Geochemical and Temporal Influences on the Enrichment of Acidophilic Iron-Oxidizing Bacterial Communities

Biogeochemical mechanisms of iron (Fe) and manganese (Mn) in groundwater and soil profiles in the Zhongning section of the Weining Plain (northwest China)

High levels of Iron (Fe) and manganese (Mn) in soils may contribute to secondary contamination of groundwater. However, there is limited understanding of the cycling mechanisms of Fe and Mn in groundwater and soil. This study aimed to investigate the biogeochemical processes constituting the Fe and Mn cycle by combining hydrochemistry, sequential extraction and microbiological techniques. The results indicated a similar vertical distribution pattern of Fe and Mn, with lower levels of the effective form (EFC-Fe/Mn) observed at the oxygenated surface, increasing near the groundwater table and decreasing below it. Generally, there was a tendency for accumulation above the water table, with Mn exhibiting a higher release potential compared to Fe. Iron‑manganese oxides (Ox-Fe/Mn) dominated the effective forms, with Fe and Mn in the soil entering groundwater through the reduction dissolution of Ox-Fe/Mn and the oxidative degradation of organic matter or sulfide (OM-Fe/Mn). Correlation analysis revealed that Fe and Mn tend to accumulate in media with fine particles and high organic carbon (TOC) contents. 16S rRNA sequencing analysis disclosed significant variation in the abundance of microorganisms associated with Fe and Mn transformations among unsaturated zone soils, saturated zone media and groundwater, with Fe/Mn content exerting an influence on microbial communities. Furthermore, functional bacterial identification results from the FAPROTAX database show a higher abundance of iron-oxidizing bacteria (9.3 %) in groundwater, while iron and manganese-reducing bacteria are scarce in both groundwater and soil environments. Finally, a conceptual model of Fe and Mn cycling was constructed, elucidating the biogeochemical processes in groundwater and soil environments. This study provides a new perspective for a deeper understanding of the environmental fate of Fe and Mn, which is crucial for mitigating Fe and Mn pollution in groundwater.

Spatiotemporal successions of N, S, C, Fe, and As cycling genes in groundwater of a wetland ecosystem: Enhanced heterogeneity in wet season

Microorganisms in wetland groundwater play an essential role in driving global biogeochemical cycles. However, largely due to the dynamics of spatiotemporal surface water-groundwater interaction, the spatiotemporal successions of biogeochemical cycling in wetland groundwater remain poorly delineated. Herein, we investigated the seasonal coevolution of hydrogeochemical variables and microbial functional genes involved in nitrogen, carbon, sulfur, iron, and arsenic cycling in groundwater within a typical wetland, located in Poyang Lake Plain, China. During the dry season, the microbial potentials for dissimilatory nitrate reduction to ammonium and ammonification were dominant, whereas the higher potentials for nitrogen fixation, denitrification, methane metabolism, and carbon fixation were identified in the wet season. A likely biogeochemical hotspot was identified in the area located in the low permeable aquifer near the lake, characterized by reducing conditions and elevated levels of Fe2+ (6.65-17.1 mg/L), NH4+ (0.57-3.98 mg/L), total organic carbon (1.02-1.99 mg/L), and functional genes. In contrast to dry season, higher dissimilarities of functional gene distribution were observed in the wet season. Multivariable statistics further indicated that the connection between the functional gene compositions and hydrogeochemical variables becomes less pronounced as the seasons transition from dry to wet. Despite this transition, Fe2+ remained the dominant driving force on gene distribution during both seasons. Gene-based co-occurrence network displayed reduced interconnectivity among coupled C-N-Fe-S cycles from the dry to the wet season, underpinning a less complex and more destabilizing occurrence pattern. The rising groundwater level may have contributed to a reduction in the stability of functional microbial communities, consequently impacting ecological functions. Our findings shed light on microbial-driven seasonal biogeochemical cycling in wetland groundwater.

Towards an understanding of the factors controlling bacterial diversity and activity in semi-passive Fe- and As-oxidizing bioreactors treating arsenic-rich acid mine drainage

Semi-passive bioreactors based on iron and arsenic oxidation and coprecipitation are promising for the treatment of As-rich acid mine drainages. However, their performance in the field remains variable and unpredictable. Two bioreactors filled with distinct biomass carriers (plastic or a mix of wood and pozzolana) were monitored during 1 year. We characterized the dynamic of the bacterial communities in these bioreactors, and explored the influence of environmental and operational drivers on their diversity and activity. Bacterial diversity was analyzed by 16S rRNA gene metabarcoding. The aioA genes and transcripts were quantified by qPCR and RT-qPCR. Bacterial communities were dominated by several iron-oxidizing genera. Shifts in the communities were attributed to operational and physiochemical parameters including the nature of the biomass carrier, the water pH, temperature, arsenic, and iron concentrations. The bioreactor filled with wood and pozzolana showed a better resilience to disturbances, related to a higher bacterial alpha diversity. We evidenced for the first time aioA expression in a treatment system, associated with the presence of active Thiomonas spp. This confirmed the contribution of biological arsenite oxidation to arsenic removal. The resilience and the functional redundancy of the communities developed in the bioreactors conferred robustness and stability to the treatment systems.

Nitrogen species and microbial community coevolution along groundwater flowpath in the southwest of Poyang Lake area, China

Nitrate and ammonia overload in groundwater can lead to eutrophication of surface water in areas where surface water is recharged by groundwater. However, this process remained elusive due to the complicated groundwater N cycling, which is governed by the co-evolution of hydrogeochemical conditions and N-cycling microbial communities. Herein, this process was studied along a generalized groundwater flowpath in Ganjing Delta, Poyang Lake area, China. From groundwater recharge to the discharge area near the lake, oxidation-reduction potential (ORP), NO₃-N, and NO₂-N decreased progressively, while NH₃-N, total organic carbon (TOC), Fe²⁺, sulfide, and TOC/NO₃^- ratio accumulated in the lakeside samples. The anthropogenic influences such as sewage and agricultural activities drove the nitrate distribution, as observed by Cl^- vs. NO₃^-/Cl^- ratio and isotopic composition of nitrate. The hydrogeochemical evolution was intimately coupled with the changes in microbial communities. Variations in microbial community structures was significantly explained by Fe²⁺, NH₃-N, and sulfide, while TOC/NO₃^- controlled the distribution of predicted N cycling gene. The absence of NH₃-N in groundwater upstream was accompanied by the enrichment in Acinetobacter capable of nitrification and aerobic denitrification. These two processes were also supported by Ca²⁺ + Mg²⁺ vs. HCO₃^- ratio and isotopic composition of NO₃^-. The DNRA process downstream was revealed by both the presence of DNRA-capable microbes such as Arthrobacter and the isotopic composition of NH₄⁺ in environments with high concentrations of NH₃-N, TOC/NO₃^-, Fe²⁺, and sulfide. This coupled evolution of N cycling and microbial community sheds new light on the N biogeochemical cycle in areas where surface water is recharged by groundwater.

Hydrochemical characteristics and microbial community evolution of Pinglu River affected by regional abandoned coal mine drainage, Guizhou Province, China

Pinglu River in southwestern China was continuously polluted by acid mine drainage (AMD) from abandoned coal mines, and AMD has become a major source of recharge to the river (43.26% of total flow), resulting in structural changes in the physicochemical properties and microbial communities of river water and sediments. In this study, we collected abandoned coal mine drainage, river water, and river sediment samples for comprehensive analysis. Results indicated that the hydrochemical types of AMD from abandoned coal mines were mainly SO₄-Ca·Mg. The pH of river water in Pinglu River decreased from upstream to downstream due to AMD, with the hydrochemical type gradually changing from SO₄·HCO₃-Ca·Mg to SO₄-Ca·Mg. The variation of pH along the river sediments was less than that of water samples, which remained weakly alkaline. However, high-throughput sequencing revealed a gradual decrease in microbial diversity in river sediments from upstream to downstream. The core bacteria groups in the upstream sediments were mainly attributed to the phylum Proteobacteria and Actinobacteriota, mainly including Geobacter, Anaeromyxobacter, Marmoricola, and Phycicoccus. The relative abundance of Gaiella, MND1, and Pseudolabrys in sediment samples gradually increased with the confluence of AMD, and the differences in microbial communities may be attributed to pH, TOC, and TP. Results of phenotype prediction demonstrated that the relative abundance of anaerobic microorganisms in river sediment gradually decreased from upstream to downstream (from 24.77 to 12.46%), presumably due to the large amount of oligotrophic AMD converge.

Convergent Community Assembly among Globally Separated Acidic Cave Biofilms

Acidophilic bacteria and archaea inhabit extreme geochemical "islands" that can tell us when and how geographic barriers affect the biogeography of microorganisms. Here, we describe microbial communities from extremely acidic (pH 0 to 1) biofilms, known as snottites, from hydrogen sulfide-rich caves. Given the extreme acidity and subsurface location of these biofilms, and in light of earlier work showing strong geographic patterns among snottite Acidithiobacillus populations, we investigated their structure and diversity in order to understand how geography might impact community assembly. We used 16S rRNA gene cloning and fluorescence in situ hybridization (FISH) to investigate 26 snottite samples from four sulfidic caves in Italy and Mexico. All samples had very low biodiversity and were dominated by sulfur-oxidizing bacteria in the genus Acidithiobacillus. Ferroplasma and other archaea in the Thermoplasmatales ranged from 0 to 50% of total cells, and relatives of the bacterial genera Acidimicrobium and Ferrimicrobium were up to 15% of total cells. Rare phylotypes included Sulfobacillus spp. and members of the phyla "Candidatus Dependentiae" and "Candidatus Saccharibacteria" (formerly TM6 and TM7). Although the same genera of acidophiles occurred in snottites on separate continents, most members of those genera represent substantially divergent populations, with 16S rRNA genes that are only 95 to 98% similar. Our findings are consistent with a model of community assembly where sulfidic caves are stochastically colonized by microorganisms from local sources, which are strongly filtered through environmental selection for extreme acid tolerance, and these different colonization histories are maintained by dispersal restrictions within and among caves. IMPORTANCE Microorganisms that are adapted to extremely acidic conditions, known as extreme acidophiles, are catalysts for rock weathering, metal cycling, and mineral formation in naturally acidic environments. They are also important drivers of large-scale industrial processes such as biomining and contaminant remediation. Understanding the factors that govern their ecology and distribution can help us better predict and utilize their activities in natural and engineered systems. However, extremely acidic habitats are unusual in that they are almost always isolated within circumneutral landscapes. So where did their acid-adapted inhabitants come from, and how do new colonists arrive and become established? In this study, we took advantage of a unique natural experiment in Earth's subsurface to show how isolation may have played a role in the colonization history, community assembly, and diversity of highly acidic microbial biofilms.

Guided by the principles of microbiome engineering: Accomplishments and perspectives for environmental use

Although the accomplishments of microbiome engineering highlight its significance for the targeted manipulation of microbial communities, knowledge and technical gaps still limit the applications of microbiome engineering in biotechnology, especially for environmental use. Addressing the environmental challenges of refractory pollutants and fluctuating environmental conditions requires an adequate understanding of the theoretical achievements and practical applications of microbiome engineering. Here, we review recent cutting-edge studies on microbiome engineering strategies and their classical applications in bioremediation. Moreover, a framework is summarized for combining both top-down and bottom-up approaches in microbiome engineering toward improved applications. A strategy to engineer microbiomes for environmental use, which avoids the build-up of toxic intermediates that pose a risk to human health, is suggested. We anticipate that the highlighted framework and strategy will be beneficial for engineering microbiomes to address difficult environmental challenges such as degrading multiple refractory pollutants and sustain the performance of engineered microbiomes in situ with indigenous microorganisms under fluctuating conditions.

Changes in the prokaryotic diversity in response to hydrochemical variations during an acid mine drainage passive treatment

Acid mine drainage (AMD) causes major environmental problems and consequently, several treatments are proposed, favoring the passive systems because of their many advantages. The main goal of these procedures is the neutralization and removal of potentially toxic elements (PTE), yet little is known about the changes in the microbial assemblages in response to the hydrochemical variations during the treatments. Therefore, the main objective of this research was to determine the changes in the diversity and structure of the prokaryotic assemblages in a hybrid abiotic and biological (wetland) passive treatment system. The 16S rRNA gene survey showed that the AMD coming from the mine (pH 2.6) was mainly composed of acidophilic genera such as Acidithiobacillus, Leptospirillum, Ferritrophicum, and Cuniculiplasma (up to 76 % relative abundance). In the abiotic treatment, Acidiphilium was dominant in the sections with limestone filters (pH 2.2-4.8), followed by Limnobacter in the subsequent dolomite/limestone and phosphoric rock filters (pH 5.2-5.8). In these abiotic passive treatment sections, the microbial assemblage showed a limited diversity and richness. However, when the treated AMD reached the two final wetlands (pH ~6.8), the microbial diversity and richness increased, suggesting that further bioattenuation mechanisms might be occurring. Limnobacter and Novosphingobium were the main bacterial genera in the water samples of the wetland sections (Arundo donax). These changes in the composition of the microbial assemblages were highly correlated with the pH and Eh values during the treatment (p-value <0.001); however, the concentration of metal(loid)s such as Al, Cd, Fe, Mn, Ni, and Zn were also significantly related (p-value <0.05). In conclusion, the studied passive AMD treatment system enhanced the chemical quality of the treated AMD, showing high removal efficiencies for Al and Fe (> 99 %), and increasing the microbial diversity and richness in the effluent.

Microbial biogeography of acid mine drainage sediments at a regional scale across Southern China

Investigations of microbial biogeography in extreme environments provide unique opportunities to disentangle the roles of environment and space in microbial community assembly. Here, we reported a comprehensive microbial biogeographic survey of 90 acid mine drainage (AMD) sediment samples from 18 mining sites of various mineral types across southern China. We found that environmental selection was strong in determining the AMD habitat species pool. However, microbial alpha diversity was primarily explained by mining sites rather than environmental factors, and microbial beta diversity correlated more strongly with geographic than environmental distance at both large and small spatial scales. Particularly, the presence/absence of widespread AMD habitat generalists was only correlated with geographic distance and independent of environmental variation. These distance-decay patterns suggested that spatial processes played a more important role in determining microbial compositional variation across space; which could be explained by the reinforced impacts of dispersal limitation in less fluid, spatially structured sediment habitat with diverse pre-existing communities. In summary, our findings suggested that the deterministic assembling and spatial constraints interact to shape microbial biogeography in AMD sediments; and provided implications that spatial processes should be considered when predicting microbial dynamics in response to severe environmental change across large spatial scales.

Groundwater quality assessment and hydrogeochemical processes in typical watersheds in Zhangjiakou region, northern China

It is of significance to elucidate the groundwater quality and hydrogeochemical processes for sustainable utilization of groundwater resources in water shortage regions. A total of 256 groundwater samples were collected in typical watersheds in Zhangjiakou, northern China. The hydrochemical parameters, conventional ions, and trace elements were measured, and δD and δ18O data were collected to delineate the groundwater quality and hydrogeochemical processes. The results showed that 32.91% of the groundwater could be directly used for drinking water sources in the Bashang Plateau, north of the study area. The F- and NO3--N were the main parameters above the standard threshold for drinking water. In contrast, the groundwater quality in the Baxia River Basins, south of the study area, was of a better scenario. Nonetheless, high concentrations of F-, total hardness, and SO42- were still observed. Most samples in the Bashang Plateau had relatively higher salinity than the Baxia River Basins. Both surface water and groundwater in the study area originated from local meteoric water with considerable hydraulic connections. The high-fluoride groundwater was primarily formed by dissolution of fluoride-rich minerals under conditions of high pH and Na+, low Ca2+, and rich in HCO3-. The dissolution of carbonate and silicate minerals accompanied by strong cation exchange and weak evaporation was the dominant water-rock interaction affecting the hydrochemical composition of groundwater, and anthropogenic NO3- input had an extra influence on hydrochemical process. This study provides a scientific guideline for the protection and allocation of local groundwater resources.

Disentangling Microbial Syntrophic Mechanisms for Hexavalent Chromium Reduction in Autotrophic Biosystems

Hexavalent chromium [Cr(VI)] is one of the common heavy-metal contaminants in groundwater, and the availability of electron donors is considered to be a key parameter for Cr(VI) biotransformation. During the autotrophic remediation process, however, much remains to be illuminated about how complex syntrophic microbial communities couple Cr(VI) reduction with other elemental cycles. Two series of Cr(VI)-reducing groundwater bioreactors were independently amended by elemental sulfur and iron and inoculated with the same inoculum. After 160 days of incubation, both bioreactors showed similar archaea-dominating microbiota compositions, whereas a higher Cr(VI)-reducing rate and more methane production were detected in the Fe⁰-driven one. Metabolic reconstruction of 23 retrieved genomes revealed complex symbiotic relationships driving distinct elemental cycles coupled with Cr(VI) reduction in bioreactors. In both bioreactors, these Cr(VI) reducers were assumed to live in syntrophy with oxidizers of sulfur, iron, hydrogen, and volatile fatty acids and methane produced by carbon fixers and multitrophic methanogens, respectively. The significant difference in methane production was mainly due to the fact that the yielded sulfate greatly retarded acetoclastic methanogenesis in the S-bioreactor. These findings provide insights into mutualistic symbioses of carbon, sulfur, iron, and chromium metabolisms in groundwater systems and have implications for bioremediation of Cr(VI)-contaminated groundwater.

Acid Mine Drainage as Energizing Microbial Niches for the Formation of Iron Stromatolites: The Tintillo River in Southwest Spain

The Iberian Pyrite Belt in southwest Spain hosts some of the largest and diverse extreme acidic environments with textural variation across rapidly changing biogeochemical gradients at multiple scales. After almost three decades of studies, mostly focused on molecular evolution and metagenomics, there is an increasing awareness of the multidisciplinary potential of these types of settings, especially for astrobiology. Since modern automatized exploration on extraterrestrial surfaces is essentially based on the morphological recognition of biosignatures, a macroscopic characterization of such sedimentary extreme environments and how they look is crucial to identify life properties, but it is a perspective that most molecular approaches frequently miss. Although acid mine drainage (AMD) systems are toxic and contaminated, they offer at the same time the bioengineering tools for natural remediation strategies. This work presents a biosedimentological characterization of the clastic iron stromatolites in the Tintillo river. They occur as laminated terraced iron formations that are the most distinctive sedimentary facies at the Tintillo river, which is polluted by AMD. Iron stromatolites originate from fluvial abiotic factors that interact with biological zonation. The authigenic precipitation of schwertmannite and jarosite results from microbial-mineral interactions between mineral and organic matrices. The Tintillo iron stromatolites are composed of bacterial filaments and diatoms as Nitzschia aurariae, Pinnularia aljustrelica, Stauroneis kriegeri, and Fragilaria sp. Furthermore, the active biosorption and bioleaching of sulfur are suggested by the black and white coloration of microbial filaments inside stromatolites. AMD systems are hazardous due to physical, chemical, and biological agents, but they also provide biogeochemical sources with which to infer past geochemical conditions on Earth and inform exploration efforts on extraterrestrial surfaces in the future.

Distinct assembly processes shape bacterial communities along unsaturated, groundwater fluctuated, and saturated zones

The subsurface soil environment through the unsaturated (vadose) zone and saturated (below groundwater table) zone is one of the most active layers in the Earth's surface with biogeochemical interactions. Geochemical variables and geographic distance are key driving forces shaping the distribution of soil microbial communities, but our understandings are mainly limited to surface soil or shallow unsaturated zone (1-3 m beneath the ground). In this study, soil and sediment samples were collected from the unsaturated zone, through groundwater fluctuated zone, to saturated zone (up to 20 m) to unravel the assembly processes mediating vertical bacterial community succession across these three zones. Our results suggested both geochemical niches and bacterial diversity had different vertical patterns in each zone. With increased depth, pH increased and nutrient levels (C, N, P, K) and bacterial diversity declined in the unsaturated zone, and nutrients and bacterial diversity remained low levels after reaching the fluctuated and saturated zones. Nutrients were the key drivers shaping bacterial variation in the unsaturated zone, but limited nutrients and only 'depth' significantly explained the variations in the fluctuated zone and saturated zone, respectively. The co-occurrence network supported a more species co-existence pattern in the unsaturated zone than that in the other two zones. Due to the geochemical variations across three zones, the assembly of phylogenetically more clustered communities was observed through deterministic processes (e.g., 55% homogenizing selection) in the unsaturated zone, but the stochastic process (e.g., 50%-70% dispersal limitation) was more important in the fluctuated and saturated zones. These findings together suggested that the vertical distribution of soil bacterial community assembly was zone-specific and shaped by the degree of deterministic vs. stochastic processes. Our results provide a novel insight into the microbial community assembly across three different ecosystems in the Earth's critical zone and shed a light on subsurface biogeochemical processes.

History of petroleum disturbance triggering the depth-resolved assembly process of microbial communities in the vadose zone

Biogeochemical gradient forms in vadose zone, yet little is known about the assembly processes of microbial communities in this zone under petroleum disturbance. This study collected vadose zone soils at three sites with 0, 5, and 30 years of petroleum contamination to unravel the vertical microbial community successions and their assembly mechanisms. The results showed that petroleum hydrocarbons exhibited higher concentrations at the long-term contaminated site, showing negative impacts on some soil properties, retarding in the surface soils and decreasing along soil depth. Cultivable fraction of heterotrophic bacteria and microbial α-diversity decreased along depth in vadose zones with short-term/no contamination history, but exhibited an opposite trend with long-term contamination history. Petroleum contamination intensified the vertical heterogeneity of microbial communities based on the contamination time. Microbial co-occurrence network revealed the lowest species co-occurrence pattern at the long-term contaminated site. The distance-decay patterns and null model analysis together suggested distinct assembly mechanisms at three sites, where dispersal limitation (42-45%) was higher and variable and homogenizing selections were lower (37-38%) in vadose zones under petroleum disturbance than those in the uncontaminated vadose zone. Our findings help to better understand the subsurface biogeochemical cycles and bioremediation of petroleum-contaminated vadose zones.

In-situ remediation of acid mine drainage from abandoned coal mine by filed pilot-scale passive treatment system: Performance and response of microbial communities to low pH and elevated Fe

A field pilot-scale passive treatment system was developed for in-situ bioremediation of acid mine drainage (AMD). The microbial community and its variation were analyzed. The data proved that 93.7% of total soluble Fe and 99% of soluble Fe(II) could be removed by the system. Principal coordinates analysis (PCoA) showed that a low pH and an elevated Fe concentration within the system created a unique microbial community that was dominated by acidophilic iron-oxidizing bacteria and iron-reducing bacteria. Canonical correlation analysis (CCA) indicated that the pH, iron content and total sulfur jointly determined the composition of the microbial communities. Species of Ferrovum, Delftia, Acinetobacter, Metallibacterium, Acidibacter and Acidiphilium were highly enriched, which promoted the removal of iron. Furthermore, the results revealed important data for the biogeochemical coupling of microbial communities and environmental parameters. These findings are beneficial for further application of in-situ field bioreactors to remediate AMD.

Functional redundancy imparts process stability to acidic Fe(II)-oxidizing microbial reactors

In previous work, lab-scale reactors designed to study microbial Fe(II) oxidation rates at low pH were found to have stable rates under a wide range of pH and Fe(II) concentrations. Since the stirred reactor environment eliminates many of the temporal and spatial variations that promote high diversity among microbial populations in nature, we were surprised that the reactors supported multiple taxa presumed to be autotrophic Fe(II) oxidizers based on their phylogeny. Metagenomic analyses of the reactor communities revealed differences in the metabolic potential of these taxa with respect to Fe(II) oxidation and carbon fixation pathways, acquisition of potentially growth-limiting substrates and the ability to form biofilms. Our findings support the hypothesis that the long-term co-existence of multiple autotrophic Fe(II)-oxidizing populations in the reactors are due to distinct metabolic potential that supports differential growth in response to limiting resources such as nitrogen, phosphorus and oxygen. Our data also highlight the role of biofilms in creating spatially distinct geochemical niches that enable the co-existence of multiple taxa that occupy the same apparent metabolic niche when the system is viewed in bulk. The distribution of key metabolic functions across different co-existing taxa supported functional redundancy and imparted process stability to these reactors.

Temperature governs the distribution of hot spring microbial community in three hydrothermal fields, Eastern Tibetan Plateau Geothermal Belt, Western China

The eastern Tibetan Plateau geothermal belt in the southwest of China hosts a number of hot springs with a wide range of temperature and hydrogeochemical conditions, which may harbor different niches for the distribution of microbial communities. In this study, we investigated hydrochemical characteristics and microbial community composition in 16 hot springs with a temperature range of 34.6 to 88.2 °C within and across three typical hydrothermal fields (Kangding, Litang, and Batang). According to aquifer lithologic and tectonic differences, the hydrochemical compositions of hot springs displayed an apparent regional-specific pattern with distinct distributions of major and trace elements (e.g., Ca²⁺, Mg²⁺, F^-/B) and were primarily formed by water-rock interaction across the three hydrothermal fields. Nonetheless, microbial communities significantly assembled with the temperature rather than the geographic locations with distinct hydrogeological features. Low temperature (<45 °C), moderate temperature (55-70 °C) and high temperature (>70 °C) groups were identified based on their community compositions. Proteobacteria and Nitrospirae were the predominant phyla in low-temperature hot springs, while in moderate to high-temperature springs they were mainly composed of Aquificae, Deinococcus-Thermus, Thermodesulfobacteria, Thermotogae and Cyanobacteria. Variation partition analysis suggested a higher explanation of temperature (29.6%) than spatial variable (1.8%) and other geochemical variables (2.5%) on the microbial distribution. Microbial co-occurrence network showed >80% negative associations hinting a low co-existence pattern and highlighted the driving force of temperature as well as F^- or total organic carbon (TOC) for microbial interactions. Microbial dissimilarity displayed significant linear correlations with environmental (temperature) and geographic distance in Batang but only with temperature in Kangding area, which might be attributed to the regional-specific hydrogeochemistry. This study may help us to better understand the distribution of the microbial community in hot spring across different hydrothermal fields.

Distinct functional microbial communities mediating the heterotrophic denitrification in response to the excessive Fe(II) stress in groundwater under wheat-rice stone and rock phosphate amendments

Denitrifying microbial community can be utilized for eliminating nitrate and Fe(II) combined contamination in groundwater, while excessive amount of Fe(II) limit the process. Natural mineral can be additional substrate for the microbial growth, whereas how it influences the microbial community that mediating the denitrification coupling with Fe(II) oxidation and balancing inhibition of excessive Fe(II) on denitrification remain unclear. In the present study, we conducted a series of microcosm experiments to explore the denitrification and Fe(II) oxidation kinetic, and used RNA-based qPCR and DNA-based high-throughput sequencing to elucidate microbial diversity, co-occurrence and metabolic profiles amended by wheat-rice stone and rock phosphate. The results showed that both minerals could extensively improve and double the denitrification rates (2.0 ± 0.03 to 2.12 ± 0.13 times), decrease the nitrite accumulation and trigger the high resistance of the denitrifiers from the stress of Fe(II), whereas only wheat-rice stone with higher surface area increased the oxidation of Fe(II) (<10%). The addition of both minerals enhanced the microbial alpha-diversity, shaped the beta-diversity and co-occurrence network, and recovered the transcription of nitrate and nitrite reductase (Nar, Nap, NirS, NirK) from the Fe(II) inhibition. Accordingly, heterotroph Methyloversatilis sp., Methylotenra sp. might contribute to the denitrification under wheat-rice stone amendment, Denitratisoma sp. contribute to the denitrification for rock phosphate, and Fe oxidation was partially catalyzed by Dechloromonas sp. or abiotically by the nitrite/nitrous oxide. These findings would be helpful for better understanding the bioremediation of nitrate and Fe contaminated groundwater.

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.

Microbiomes in an acidic rock-water cave system

Belowground ecosystems are accessible by mining, where a specific microbial community can be discovered. The biodiversity of a former alum mine rich in carbon, but with a low pH of 2.6-3.7, was evaluated by DNA- and cultivation-dependent methods using samples of the black slate rock material, secondary mineralization phases and seepage water. Pyrite oxidation within the low-grade metamorphic Silurian black slate established high concentrations of Fe and $\rm{SO}_4^{2-}$ forming the extreme conditions visible with acidophilic and Fe-oxidizing microorganisms. In addition, an unexpected predominance of fungi in this C-rich and acidic cave ecosystem, including high numbers of Mucoromycota and Mortierellomycota, was detected. Therefore, fungal cultures were obtained, mainly from the secondary mineral phases that are iron phosphates. Hence, the fungi might well have been involved in phosphate mobilization there. The rock material itself is rich in organic carbon that can be used by oxidase activity. The cultivation setup mimicked the cave conditions (low temperature, low pH, oxic conditions), with one oligotrophic and one medium rich in nutrients that allowed for isolation of different fungal (and eutrophic bacterial) groups. The acidic conditions prevented the occurrence of many basidiomycetes, while the isolated fungi could survive these adverse conditions.

The Study of Hydrogeochemical Environments and Microbial Communities along a Groundwater Salinity Gradient in the Pearl River Delta, China

The salinization of groundwater is an issue in coastal areas because it causes the deterioration of freshwater resources, significantly impacting human livelihoods and ecosystems. This study integrated isotopic geochemical measurements with high-throughput sequencing of 16S rRNA gene amplicons to evaluate the source of groundwater salinity and the influence of hydrogeochemical variations on microbial communities under different salinity gradients in the Pearl River Delta of China. Results showed that the groundwater salinity in this area varied from fresh water in the inland area to brackish water, and then to saline water close to the southeast shoreline. The major ions (Na+, K+, Ca2+, Mg2+, Cl−, NO3−, SO42−, and HCO3−) and isotope analyses (2H, 3H, 18O, and 14C) indicated that the groundwater in the confined aquifer was recharged by local precipitation and seawater. A further 14C analysis showed that the salinity of the groundwater was likely attributed to the Holocene transgression. Analysis of the microbial community showed that γ-proteobacteria were frequently observed in all the groundwater samples, while the other main microbial community at class level varied greatly, from β-proteobacteria in the freshwater wells to ε-proteobacteria in the brackish wells and to Bacilli in the saline wells. Exiguobacterium and Acinetobacter were dominant in saline water and the brackish water sample of Q144, while Sulfuricurvum dominated in the brackish water sample of Q143. Aeromonas, no rank Gallionellaceae, no rank Methylophilaceae, Acidovorax, and Comamonas unevenly thrived in the freshwater samples collected from different locations. Therefore, the distribution of microbial communities reflected the salinity and hydrogeochemical characteristics of a groundwater aquifer, and can be regarded as a potential environmental indicator in the groundwater.

Effect of Fe(II) on reactivity of heterotrophic denitrifiers in the remediation of nitrate- and Fe(II)-contaminated groundwater

Heterotrophic denitrifiers, capable of simultaneous nitrate reduction and Fe(II) oxidation, can be applied for the remediation of nitrate and Fe(II) combined contamination in groundwater. Under strictly anaerobic condition, denitrifying microbial communities were enriched with the coexistence of soluble nitrate, Fe(II) and associated nutrient elements to monitor the denitrification process. Low abundance of Fe(II) (e.g., 10 mg L^-1 in this study) tended to stimulate the activity of denitrifying microbial communities. However, elevated Fe(II) concentration (50 and 100 mg L^-1 in this study), acted as a stress, strongly inhibited the activity and reproduction of denitrifiers. Besides, through thermodynamics calculations, methanol rather than Fe(II) was proved to be the preferable electron donors for both energy metabolism and anabolism. Betaproteobacteria was found to be the most predominant (sub)phylum in all enriched microbial assemblages. Methylovesartilis was the most predominant group mainly catalyzed for methanol based denitrification, and others denitrifiers included Methylophilaceae, Dechloromonas and Denitratisoma. Excessive Fe(II) in the solution greatly reduced the proportions of these denitrifying groups, while the influence seemed to be less apparent on functional genes composition. As such, a conceptional metabolism pathway of the most dominant genus (i.e., Methylovesartilis) for nitrate reducing as well as methanol and Fe(II) oxidation confirmed that biotic nitrate reducing and Fe(II) oxidizing were potentially proceeded in cytoplasm by enzymes such as NarGHI. The Fe(II) oxidation rate depended on the rate of Fe(II) entering into the cell. These findings provide a clear mechanistic understanding of heterotrophic denitrification coupling with Fe(II) oxidation, and environmental implication for the bioremediation of nitrate and Fe(II) contaminated groundwater.

Dynamics of Bacterial Communities Mediating the Treatment of an As-Rich Acid Mine Drainage in a Field Pilot

Passive treatment based on iron biological oxidation is a promising strategy for Arsenic (As)-rich acid mine drainage (AMD) remediation. In the present study, we characterized by 16S rRNA metabarcoding the bacterial diversity in a field-pilot bioreactor treating extremely As-rich AMD in situ, over a 6 months monitoring period. Inside the bioreactor, the bacterial communities responsible for iron and arsenic removal formed a biofilm (“biogenic precipitate”) whose composition varied in time and space. These communities evolved from a structure at first similar to the one of the feed water used as an inoculum to a structure quite similar to the natural biofilm developing in situ in the AMD. Over the monitoring period, iron-oxidizing bacteria always largely dominated the biogenic precipitate, with distinct populations (Gallionella, Ferrovum, Leptospirillum, Acidithiobacillus, Ferritrophicum), whose relative proportions extensively varied among time and space. A spatial structuring was observed inside the trays (arranged in series) composing the bioreactor. This spatial dynamic could be linked to the variation of the physico-chemistry of the AMD water between the raw water entering and the treated water exiting the pilot. According to redundancy analysis (RDA), the following parameters exerted a control on the bacterial communities potentially involved in the water treatment process: dissolved oxygen, temperature, pH, dissolved sulfates, arsenic and Fe(II) concentrations and redox potential. Appreciable arsenite oxidation occurring in the bioreactor could be linked to the stable presence of two distinct monophylogenetic groups of Thiomonas related bacteria. The ubiquity and the physiological diversity of the bacteria identified, as well as the presence of bacteria of biotechnological relevance, suggested that this treatment system could be applied to the treatment of other AMD.

Groundwater Microbial Communities Along a Generalized Flowpath in Nomhon Area, Qaidam Basin, China

Spatial distribution (horizonal and vertical) of groundwater microbial communities and the hydrogeochemistry in confined aquifers were studied approximately along the groundwater flow path from coteau to plain in the Nomhon area, Qinghai-Tibet plateau, China. The confined groundwater samples at different depths and locations were collected in three boreholes through a hydrogeological section in this arid and semi-arid area. The phylogenetic analysis of 16S rRNA genes and multivariate statistical analysis were used to elucidate similarities and differences between groundwater microbial communities and hydrogeochemical properties. The integrated isotopic geochemical measurements were applied to estimate the source and recharge characteristics of groundwater. The results showed that groundwater varied from fresh to saline water, and modern water to ancient water following the flowpath. The recharge characteristics of the saline water was distinct with that of fresh water. Cell abundance did not vary greatly along the hydrogeochemical zonality; however, dissimilarities in habitat-based microbial community structures were evident, changing from Betaproteobacteria in the apex of alluvial fan to Gammaproteobacteria and then to Epsilonproteobacteria in the core of the basin (alluvial-lacustrine plain). Rhodoferax, Hydrogenophaga, Pseudomonas, and bacterium isolated from similar habitats unevenly thrived in the spatially distinct fresh water environments, while Sulfurimonas dominanted in the saline water environment. The microbial communities presented likely reflected to the hydrogeochemical similarities and zonalities along groundwater flowpath.

Hydraulic retention time affects bacterial community structure in an As-rich acid mine drainage (AMD) biotreatment process

Arsenic removal consecutive to biological iron oxidation and precipitation is an effective process for treating As-rich acid mine drainage (AMD). We studied the effect of hydraulic retention time (HRT)-from 74 to 456 min-in a bench-scale bioreactor exploiting such process. The treatment efficiency was monitored during 19 days, and the final mineralogy and bacterial communities of the biogenic precipitates were characterized by X-ray absorption spectroscopy and high-throughput 16S rRNA gene sequencing. The percentage of Fe(II) oxidation (10-47%) and As removal (19-37%) increased with increasing HRT. Arsenic was trapped in the biogenic precipitates as As(III)-bearing schwertmannite and amorphous ferric arsenate, with a decrease of As/Fe ratio with increasing HRT. The bacterial community in the biogenic precipitate was dominated by Fe-oxidizing bacteria whatever the HRT. The proportion of Gallionella and Ferrovum genera shifted from respectively 65 and 12% at low HRT to 23 and 51% at high HRT, in relation with physicochemical changes in the treated water. aioA genes and Thiomonas genus were detected at all HRT although As(III) oxidation was not evidenced. To our knowledge, this is the first evidence of the role of HRT as a driver of bacterial community structure in bioreactors exploiting microbial Fe(II) oxidation for AMD treatment.

Function and functional redundancy in microbial systems

Microbial communities often exhibit incredible taxonomic diversity, raising questions regarding the mechanisms enabling species coexistence and the role of this diversity in community functioning. On the one hand, many coexisting but taxonomically distinct microorganisms can encode the same energy-yielding metabolic functions, and this functional redundancy contrasts with the expectation that species should occupy distinct metabolic niches. On the other hand, the identity of taxa encoding each function can vary substantially across space or time with little effect on the function, and this taxonomic variability is frequently thought to result from ecological drift between equivalent organisms. Here, we synthesize the powerful paradigm emerging from these two patterns, connecting the roles of function, functional redundancy and taxonomy in microbial systems. We conclude that both patterns are unlikely to be the result of ecological drift, but are inevitable emergent properties of open microbial systems resulting mainly from biotic interactions and environmental and spatial processes.

Biological attenuation of arsenic and iron in a continuous flow bioreactor treating acid mine drainage (AMD)

Passive water treatments based on biological attenuation can be effective for arsenic-rich acid mine drainage (AMD). However, the key factors driving the biological processes involved in this attenuation are not well-known. Here, the efficiency of arsenic (As) removal was investigated in a bench-scale continuous flow channel bioreactor treating As-rich AMD (∼30-40 mg L^-1). In this bioreactor, As removal proceeds via the formation of biogenic precipitates consisting of iron- and arsenic-rich mineral phases encrusting a microbial biofilm. Ferrous iron (Fe(II)) oxidation and iron (Fe) and arsenic removal rates were monitored at two different water heights (4 and 25 mm) and with/without forced aeration. A maximum of 80% As removal was achieved within 500 min at the lowest water height. This operating condition promoted intense Fe(II) microbial oxidation and subsequent precipitation of As-bearing schwertmannite and amorphous ferric arsenate. Higher water height slowed down Fe(II) oxidation, Fe precipitation and As removal, in relation with limited oxygen transfer through the water column. The lower oxygen transfer at higher water height could be partly counteracted by aeration. The presence of an iridescent floating film that developed at the water surface was found to limit oxygen transfer to the water column and delayed Fe(II) oxidation, but did not affect As removal. The bacterial community structure in the biogenic precipitates in the bottom of the bioreactor differed from that of the inlet water and was influenced to some extent by water height and aeration. Although potential for microbial mediated As oxidation was revealed by the detection of aioA genes, removal of Fe and As was mainly attributable to microbial Fe oxidation activity. Increasing the proportion of dissolved As(V) in the inlet water improved As removal and favoured the formation of amorphous ferric arsenate over As-sorbed schwertmannite. This study proved the ability of this bioreactor-system to treat extreme As concentrations and may serve in the design of future in-situ bioremediation system able to treat As-rich AMD.

Novel Microbial Assemblages Dominate Weathered Sulfide-Bearing Rock from Copper-Nickel Deposits in the Duluth Complex, Minnesota, USA

The Duluth Complex in northeastern Minnesota hosts economically significant deposits of copper, nickel, and platinum group elements (PGEs). The primary sulfide mineralogy of these deposits includes the minerals pyrrhotite, chalcopyrite, pentlandite, and cubanite, and weathering experiments show that most sulfide-bearing rock from the Duluth Complex generates moderately acidic leachate (pH 4 to 6). Microorganisms are important catalysts for metal sulfide oxidation and could influence the quality of water from mines in the Duluth Complex. Nevertheless, compared with that of extremely acidic environments, much less is known about the microbial ecology of moderately acidic sulfide-bearing mine waste, and so existing information may have little relevance to those microorganisms catalyzing oxidation reactions in the Duluth Complex. Here, we characterized the microbial communities in decade-long weathering experiments (kinetic tests) conducted on crushed rock and tailings from the Duluth Complex. Analyses of 16S rRNA genes and transcripts showed that differences among microbial communities correspond to pH, rock type, and experimental treatment. Moreover, microbial communities from the weathered Duluth Complex rock were dominated by taxa that are not typically associated with acidic mine waste. The most abundant operational taxonomic units (OTUs) were from the genera Meiothermus and Sulfuriferula, as well as from diverse clades of uncultivated Chloroflexi, Acidobacteria, and Betaproteobacteria Specific taxa, including putative sulfur-oxidizing Sulfuriferula spp., appeared to be primarily associated with Duluth Complex rock, but not pyrite-bearing rocks subjected to the same experimental treatment. We discuss the implications of these results for the microbial ecology of moderately acidic mine waste with low sulfide content, as well as for kinetic testing of mine waste.IMPORTANCE Economic sulfide mineral deposits in the Duluth Complex may represent the largest undeveloped source of copper and nickel on Earth. Microorganisms are important catalysts for sulfide mineral oxidation, and research on extreme acidophiles has improved our ability to manage and remediate mine wastes. We found that the microbial assemblages associated with weathered rock from the Duluth Complex are dominated by organisms not widely associated with mine waste or mining-impacted environments, and we describe geochemical and experimental influences on community composition. This report will be a useful foundation for understanding the microbial biogeochemistry of moderately acidic mine waste from these and similar deposits.

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.

Efficient Low-pH Iron Removal by a Microbial Iron Oxide Mound Ecosystem at Scalp Level Run

Acid mine drainage (AMD) is a major environmental problem affecting tens of thousands of kilometers of waterways worldwide. Passive bioremediation of AMD relies on microbial communities to oxidize and remove iron from the system; however, iron oxidation rates in AMD environments are highly variable among sites. At Scalp Level Run (Cambria County, PA), first-order iron oxidation rates are 10 times greater than at other coal-associated iron mounds in the Appalachians. We examined the bacterial community at Scalp Level Run to determine whether a unique community is responsible for the rapid iron oxidation rate. Despite strong geochemical gradients, including a >10-fold change in the concentration of ferrous iron from 57.3 mg/liter at the emergence to 2.5 mg/liter at the base of the coal tailings pile, the bacterial community composition was nearly constant with distance from the spring outflow. Scalp Level Run contains many of the same taxa present in other AMD sites, but the community is dominated by two strains of Ferrovum myxofaciens, a species that is associated with high rates of Fe(II) oxidation in laboratory studies.IMPORTANCE Acid mine drainage pollutes more than 19,300 km of rivers and streams and 72,000 ha of lakes worldwide. Remediation is frequently ineffective and costly, upwards of $100 billion globally and nearly $5 billion in Pennsylvania alone. Microbial Fe(II) oxidation is more efficient than abiotic Fe(II) oxidation at low pH (P. C. Singer and W. Stumm, Science 167:1121-1123, 1970, https://doi.org/10.1126/science.167.3921.1121). Therefore, AMD bioremediation could harness microbial Fe(II) oxidation to fuel more-cost-effective treatments. Advances will require a deeper understanding of the ecology of Fe(II)-oxidizing microbial communities and the factors that control their distribution and rates of Fe(II) oxidation. We investigated bacterial communities that inhabit an AMD site with rapid Fe(II) oxidation and found that they were dominated by two operational taxonomic units (OTUs) of Ferrovum myxofaciens, a taxon associated with high laboratory rates of iron oxidation. This research represents a step forward in identifying taxa that can be used to enhance cost-effective AMD bioremediation.

Enriching Acidophilic Fe(II)-oxidizing Bacteria in No-flow, Fed-batch Systems

Low-pH microbial Fe(II) oxidation occurs naturally in some Fe(II)-rich acid mine drainage (AMD) ecosystems across so-called terraced iron formations. Indigenous acidophilic Fe(II)-oxidizing bacterial communities can be incorporated into both passive and active treatments to remove Fe from the AMD solution. Here, we present a protocol of enriching acidophilic Fe(II)-oxidizing bacteria in no-flow, fed-batch systems. Mixed cultures of naturally occurring microbes are enriched from the fresh surface sediments at AMD sites using a chemo-static bioreactor (Eppendorf BioFlo^®/Celligen^® 115 Fermentor) with respect to constant stirring speed, temperature, pH and unlimited dissolved oxygen. Ferrous sulfate is discontinuously added to the reactor as the primary substrate to enrich for acidophilic Fe(II)-oxidizing bacteria. Successfully and efficiently enriching acidophilic Fe(II)-oxidizing bacteria helps to exploit this biogeochemical process into AMD treatment systems.

Bioreactors for low-pH iron(ii) oxidation remove considerable amounts of total iron

Rates of Fe(ii) oxidation in chemostatic bioreactors can be predicted based only on the influent Fe(ii) concentration and pH value.

Bioremediation of nitrate and Fe(ii) combined contamination in groundwater by heterotrophic denitrifying bacteria and microbial community analysis

The optimal condition range was determined for the simultaneous removal of nitrate and Fe(ii) in groundwater mediated by denitrifying Betaproteobacterial communities.