below. Chloroflexota would have developed analogous primeval features due to oxygen fluctuations in ancient ferruginous ecosystems.

Enrichment of acid-tolerant sulfide-producing microbes from an acidic pit lake

High concentrations of harmful metal(loid)s and extreme acidity are persistent environmental concerns in acidic pit lakes. In this study, we examine Cueva de la Mora (CM), a meromictic pit lake in the Iberian Pyrite Belt, Spain, as a model system. Our research aims to explore potential bioremediation strategies to mitigate the impacts of metal(loid)s and acidity in such environments. The major strategy applied in this research is to biologically stimulate sulfate reduction (i.e., biosulfidogenesis) in the deep layer of the lake to promote the formation of low-solubility sulfide minerals. Previous omics-based studies of CM have shown that several sulfate-reducing bacteria (SRB) taxa are present in the deep layer. However, their activities are likely limited by the availability of electron donors for sulfide production. Therefore, different amendments (glycerol, elemental sulfur, and glycerol + elemental sulfur) were tested to promote sulfide production and enrich acid-tolerant sulfide-producing microbes. Our results showed that glycerol stimulated dissimilatory sulfate reduction much faster than elemental sulfur alone, suggesting that electron donor limitations control sulfide production. Furthermore, the combined addition of glycerol and elemental sulfur (S(0)) resulted in the highest level of sulfide production. This indicates that S(0) can play a significant role as an electron acceptor in further promoting sulfide production when a suitable electron donor is present. Microbial community analysis revealed that Desulfosporosinus acididurans, a previously discovered acid-tolerant SRB, was enriched and became the dominant species in incubations with glycerol only (~76-96% abundance) or the combination of glycerol and S(0) (~93-99% abundance).

Deciphering microbial metabolic interactions and their implications for community dynamics in acid mine drainage sediments

The microbially-mediated reduction processes have potential for the bioremediation of acid mine drainage (AMD), which represents a worldwide environment problem. However, we know little about the microbial interactions in anaerobic AMD sediments. Here we utilized genome-resolved metagenomics to uncover the nature of cooperative and competitive metabolic interactions in 90 AMD sediments across Southern China. Our analyses recovered well-represented prokaryotic communities through the reconstruction of 2625 population genomes. Functional analyses of these genomes revealed extensive metabolic handoffs which occurred more frequently in nitrogen metabolism than in sulfur metabolism, as well as stable functional redundancy across sediments resulting from populations with low genomic relatedness. Genome-scale metabolic modeling showed that metabolic competition promoted microbial co-occurrence relationships, suggesting that community assembly was dominated by habitat filtering in sediments. Notably, communities colonizing more extreme conditions tended to be highly competitive, which was typically accompanied with increased network complexity but decreased stability of the microbiome. Finally, our results demonstrated that heterotrophic Thermoplasmatota associated with ferric iron and sulfate reduction contributed most to the elevated levels of competition. Our study shed light on the cooperative and competitive metabolisms of microbiome in the hazardous AMD sediments, which may provide preliminary clues for the AMD bioremediation in the future.

Acidophilic sulphate-reducing bacteria: Diversity, ecophysiology, and applications

Acidophilic sulphate-reducing bacteria (aSRB) are widespread anaerobic microorganisms that perform dissimilatory sulphate reduction and have key adaptations to tolerate acidic environments (pH <5.0), such as proton impermeability and Donnan potential. This diverse prokaryotic group is of interest from physiological, ecological, and applicational viewpoints. In this review, we summarize the interactions between aSRB and other microbial guilds, such as syntrophy, and their roles in the biogeochemical cycling of sulphur, iron, carbon, and other elements. We discuss the biotechnological applications of aSRB in treating acid mine drainage (AMD, pH <3), focusing on their ability to produce biogenic sulphide and precipitate metals, particularly in the context of utilizing microbial consortia instead of pure isolates. Metal sulphide nanoparticles recovered after AMD treatment have multiple potential technological uses, including in electronics and biomedicine, contributing to a cost-effective circular economy. The products of aSRB metabolisms, such as biominerals and isotopes, could also serve as biosignatures to understand ancient and extant microbial life in the universe. Overall, aSRB are active components of the sulphur and carbon cycles under acidic conditions, with potential natural and technological implications for the world around us.

Bacterial and Archaeal Communities in Erhai Lake Sediments: Abundance and Metabolic Insight into a Plateau Lake at the Edge of Eutrophication

The littoral zones of lakes are potential hotspots for local algal blooms and biogeochemical cycles; however, the microbial communities within the littoral sediments of eutrophic plateau lakes remain poorly understood. Here, we investigated the taxonomic composition, co-occurrence networks, and potential functional roles of both abundant and rare taxa within bacterial and archaeal communities, as well as physicochemical parameters, in littoral sediments from Erhai Lake, a mesotrophic lake transitioning towards eutrophy located in the Yunnan-Guizhou Plateau. 16S rRNA gene sequencing revealed that bacterial communities were dominated by Proteobacteria, Bacteroidetes, and Chloroflexi, while Euryarchaeota was the main archaeal phylum. Co-occurrence network analysis revealed that keystone taxa mainly belonged to rare species in the bacterial domain, but in the archaeal domain, over half of keystone taxa were abundant species, demonstrating their fundamental roles in network persistence. The rare bacterial taxa contributed substantially to the overall abundance (81.52%), whereas a smaller subset of abundant archaeal taxa accounted for up to 82.70% of the overall abundance. Functional predictions highlighted a divergence in metabolic potentials, with abundant bacterial sub-communities enriched in pathways for nitrogen cycling, sulfur cycling, and chlorate reduction, while rare bacterial sub-communities were linked to carbon cycling processes such as methanotrophy. Abundant archaeal sub-communities exhibited a high potential for methanogenesis, chemoheterotrophy, and dark hydrogen oxidation. Spearman correlation analysis showed that genera such as Candidatus competibacter, Geobacter, Syntrophobacter, Methanocella, and Methanosarcina may serve as potential indicators of eutrophication. Overall, this study provides insight into the distinct roles that rare and abundant taxa play in the littoral sediments of mesotrophic plateau lakes.

Multi-omics insights into biogeochemical responses to organic matter addition in an acidic pit lake: Implications for bioremediation

Acidic pit lakes (APLs) emerge as reservoirs of acid mine drainage in flooded open-pit mines, representing extreme ecosystems and environmental challenges worldwide. The bioremediation of these oligotrophic waters necessitates the addition of organic matter, but the biogeochemical response of APLs to exogenous organic matter remains inadequately comprehended. This study delves into the biogeochemical impacts and remediation effects of digestate-derived organic matter within an APL, employing a multi-omics approach encompassing geochemical analyses, amplicon and metagenome sequencing, and ultra-high resolution mass spectrometry. The results indicated that digestate addition first stimulated fungal proliferation, particularly Ascomycetes and Basidiomycetes, which generated organic acids through lignocellulosic hydrolysis and fermentation. These simple compounds further supported heterotrophic growth, including Acidiphilium, Acidithrix, and Clostridium, thereby facilitating nitrate, iron, and sulfate reduction linked with acidity consumption. Nutrients derived from digestate also promoted the macroscopic development of acidophilic algae. Notably, the increased sulfate reduction-related genes primarily originated from assimilatory metabolism, thus connecting sulfate decrease to organosulfur increase. Assimilatory and dissimilatory sulfate reduction collectively contributed to sulfate removal and metal fixation. These findings yield multi-omics insights into APL biogeochemical responses to organic matter addition, enhancing the understanding of carbon-centered biogeochemical cycling in extreme ecosystems and guiding organic amendment-based bioremediation in oligotrophic polluted environments.

Sulfate-reducing bacteria unearthed: ecological functions of the diverse prokaryotic group in terrestrial environments

Sulfate-reducing prokaryotes (SRPs) are essential microorganisms that play crucial roles in various ecological processes. Even though SRPs have been studied for over a century, there are still gaps in our understanding of their biology. In the past two decades, a significant amount of data on SRP ecology has been accumulated. This review aims to consolidate that information, focusing on SRPs in soils, their relation to the rare biosphere, uncultured sulfate reducers, and their interactions with other organisms in terrestrial ecosystems. SRPs in soils form part of the rare biosphere and contribute to various processes as a low-density population. The data reveal a diverse range of sulfate-reducing taxa intricately involved in terrestrial carbon and sulfur cycles. While some taxa like Desulfitobacterium and Desulfosporosinus are well studied, others are more enigmatic. For example, members of the Acidobacteriota phylum appear to hold significant importance for the terrestrial sulfur cycle. Many aspects of SRP ecology remain mysterious, including sulfate reduction in different bacterial phyla, interactions with bacteria and fungi in soils, and the existence of soil sulfate-reducing archaea. Utilizing metagenomic, metatranscriptomic, and culture-dependent approaches will help uncover the diversity, functional potential, and adaptations of SRPs in the global environment.

Metagenomic insight into the acidophilic functional communities driving elemental geochemical cycles in an acid mine drainage lake

Acidophiles play a key role in the generation, evolution and attenuation of acid mine drainage (AMD), which is characterized by strong acidity (pH<3.5) and high metal concentrations. In this study, the seasonal changes of acidophilic communities and their roles in elemental cycling in an AMD lake (pH∼3.0) in China were analyzed through metagenomics. The results showed eukaryotic algae thrived in the lake, and Coccomyxa was dominant in January (38.1%) and May (33.9%), while Chlorella in July (9.5%). The extensive growth of Chlamydomonas in December (22.7%) resulted in an ultrahigh chlorophyll a concentration (587 μg/L), providing abundant organic carbon for the ecosystem. In addition, the iron-oxidizing and nitrogen-fixing bacterium Ferrovum contributed to carbon fixation. Ammonia oxidation likely occurred in the acidic lake, as was revealed by archaea Ca. Nitrosotalea. To gain a competitive advantage in the nutrient-poor environment, some acidophiles exhibited facultative characteristics, e.g. the most abundant bacterium Acidiphilium utilized both organic and inorganic carbon, and obtained energy from organic matter, inorganic sulfur, and sunlight simultaneously. It was suggested that sunlight, rather than chemical energy of reduced iron-sulfur was the major driver of elemental cycling in the AMD lake. The results are beneficial to the development of bioremediation strategies for AMD.

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.

Reversed oxidative TCA (roTCA) for carbon fixation by an Acidimicrobiia strain from a saline lake

Acidimicrobiia are widely distributed in nature and suggested to be autotrophic via the Calvin-Benson-Bassham (CBB) cycle. However, direct evidence of chemolithoautotrophy in Acidimicrobiia is lacking. Here, we report a chemolithoautotrophic enrichment from a saline lake, and the subsequent isolation and characterization of a chemolithoautotroph, Salinilacustristhrix flava EGI L10123T, which belongs to a new Acidimicrobiia family. Although strain EGI L10123T is autotrophic, neither its genome nor Acidimicrobiia metagenome-assembled genomes from the enrichment culture encode genes necessary for the CBB cycle. Instead, genomic, transcriptomic, enzymatic, and stable-isotope probing data hinted at the activity of the reversed oxidative TCA (roTCA) coupled with the oxidation of sulfide as the electron donor. Phylogenetic analysis and ancestral character reconstructions of Acidimicrobiia suggested that the essential CBB gene rbcL was acquired through multiple horizontal gene transfer events from diverse microbial taxa. In contrast, genes responsible for sulfide- or hydrogen-dependent roTCA carbon fixation were already present in the last common ancestor of extant Acidimicrobiia. These findings imply the possibility of roTCA carbon fixation in Acidimicrobiia and the ecological importance of Acidimicrobiia. Further research in the future is necessary to confirm whether these characteristics are truly widespread across the clade.

Decadal evolution of an acidic pit lake: Insights into the biogeochemical impacts of microbial community succession

Acidic pit lakes represent hydrological features resulting from the accumulation of acid mine drainage in mining operations. Long-term monitoring is essential for these extreme and contaminated environments, yet tracking investigations integrating microbial geochemical dynamics in acidic pit lakes have been lacking thus far. This study integrated historical data with field sampling to track decadal biogeochemical changes in an acidic pit lake. With limited artificial disturbance, significant and sustained biogeochemical changes were observed over the past decade. Surface water pH slowly increased from 2.8 to a maximum of 3.6, with a corresponding increase in bottom water pH to around 3.9, despite the accumulation of externally imported sulfate and metals. Elevated nutrient levels stimulated the macroscopic growth of Chlorophyta, resulting in a shift from reddish-brown to green water with floating algal bodies. Furthermore, microalgae-fixed organic carbon promoted the transition from the initial chemolithotrophy-based population dominated by Acidiphilium and Ferrovum to a heterotrophic community. The increase in heterotrophic iron- and sulfate-reducers may cause an elevation in ferrous levels and a decline in copper concentrations. However, most metals were not removed from the water column, potentially due to insufficient biosulfidogenesis or sulfide reoxidation. These findings offer novel insights into microbial succession in extreme ecosystem evolution and contribute to the management and remediation of acidic pit lakes.

Eukaryotic Community Structure and Interspecific Interactions in a Stratified Acidic Pit Lake Water in Anhui Province

The stratified acidic pit lake formed by the confluence of acid mine drainage has a unique ecological niche and is a model system for extreme microbial studies. Eukaryotes are a component of the AMD community, with the main members including microalgae, fungi, and a small number of protozoa. In this study, we analyzed the structural traits and interactions of eukaryotes (primarily fungi and microalgae) in acidic pit lakes subjected to environmental gradients. Based on the findings, microalgae and fungi were found to dominate different water layers. Specifically, Chlorophyta showed dominance in the well-lit aerobic surface layer, whereas Basidiomycota was more abundant in the dark anoxic lower layer. Co-occurrence network analysis showed that reciprocal relationships between fungi and microalgae were prevalent in extremely acidic environments. Highly connected taxa within this network were Chlamydomonadaceae, Sporidiobolaceae, Filobasidiaceae, and unclassified Eukaryotes. Redundancy analysis (RDA) and random forest models revealed that Chlorophyta and Basidiomycota responded strongly to environmental gradients. Further analysis indicated that eukaryotic community structure was mainly determined by nutrient and metal concentrations. This study investigates the potential symbiosis between fungi and microalgae in the acidic pit lake, providing valuable insights for future eukaryotic biodiversity studies on AMD remediation.

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.

An overview of experimental simulations of microbial activity in early Earth

Microbial activity has shaped the evolution of the ocean and atmosphere throughout the Earth history. Thus, experimental simulations of microbial metabolism under the environment conditions of the early Earth can provide vital information regarding biogeochemical cycles and the interaction and coevolution between life and environment, with important implications for extraterrestrial exploration. In this review, we discuss the current scope and knowledge of experimental simulations of microbial activity in environments representative of those of early Earth, with perspectives on future studies. Inclusive experimental simulations involving multiple species, and cultivation experiments with more constraints on environmental conditions similar to early Earth would significantly advance our understanding of the biogeochemical cycles of the geological past.