Population dynamics of iron-oxidizing communities in pilot plants for the treatment of acid mine waters

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.

Hydroecology of Argyroneta aquatica’s Habitat in Hantangang River Geopark, South Korea

The water spider (Argyroneta aquatic) is the only known spider to live a fully aquatic life. Therefore, it has been the subject of a series of studies on various aspects of its unique biology such as its reproductive behavior, sexual dimorphism, physiology, genetics, and silk. However, there have been relatively few studies on the hydroecology of where water spiders live. The water spider habitat in Eundae-ri, Yeoncheon is the only habitat for A. aquatica, a globally rare species, in South Korea. In this region, the water level of the wetland is automatically adjusted to groundwater owing to continued drying. Here, the surface water, wetland, and groundwater near the A. aquatica habitat were studied using hydrochemical, microbiological, and correlation analyses. The hydrochemical properties—water temperature, pH, electrical conductivity, dissolved oxygen (DO), oxidation reduction potential, and turbidity—of the surface water and wetland were similar. The Piper diagrams revealed that the wetlands, surface water, and most of the groundwater portrayed Ca-HCO3-type properties, whereas only areas where the water level of the wetland was controlled displayed Na-HCO3-type properties. Furthermore, the NO3 content was too low to be detected in the wetland, indicating clean and non-polluted water conditions; additionally, heavier oxygen-hydrogen isotopes were observed because these regions were climatically affected by the wetland. The dominant bacteria were Proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Verrucomicrobia, and Nitrospirae. The correlation analysis revealed that the major environmental control factors of the A. aquatica habitat were DO, temperature, and pH, and the related bacteria were Cyanobacteria, Actinobacteria, and Verrucomicrobia.

Prokaryotic communities in the historic silver mine Reiche Zeche

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

Rhizosphere effect and its associated soil-microbe interactions drive iron fraction dynamics in tidal wetland soils

It is becoming increasingly clear that plants can affect iron (Fe) dynamics in tidal wetland soils, but whether this is rhizosphere effect-dependent remains unclear. To assess rhizosphere effects on soil Fe cycling, in-situ rhizosphere and bulk soil samples (0-60-cm) were collected from a tidal wetland across plant growth stages (regreening, shooting, and senescence). Changes in Fe fractions, the abundance of Fe-oxidizing/reducing bacteria (16S rRNA gene), root morphology traits, and soil and porewater geochemistry were examined. Overall, the rhizosphere effect decreased soil pH but increased the concentrations of dissolved organic carbon (DOC), porewater Fe²⁺, and bicarbonates (HCO₃^-). Both Fe-oxidizing and Fe-reducing bacteria were more enriched in the rhizosphere than those in the bulk soil. The rhizosphere effect increased the concentrations of amorphous and crystalline Fe(III), and also enhanced the proportion of amorphous Fe(III). The rhizosphere had higher concentrations of non-sulfidic ferrous iron [Fe(II)] but lower concentrations of ferrous sulfide (FeS) and pyrites (FeS₂) than those in bulk soils, suggesting that the rhizosphere effect favors microbial Fe(III) reduction but suppresses microbial sulfate reduction. Moreover, the rhizosphere amorphous Fe(III) levels changed following the patterns of root porosity, which attained peak values at the root tips. The abundance of Fe-reducing bacteria was controlled by both DOC and amorphous Fe(III) concentrations, which were relatively higher during the regreening and shooting stages than those during the senescence stage. Taken together, our findings highlight that the rhizosphere effect transfer Fe from the bulk soil to the rhizosphere and especially redirects it from FeS associations to microbially-mediated Fe redox cycling. This rapid Fe redox cycling could be responsible for buffering soils and organisms from sulfide accumulation and stimulate C mineralization in the tidal wetland ecosystem.

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

Acid mine drainage (AMD) is generated by the bio-oxidation of sulfide minerals. To understand the AMD formation and evolution, it is necessary to determine the composition and variation of acidophilic community, and their role in AMD ecosystem. In this study, we compared seasonal variations of geochemistry and microbial composition of two adjacent AMD lakes with different formation histories in Anhui Province, China. Lake Paitu (PT) formed in 1970s near a mine dump and the pH was in the range of 3.01-3.16, with the lowest in spring and summer while the highest in winter. The main ions in PT were Al and SO₄^2-, whereas Fe concentration was relatively low. The concentrations of these ions were the lowest in summer and the highest in winter. Lake Tafang (TF) formed in around 2013 in a pit was more acidic (pH 2.43-2.75), but the seasonal variation of pH was the same as PT. Compared with Lake PT, TF had higher Fe, lower Al and SO₄^2- concentrations, and showed no significant seasonal changes. Despite salient seasonal variations of prokaryotic composition in Lake PT, Ferrovum was the major iron-oxidizing bacterium in most seasons. Furthermore, Lake PT was also rich in heterotrophic bacteria (48.6 ± 15.9%). Both prokaryotic diversity and evenness of Lake TF were lower than PT, and chemolithotrophic iron-oxidizing bacteria (71.7 ± 25.4%) were dominant in almost all samples. Besides Ferrovum, more acid tolerant iron-oxidizer Leptospirillum and Acidithiobacillus were also abundant in Lake TF. Chlamydomonas was the major eukaryote in Lake PT and it flourished repeatedly at the end of December, causing an extremely high chlorophyll a concentration (587 μg/L) at one sampling site in 2016, which provided rich nutrients for heterotrophic bacteria. The main alga in Lake TF was Chrysonebula, but its concentration was low, apparently because of the strong acidity and dark red color of lake water.

Microbial Fe(II) oxidation by Sideroxydans lithotrophicus ES-1 in the presence of Schlöppnerbrunnen fen-derived humic acids

Controlled laboratory experiments were combined with field measurements to better understand the interactions between dissolved organic matter (DOM) and reduced iron in organic-rich peatlands. Addition of peat-derived humic acid extract (HA) to Sideroxydans lithotrophicus ES-1 liquid cultures led to higher cell numbers and up to 1.4 times higher Fe(II) oxidation rates compared to chemical controls. This effect was positively correlated with increasing HA concentrations. Similar Fe(III) (oxyhydr)oxide mineralogies were formed both abiotically and biotically irrespective of HA amendment, but minerals formed in the presence of ES-1 and HA were smaller. ES-1 growth with HA promoted aggregation of Fe(III) products in agarose-stabilized gradient tubes as shown by voltammetric profiling. In situ voltammetry in an acidic, iron-rich peatland revealed a gap between oxygen penetration and iron reduction that may reflect active Fe(II)-oxidizing microorganisms. The highest abundance of Fe(II) oxidizers Sideroxydans (4.9 × 107 gene copies gww-1) and Gallionella (1.5 × 107 gene copies gww-1) in the upper peat layer coincided with small-sized minerals resembling nanoparticulate ferrihydrite or goethite. Our results suggest that microbially mediated Fe(II) oxidation dominates in the presence of DOM leading to the formation of nano-sized biogenic Fe(III) (oxyhydr)oxides that might be readily bioavailable and likely important to iron and carbon cycling.

The association of microbial activity with Fe, S and trace element distribution in sediment cores within a natural wetland polluted by acid mine drainage

Natural recovery and remediation of acid mine drainage (AMD) reduces the generation of acidity and transport of trace elements in the runoff. A natural wetland that receives and remediates AMD from an abandoned copper mine at Parys Mountain (Anglesey, UK) was investigated for better understanding of the remediation mechanisms. Water column concentrations of dissolved Fe and S species, trace metal (loid)s and acidity decreased markedly as the mine drainage stream passed through the wetland. The metal (loid)s were removed from the water column by deposition into the sediment. Fe typically accumulated to higher concentrations in the surface layers of sediment while S and trace metal (loid)s were deposited at higher concentration within deeper (20-50 cm) sediments. High resolution X-ray fluorescence scans of sediment cores taken at three sites along the wetland indicates co-immobilization of Zn, Cu and S with sediment depth as each element showed a similar core profile. To examine the role of bacteria in sediment elemental deposition, marker genes for Fe and S metabolism were quantified. Increased expression of marker genes for S and Fe oxidation was detected at the same location within the middle of the wetland where significant decrease in SO₄^2- and Fe²⁺ was observed and where generation of particulate Fe occurs. This suggests that the distribution and speciation of Fe and S that mediates the immobilization and deposition of trace elements within the natural wetland sediments is mediated in part by bacterial activity.

Response of microbial communities and interactions to thallium in contaminated sediments near a pyrite mining area

Thallium (Tl) is a well-recognized hazardous heavy metal with very high toxicity. It is usually concentrated in sulfide minerals, such as pyrite (FeS₂), sphalerite (ZnS), chalcopyrite (CuS) and galena (PbS). Here, this study was carried out to investigate the indigenous microbial communities via 16S rRNA gene sequence analysis in typical surface sediments with various levels of Tl pollution (1.8-16.1 mg/kg) due to acid mine drainage from an active Tl-containing pyrite mining site in South China. It was found with more than 50 phyla from the domain Bacteria and 1 phyla from the domain Archaea. Sequences assigned to the genera Ferroplasma, Leptospirillum, Ferrovum, Metallibacterium, Acidithiobacillus, and Sulfuriferula manifested high relative abundances in all sequencing libraries from the relatively high Tl contamination. Canonical correspondence analysis further uncovered that the overall microbial community in this area was dominantly structured by the geochemical fractionation of Tl and geochemical parameters such as pH and Eh. Spearman's rank correlation analysis indicated a strong positive correlation between acidophilic Fe-metabolizing species and Tl_total, Tl_oxi, and Tl_res. The findings clarify potential roles of such phylotypes in the biogeochemical cycling of Tl, which may facilitate the development of in-situ bioremediation technology for Tl-contaminated sediments.

A novel approach coupling ferrous iron bio-oxidation and ferric iron chemo-reduction to promote biomineralization in simulated acidic mine drainage

A novel Acidithiobacillus ferrooxidans-mediated approach coupling biological oxidation and chemical reduction for treating acid mine drainage (AMD) was investigated. The results showed that controlled addition of zero valent iron (ZVI) into the coupling system did not exhibit a significant adverse influence on the bacterial activity of Acidithiobacillus ferrooxidans but markedly increased the formation of secondary Fe-minerals. Nutrition did not affect the efficiency of coupling process, except for the bacteria density of A. ferrooxidans. 2 days cyclic treatment performed better than that of 4 and 8 days. After 14 cycles of the coupling process, 89.4% of total iron (2.23 g L-1) was transferred into Fe-minerals finally. In addition, the combined system was highly effective in removing sulfate (63%) from a simulated AMD that contained soluble Cu, Zn, Al, and Mn. Valuable iron-sulfate material e.g. schwertmannite was formed with little co-precipitation of other metals. Therefore, the integration of A. ferrooxidans into the reduction by ZVI may have considerable potential in the enhancement of biomineralization efficiency, which may further decrease soluble TFe and sulfate loads in AMD before lime neutralization.

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.

Diversity of Iron Oxidizers in Groundwater-Fed Rapid Sand Filters: Evidence of Fe(II)-Dependent Growth by Curvibacter and Undibacterium spp

Although earlier circumstantial observations have suggested the presence of iron oxidizing bacteria (IOB) in groundwater-fed rapid sand filters (RSF), ferrous iron (Fe(II)) oxidation in this environment is often considered a chemical process due to the highly oxic and circumneutral pH conditions. The low water temperature (5-10°C), typical of groundwaters, on the other hand, may reduce the rates of chemical Fe(II) oxidation, which may allow IOB to grow and compete with chemical Fe(II) oxidation. Hence, we hypothesized that IOB are active and abundant in groundwater-fed RSFs. Here, we applied a combination of cultivation and molecular approaches to isolate, quantify, and confirm the growth of IOB from groundwater-fed RSFs, operated at different influent Fe(II) concentrations. Isolates related to Undibacterium and Curvibacter were identified as novel IOB lineages. Gallionella spp. were dominant in all waterworks, whereas Ferriphaselus and Undibacterium were dominant at pre-filters of waterworks receiving groundwaters with high (>2 mg/l) Fe(II) concentrations. The high density and diversity of IOB in groundwater-fed RSFs suggest that neutrophilic IOB may not be limited to oxic/anoxic interfaces.

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.

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.

Reconstruction of the Metabolic Potential of Acidophilic Sideroxydans Strains from the Metagenome of an Microaerophilic Enrichment Culture of Acidophilic Iron-Oxidizing Bacteria from a Pilot Plant for the Treatment of Acid Mine Drainage Reveals Metabolic Versatility and Adaptation to Life at Low pH

Bacterial community analyses of samples from a pilot plant for the treatment of acid mine drainage (AMD) from the lignite-mining district in Lusatia (East Germany) had previously demonstrated the dominance of two groups of acidophilic iron oxidizers: the novel candidate genus "Ferrovum" and a group comprising Gallionella-like strains. Since pure culture had proven difficult, previous studies have used genome analyses of co-cultures consisting of "Ferrovum" and a strain of the heterotrophic acidophile Acidiphilium in order to obtain insight into the life style of these novel bacteria. Here we report on attempts to undertake a similar study on Gallionella-like acidophiles from AMD. Isolates belonging to the family Gallionellaceae are still restricted to the microaerophilic and neutrophilic iron oxidizers Sideroxydans and Gallionella. Availability of genomic or metagenomic sequence data of acidophilic strains of these genera should, therefore, be relevant for defining adaptive strategies in pH homeostasis. This is particularly the case since complete genome sequences of the neutrophilic strains G. capsiferriformans ES-2 and S. lithotrophicus ES-1 permit the direct comparison of the metabolic capacity of neutrophilic and acidophilic members of the same genus and, thus, the detection of biochemical features that are specific to acidophilic strains to support life under acidic conditions. Isolation attempts undertaken in this study resulted in the microaerophilic enrichment culture ADE-12-1 which, based on 16S rRNA gene sequence analysis, consisted of at least three to four distinct Gallionellaceae strains that appear to be closely related to the neutrophilic iron oxidizer S. lithotrophicus ES-1. Key hypotheses inferred from the metabolic reconstruction of the metagenomic sequence data of these acidophilic Sideroxydans strains include the putative role of urea hydrolysis, formate oxidation and cyanophycin decarboxylation in pH homeostasis.

Iron Kinetics and Evolution of Microbial Populations in Low-pH, Ferrous Iron-Oxidizing Bioreactors

Iron-rich, acidic wastewaters are commonplace pollutants associated with metal and coal mining. Continuous-flow bioreactors were commissioned and tested for their capacities to oxidize ferrous iron in synthetic and actual acid mine drainage waters using (initially) pure cultures of the recently described acidophilic, iron-oxidizing heterotrophic bacterium Acidithrix ferrooxidans grown in the presence of glucose and yeast extract. The bioreactors became rapidly colonized by this bacterium, which formed macroscopic streamer growths in the flowing waters. Over 97% of ferrous iron in pH 2.0-2.2 synthetic mine water was oxidized (at up to 225 mg L(-1) h(-1)) at dilution rates (D) of 0.6 h(-1). Rates of iron oxidation decreased with pH but were still significant, with influent liquors as low as pH 1.37. When fed with actual mine water, >90% of ferrous iron was oxidized at D values of 0.4 h(-1), and microbial communities within the bioreactors changed over time, with Atx. ferrooxidans becoming increasingly displaced by the autotrophic iron-oxidizing acidophiles Ferrovum myxofaciens, Acidithiobacillus ferrivorans, and Leptospirillum ferrooxidans (which were all indigenous to the mine water), although this did not have a negative impact on net ferrous-iron oxidation. The results confirmed the potential of using a heterotrophic acidophile to facilitate the rapid commissioning of iron-oxidizing bioreactors and illustrated how microbial communities within them can evolve without compromising the performances of the bioreactors.

Remediation of antimony-rich mine waters: Assessment of antimony removal and shifts in the microbial community of an onsite field-scale bioreactor

An on-site field-scale bioreactor for passive treatment of antimony (Sb) contamination was installed downstream of an active Sb mine in Southwest China, and operated for one year (including a six month monitoring period). This bioreactor consisted of five treatment units, including one pre-aerobic cell, two aerobic cells, and two microaerobic cells. With the aerobic cells inoculated with indigenous mine water microflora, the bioreactor removed more than 90% of total soluble Sb and 80% of soluble antimonite (Sb(III)). An increase in pH and decrease of oxidation-reduction potential (Eh) was also observed along the flow direction. High-throughput sequencing of the small subunit ribosomal RNA (SSU rRNA) gene variable (V4) region revealed that taxonomically diverse microbial communities developed in the bioreactor. Metal (loid)-oxidizing bacteria including Ferrovum, Thiomonas, Gallionella, and Leptospirillum, were highly enriched in the bioreactor cells where the highest total Sb and Sb(III) removal occurred. Canonical correspondence analysis (CCA) indicated that a suite of in situ physicochemical parameters including pH and Eh were substantially correlated with the overall microbial communities. Based on an UPGMA (Unweighted Pair Group Method with Arithmetic Mean) tree and PCoA (Principal Coordinates Analysis), the microbial composition of each cell was distinct, indicating these in situ physicochemical parameters had an effect in shaping the indigenous microbial communities. Overall, this study was the first to employ a field-scale bioreactor to treat Sb-rich mine water onsite and, moreover, the findings suggest the feasibility of the bioreactor in removing elevated Sb from mine waters.

Substantial Variability of Multiple Microbial Communities Collected at Similar Acidic Mine Water Outlets

Deep sequencing of prokaryotic 16S rDNA regularly reveals thousands of microbial species thriving in many common habitats. It is still unknown how this huge microbial diversity, including many potentially competing organisms, may persist at a single site. One of plausible hypotheses is that a large number of spatially separated microcommunities exist within each complex habitat. Smaller subset of the species may exist in each microcommunity and actually interact with each other. We sampled two groups of microbial stalactites growing at a single acidic mine drainage outlet as a model of multiplicated, low-complexity microhabitat. Samples from six other sites were added for comparison. Both tRFLP and 16S rDNA pyrosequencing showed that microbial communities containing 6 to 51 species-level operational taxonomic units (OTU) inhabited all stalactites. Interestingly, most OTUs including the highly abundant ones unpredictably alternated regardless of physical and environmental distance of the stalactites. As a result, the communities clustered independently on sample site and other variables when using both phylogenetic dissimilarity and OTU abundance metrics. Interestingly, artificial communities generated by pooling the biota of several adjacent stalactites together clustered by the locality more strongly than when the stalactites were analyzed separately. The most probable interpretation is that each stalactite contains likely random selection from the pool of plausible species. Such degree of stochasticity in assembly of extremophilic microbial communities is significantly greater than commonly proposed and requires caution when interpreting microbial diversity.

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

Two acid mine drainage (AMD) sites in the Appalachian bituminous coal basin were selected to enrich for Fe(II)-oxidizing microbes and measure rates of low-pH Fe(II) oxidation in chemostatic bioreactors. Microbial communities were enriched for 74 to 128 days in fed-batch mode, then switched to flowthrough mode (additional 52 to 138 d) to measure rates of Fe(II) oxidation as a function of pH (2.1 to 4.2) and influent Fe(II) concentration (80 to 2,400 mg/liter). Biofilm samples were collected throughout these operations, and the microbial community structure was analyzed to evaluate impacts of geochemistry and incubation time. Alpha diversity decreased as the pH decreased and as the Fe(II) concentration increased, coincident with conditions that attained the highest rates of Fe(II) oxidation. The distribution of the seven most abundant bacterial genera could be explained by a combination of pH and Fe(II) concentration. Acidithiobacillus, Ferrovum, Gallionella, Leptospirillum, Ferrimicrobium, Acidiphilium, and Acidocella were all found to be restricted within specific bounds of pH and Fe(II) concentration. Temporal distance, defined as the cumulative number of pore volumes from the start of flowthrough mode, appeared to be as important as geochemical conditions in controlling microbial community structure. Both alpha and beta diversities of microbial communities were significantly correlated to temporal distance in the flowthrough experiments. Even after long-term operation under nearly identical geochemical conditions, microbial communities enriched from the different sites remained distinct. While these microbial communities were enriched from sites that displayed markedly different field rates of Fe(II) oxidation, rates of Fe(II) oxidation measured in laboratory bioreactors were essentially the same. These results suggest that the performance of suspended-growth bioreactors for AMD treatment may not be strongly dependent on the inoculum used for reactor startup.

IMPORTANCE

This study showed that different microbial communities enriched from two sites maintained distinct microbial community traits inherited from their respective seed materials. Long-term operation (up to 128 days of fed-batch enrichment followed by up to 138 days of flowthrough experiments) of these two systems did not lead to the same, or even more similar, microbial communities. However, these bioreactors did oxidize Fe(II) and remove total iron [Fe(T)] at very similar rates. These results suggest that the performance of suspended-growth bioreactors for AMD treatment may not be strongly dependent on the inoculum used for reactor startup. This would be advantageous, because system performance should be well constrained and predictable for many different sites.

Gene Loss and Horizontal Gene Transfer Contributed to the Genome Evolution of the Extreme Acidophile "Ferrovum"

Acid mine drainage (AMD), associated with active and abandoned mining sites, is a habitat for acidophilic microorganisms that gain energy from the oxidation of reduced sulfur compounds and ferrous iron and that thrive at pH below 4. Members of the recently proposed genus “Ferrovum” are the first acidophilic iron oxidizers to be described within the Betaproteobacteria. Although they have been detected as typical community members in AMD habitats worldwide, knowledge of their phylogenetic and metabolic diversity is scarce. Genomics approaches appear to be most promising in addressing this lacuna since isolation and cultivation of “Ferrovum” has proven to be extremely difficult and has so far only been successful for the designated type strain “Ferrovum myxofaciens” P3G. In this study, the genomes of two novel strains of “Ferrovum” (PN-J185 and Z-31) derived from water samples of a mine water treatment plant were sequenced. These genomes were compared with those of “Ferrovum” sp. JA12 that also originated from the mine water treatment plant, and of the type strain (P3G). Phylogenomic scrutiny suggests that the four strains represent three “Ferrovum” species that cluster in two groups (1 and 2). Comprehensive analysis of their predicted metabolic pathways revealed that these groups harbor characteristic metabolic profiles, notably with respect to motility, chemotaxis, nitrogen metabolism, biofilm formation and their potential strategies to cope with the acidic environment. For example, while the “F. myxofaciens” strains (group 1) appear to be motile and diazotrophic, the non-motile group 2 strains have the predicted potential to use a greater variety of fixed nitrogen sources. Furthermore, analysis of their genome synteny provides first insights into their genome evolution, suggesting that horizontal gene transfer and genome reduction in the group 2 strains by loss of genes encoding complete metabolic pathways or physiological features contributed to the observed diversification.

Genome Analysis of the Biotechnologically Relevant Acidophilic Iron Oxidising Strain JA12 Indicates Phylogenetic and Metabolic Diversity within the Novel Genus "Ferrovum"

Background

Members of the genus “Ferrovum” are ubiquitously distributed in acid mine drainage (AMD) waters which are characterised by their high metal and sulfate loads. So far isolation and microbiological characterisation have only been successful for the designated type strain “Ferrovum myxofaciens” P3G. Thus, knowledge about physiological characteristics and the phylogeny of the genus “Ferrovum” is extremely scarce.

Objective

In order to access the wider genetic pool of the genus “Ferrovum” we sequenced the genome of a “Ferrovum”-containing mixed culture and successfully assembled the almost complete genome sequence of the novel “Ferrovum” strain JA12.

Phylogeny and Lifestyle

The genome-based phylogenetic analysis indicates that strain JA12 and the type strain represent two distinct “Ferrovum” species. “Ferrovum” strain JA12 is characterised by an unusually small genome in comparison to the type strain and other iron oxidising bacteria. The prediction of nutrient assimilation pathways suggests that “Ferrovum” strain JA12 maintains a chemolithoautotrophic lifestyle utilising carbon dioxide and bicarbonate, ammonium and urea, sulfate, phosphate and ferrous iron as carbon, nitrogen, sulfur, phosphorous and energy sources, respectively.

Unique Metabolic Features

The potential utilisation of urea by “Ferrovum” strain JA12 is moreover remarkable since it may furthermore represent a strategy among extreme acidophiles to cope with the acidic environment. Unlike other acidophilic chemolithoautotrophs “Ferrovum” strain JA12 exhibits a complete tricarboxylic acid cycle, a metabolic feature shared with the closer related neutrophilic iron oxidisers among the Betaproteobacteria including Sideroxydans lithotrophicus and Thiobacillus denitrificans. Furthermore, the absence of characteristic redox proteins involved in iron oxidation in the well-studied acidophiles Acidithiobacillus ferrooxidans (rusticyanin) and Acidithiobacillus ferrivorans (iron oxidase) indicates the existence of a modified pathway in “Ferrovum” strain JA12. Therefore, the results of the present study extend our understanding of the genus “Ferrovum” and provide a comprehensive framework for future comparative genome and metagenome studies.

Geochemical niches of iron-oxidizing acidophiles in acidic coal mine drainage

A legacy of coal mining in the Appalachians has provided a unique opportunity to study the ecological niches of iron-oxidizing microorganisms. Mine-impacted, anoxic groundwater with high dissolved-metal concentrations emerges at springs and seeps associated with iron oxide mounds and deposits. These deposits are colonized by iron-oxidizing microorganisms that in some cases efficiently remove most of the dissolved iron at low pH, making subsequent treatment of the polluted stream water less expensive. We used full-cycle rRNA methods to describe the composition of sediment communities at two geochemically similar acidic discharges, Upper and Lower Red Eyes in Somerset County, PA, USA. The dominant microorganisms at both discharges were acidophilic Gallionella-like organisms, “Ferrovum” spp., and Acidithiobacillus spp. Archaea and Leptospirillum spp. accounted for less than 2% of cells. The distribution of microorganisms at the two sites could be best explained by a combination of iron(II) concentration and pH. Populations of the Gallionella-like organisms were restricted to locations with pH>3 and iron(II) concentration of >4 mM, while Acidithiobacillus spp. were restricted to pH<3 and iron(II) concentration of <4 mM. Ferrovum spp. were present at low levels in most samples but dominated sediment communities at pH<3 and iron(II) concentration of >4 mM. Our findings offer a predictive framework that could prove useful for describing the distribution of microorganisms in acid mine drainage, based on readily accessible geochemical parameters.

Novel and Unexpected Microbial Diversity in Acid Mine Drainage in Svalbard (78° N), Revealed by Culture-Independent Approaches

Svalbard, situated in the high Arctic, is an important past and present coal mining area. Dozens of abandoned waste rock piles can be found in the proximity of Longyearbyen. This environment offers a unique opportunity for studying the biological control over the weathering of sulphide rocks at low temperatures. Although the extension and impact of acid mine drainage (AMD) in this area is known, the native microbial communities involved in this process are still scarcely studied and uncharacterized. Several abandoned mining areas were explored in the search for active AMD and a culture-independent approach was applied with samples from two different runoffs for the identification and quantification of the native microbial communities. The results obtained revealed two distinct microbial communities. One of the runoffs was more extreme with regards to pH and higher concentration of soluble iron and heavy metals. These conditions favored the development of algal-dominated microbial mats. Typical AMD microorganisms related to known iron-oxidizing bacteria (Acidithiobacillus ferrivorans, Acidobacteria and Actinobacteria) dominated the bacterial community although some unexpected populations related to Chloroflexi were also significant. No microbial mats were found in the second area. The geochemistry here showed less extreme drainage, most likely in direct contact with the ore under the waste pile. Large deposits of secondary minerals were found and the presence of iron stalks was revealed by microscopy analysis. Although typical AMD microorganisms were also detected here, the microbial community was dominated by other populations, some of them new to this type of system (Saccharibacteria, Gallionellaceae). These were absent or lowered in numbers the farther from the spring source and they could represent native populations involved in the oxidation of sulphide rocks within the waste rock pile. This environment appears thus as a highly interesting field of potential novelty in terms of both phylogenetic/taxonomic and functional diversity.

Permanent draft genome sequence of Acidiphilium sp. JA12-A1

The tenacious association between strains of the heterotrophic alphaproteobacterial genus Acidiphilium and chemolithotrophic iron oxidizing bacteria has long been known. In this context the genome of the heterotroph Acidiphilium sp. JA12-A1, an isolate from an iron oxidizing mixed culture derived from a pilot plant for bioremediation of acid mine drainage, was determined with the aim to reveal metabolic properties that are fundamental for the syntrophic interaction between Acidiphilium sp. JA12-A1 and the co-occurring chemolithoautotrophic iron oxidizer. The genome sequence consists of 4.18 Mbp on 297 contigs and harbors 4015 protein-coding genes and 50 RNA genes. Additionally, the molecular and functional organization of the Acidiphilium sp. JA12-A1 draft genome was compared to those of the close relatives Acidiphilium cryptum JF-5, Acidiphilium multivorum AIU301 and Acidiphilium sp. PM DSM 24941. The comparative genome analysis underlines the close relationship between these strains and the highly similar metabolic potential supports the idea that other Acidiphilium strains play a similar role in various acid mine drainage communities. Nevertheless, in contrast to other closely related strains Acidiphilium sp. JA12-A1 may be able to take up phosphonates as an additional source of phosphor.

Revealing the microbial community structure of clogging materials in dewatering wells differing in physico-chemical parameters in an open-cast mining area

Iron rich deposits cause clogging the pumps and pipes of dewatering wells in open-cast mines, interfering with their function; however, little is known about either the microbial community structure or their potential role in the formation of these deposits. The microbial diversity and abundance of iron-oxidizing and -reducing bacteria were compared in pipe deposit samples with different levels of encrustation from 16 wells at three lignite mining sites. The groundwater varied in pH values from slightly acidic (4.5) to neutral (7.3), Fe(II) concentrations from 0.48 to 7.55 mM, oxygen content from 1.8 to 5.8 mg L(-1), and dissolved organic carbon (DOC) from 1.43 to 12.59 mg L(-1). There were high numbers of bacterial 16S rRNA gene copies in deposits, up to 2.5 × 10(10) copies g(-1) wet weight. Pyrosequencing analysis of bacterial 16S rRNA genes revealed that Proteobacteria was the most abundant phylum (63.3% of the total reads on average), followed by Actinobacteria (10.2%) and Chloroflexi (6.4%). Gallionella-related sequences dominated the bacterial community of pipe deposits and accounted for 48% of total sequence reads. Pipe deposits with amorphous ferrihydrite and schwertmannite mostly contained Gallionella (up to 1.51 × 10(10) 16S rRNA gene copies g(-1) wet weight), while more crystalline deposits showed a higher bacterial diversity. Surprisingly, the abundance of Gallionella was not correlated with groundwater pH, oxygen, or DOC content. Sideroxydans-related 16S rRNA gene copy numbers were one order of magnitude less than Gallionella, followed by acidophilic Ferrovum-related groups. Iron reducing bacteria were detected at rather low abundance, as was expected given the low iron reduction potential, although they could be stimulated by lactate amendment. The overall high abundance of Gallionella suggests that microbes may make major contributions to pipe deposit formation irrespective of the water geochemistry. Their iron oxidation activity might initiate the formation of amorphous iron oxides, potentially providing niches for other microorganisms later after crystallization, and leading to higher bacterial diversity along with deposit accumulation in later stages of clogging.

Analysis of the microbial community in moderately acidic drainage from the Yanahara pyrite mine in Japan

Acid rock drainage (ARD) originating from the Yasumi-ishi tunnel near the main tunnel of the Yanahara mine in Japan was characterized to be moderately acidic (pH 4.1) and contained iron at a low concentration (51 mg/L). The composition of the microbial community was determined by sequence analysis of 16S rRNA genes using PCR and denaturing gradient gel electrophoresis. The analysis of the obtained sequences showed their similarity to clones recently detected in other moderately acidic mine drainages. Uncultured bacteria related to Ferrovum- and Gallionella-like clones were dominant in the microbial community. Analyses using specific primers for acidophilic iron- or sulfur-oxidizing bacteria, Acidithiobacillus ferrooxidans, Leptospirillum spp., Acidithiobacillus caldus, Acidithiobacillus thiooxidans, and Sulfobacillus spp. revealed the absence of these bacteria in the microbial community in ARD from the Yasumi-ishi tunnel. Clones affiliated with a member of the order Thermoplasmatales were detected as the dominant archaea in the ARD microbial population.

Bench-scale study of the effect of phosphate on an aerobic iron oxidation plant for mine water treatment

At the opencast pit Nochten acidic iron- and sulfate-rich mine waters are treated biotechnologically in a mine-water treatment plant by microbial iron oxidation. Due to the low phosphate concentration in such waters the treatment plant was simulated in bench-scale to investigate the influence of addition of potassium dihydrogen phosphate on chemical and biological parameters of the mine-water treatment. As a result of the phosphate addition the number of cells increased, which resulted in an increase of the iron oxidation rate in the reactor with phosphate addition by a factor of 1.7 compared to a reference approach without phosphate addition. Terminal restriction fragment length polymorphism (T-RFLP) analysis during the cultivation revealed a shift of the microbial community depending on the phosphate addition. While almost exclusively iron-oxidizing bacteria related to "Ferrovum" sp. were detected with phosphate addition, the microbial community was more diverse without phosphate addition. In the latter case, iron-oxidizing bacteria ("Ferrovum" sp., Acidithiobacillus spp.) as well as non-iron-oxidizing bacteria (Acidiphilium sp.) were identified.

Surprising abundance of Gallionella-related iron oxidizers in creek sediments at pH 4.4 or at high heavy metal concentrations

We identified and quantified abundant iron-oxidizing bacteria (FeOB) at three iron-rich, metal-contaminated creek sites with increasing sediment pH from extremely acidic (R1, pH 2.7), to moderately acidic (R2, pH 4.4), to slightly acidic (R3, pH 6.3) in a former uranium-mining district. The geochemical parameters showed little variations over the 1.5 year study period. The highest metal concentrations found in creek sediments always coincided with the lowest metal concentrations in creek water at the slightly acidic site R3. Sequential extractions of R3 sediment revealed large portions of heavy metals (Ni, Cu, Zn, Pb, U) bound to the iron oxide fraction. Light microscopy of glass slides exposed in creeks detected twisted stalks characteristic of microaerobic FeOB of the family Gallionellaceae at R3 but also at the acidic site R2. Sequences related to FeOB such as Gallionella ferruginea, Sideroxydans sp. CL21, Ferritrophicum radicicola, and Acidovorax sp. BrG1 were identified in the sediments. The highest fraction of clone sequences similar to the acidophilic "Ferrovum myxofaciens" was detected in R1. Quantitative PCR using primer sets specific for Gallionella spp., Sideroxydans spp., and "Ferrovum myxofaciens" revealed that ~72% (R2 sediment) and 37% (R3 sediment) of total bacterial 16S rRNA gene copies could be assigned to groups of FeOB with dominance of microaerobic Gallionella spp. at both sites. Gallionella spp. had similar and very high absolute and relative gene copy numbers in both sediment communities. Thus, Gallionella-like organisms appear to exhibit a greater acid and metal tolerance than shown before. Microaerobic FeOB from R3 creek sediment enriched in newly developed metal gradient tubes tolerated metal concentrations of 35 mM Co, 24 mM Ni, and 1.3 mM Cd, higher than those in sediments. Our results will extend the limited knowledge of FeOB at contaminated, moderately to slightly acidic environments.

Development and application of biotechnologies in the metal mining industry

Metal mining faces a number of significant economic and environmental challenges in the twenty-first century for which established and emerging biotechnologies may, at least in part, provide the answers. Bioprocessing of mineral ores and concentrates is already used in variously engineered formats to extract base (e.g., copper, cobalt, and nickel) and precious (gold and silver) metals in mines throughout the world, though it remains a niche technology. However, current projections of an increasing future need to use low-grade primary metal ores, to reprocess mine wastes, and to develop in situ leaching technologies to extract metals from deep-buried ore bodies, all of which are economically more amenable to bioprocessing than conventional approaches (e.g., pyrometallurgy), would suggest that biomining will become more extensively utilized in the future. Recent research has also shown that bioleaching could be used to process a far wider range of metal ores (e.g., oxidized ores) than has previously been the case. Biotechnologies are also being developed to control mine-related pollution, including securing mine wastes (rocks and tailings) by using "ecological engineering" approaches, and also to remediate and recover metals from waste waters, such as acid mine drainage. This article reviews the current status of biotechnologies within the mining sector and considers how these may be developed and applied in future years.

New cultivation medium for "Ferrovum" and Gallionella-related strains

Since the first isolation of the well-known iron oxidizer Acidithiobacillus ferrooxidans various media and techniques have been developed to isolate new species of acidophilic iron-oxidizing bacteria. A successful strategy in many cases was the use of iFeo medium in double-layer plates with a heterotrophic strain in the underlayer. However, even with samples which had been shown by molecular techniques to be dominated by "Ferrovum myxofaciens" and Gallionella-related bacteria, these bacteria were isolated considerably less frequently than Acidithiobacillus spp. on iFeo. Therefore, a new medium was designed which corresponded largely to the chemical composition of the mine water in a treatment plant dominated by the bacterial groups mentioned and was called artificial pilot-plant water (APPW). The analyses of approximately 500 colonies obtained from mine waters of two different sampling sites by PCR with primers specific for Acidithiobacillus spp., "Ferrovum" spp., Gallionella relatives, and Acidiphilium spp. revealed higher abundances of "Ferrovum" spp. and Gallionella relatives on the newly designed APPW medium than on iFeo which favored Acidithiobacillus spp. Molecular analysis of the colonies obtained indicated the occurrence of at least two species of iron-oxidizing bacteria and/or the heterotrophic Acidiphilium spp. in most of the colonies. Furthermore, the influence on the isolation of the concentrations of iron, phosphate, and ammonium of APPW, in levels of the iFeo medium previously described was studied.

Microbial life associated with low-temperature alteration of ultramafic rocks in the Leka ophiolite complex

Water-rock interactions in ultramafic lithosphere generate reduced chemical species such as hydrogen that can fuel subsurface microbial communities. Sampling of this environment is expensive and technically demanding. However, highly accessible, uplifted oceanic lithospheres emplaced onto continental margins (ophiolites) are potential model systems for studies of the subsurface biosphere in ultramafic rocks. Here, we describe a microbiological investigation of partially serpentinized dunite from the Leka ophiolite (Norway). We analysed samples of mineral coatings on subsurface fracture surfaces from different depths (10-160 cm) and groundwater from a 50-m-deep borehole that penetrates several major fracture zones in the rock. The samples are suggested to represent subsurface habitats ranging from highly anaerobic to aerobic conditions. Water from a surface pond was analysed for comparison. To explore the microbial diversity and to make assessments about potential metabolisms, the samples were analysed by microscopy, construction of small subunit ribosomal RNA gene clone libraries, culturing and quantitative-PCR. Different microbial communities were observed in the groundwater, the fracture-coating material and the surface water, indicating that distinct microbial ecosystems exist in the rock. Close relatives of hydrogen-oxidizing Hydrogenophaga dominated (30% of the bacterial clones) in the oxic groundwater, indicating that microbial communities in ultramafic rocks at Leka could partially be driven by H2 produced by low-temperature water-rock reactions. Heterotrophic organisms, including close relatives of hydrocarbon degraders possibly feeding on products from Fischer-Tropsch-type reactions, dominated in the fracture-coating material. Putative hydrogen-, ammonia-, manganese- and iron-oxidizers were also detected in fracture coatings and the groundwater. The microbial communities reflect the existence of different subsurface redox conditions generated by differences in fracture size and distribution, and mixing of fluids. The particularly dense microbial communities in the shallow fracture coatings seem to be fuelled by both photosynthesis and oxidation of reduced chemical species produced by water-rock reactions.

Contemporary environmental variation determines microbial diversity patterns in acid mine drainage

A wide array of microorganisms survive and thrive in extreme environments. However, we know little about the patterns of, and controls over, their large-scale ecological distribution. To this end, we have applied a bar-coded 16S rRNA pyrosequencing technology to explore the phylogenetic differentiation among 59 microbial communities from physically and geochemically diverse acid mine drainage (AMD) sites across Southeast China, revealing for the first time environmental variation as the major factor explaining community differences in these harsh environments. Our data showed that overall microbial diversity estimates, including phylogenetic diversity, phylotype richness and pairwise UniFrac distance, were largely correlated with pH conditions. Furthermore, multivariate regression tree analysis also identified solution pH as a strong predictor of relative lineage abundance. Betaproteobacteria, mostly affiliated with the 'Ferrovum' genus, were explicitly predominant in assemblages under moderate pH conditions, whereas Alphaproteobacteria, Euryarchaeota, Gammaproteobacteria and Nitrospira exhibited a strong adaptation to more acidic environments. Strikingly, such pH-dependent patterns could also be observed in a subsequent comprehensive analysis of the environmental distribution of acidophilic microorganisms based on 16S rRNA gene sequences previously retrieved from globally distributed AMD and associated environments, regardless of the long-distance isolation and the distinct substrate types. Collectively, our results suggest that microbial diversity patterns are better predicted by contemporary environmental variation rather than geographical distance in extreme AMD systems.

Evolution of microbial "streamer" growths in an acidic, metal-contaminated stream draining an abandoned underground copper mine

A nine year study was carried out on the evolution of macroscopic “acid streamer” growths in acidic, metal-rich mine water from the point of construction of a new channel to drain an abandoned underground copper mine. The new channel became rapidly colonized by acidophilic bacteria: two species of autotrophic iron-oxidizers (Acidithiobacillus ferrivorans and “Ferrovum myxofaciens”) and a heterotrophic iron-oxidizer (a novel genus/species with the proposed name “Acidithrix ferrooxidans”). The same bacteria dominated the acid streamer communities for the entire nine year period, with the autotrophic species accounting for ~80% of the micro-organisms in the streamer growths (as determined by terminal restriction enzyme fragment length polymorphism (T-RFLP) analysis). Biodiversity of the acid streamers became somewhat greater in time, and included species of heterotrophic acidophiles that reduce ferric iron (Acidiphilium, Acidobacterium, Acidocella and gammaproteobacterium WJ2) and other autotrophic iron-oxidizers (Acidithiobacillus ferrooxidans and Leptospirillum ferrooxidans). The diversity of archaea in the acid streamers was far more limited; relatively few clones were obtained, all of which were very distantly related to known species of euryarchaeotes. Some differences were apparent between the acid streamer community and planktonic-phase bacteria. This study has provided unique insights into the evolution of an extremophilic microbial community, and identified several novel species of acidophilic prokaryotes.

Bioremediation of mine water

Caused by the oxidative dissolution of sulfide minerals, mine waters are often acidic and contaminated with high concentrations of sulfates, metals, and metalloids. Because the so-called acid mine drainage (AMD) affects the environment or poses severe problems for later use, treatment of these waters is required. Therefore, various remediation strategies have been developed to remove soluble metals and sulfates through immobilization using physical, chemical, and biological approaches. Conventionally, iron and sulfate-the main pollutants in mine waters-are removed by addition of neutralization reagents and subsequent chemical iron oxidation and sulfate mineral precipitation. Biological treatment strategies take advantage of the ability of microorganisms that occur in mine waters to metabolize iron and sulfate. As a rule, these can be grouped into oxidative and reductive processes, reflecting the redox state of mobilized iron (reduced form) and sulfur (oxidized form) in AMD. Changing the redox states of iron and sulfur results in iron and sulfur compounds with low solubility, thus leading to their precipitation and removal. Various techniques have been developed to enhance the efficacy of these microbial processes, as outlined in this review.

Metal-containing residues from industry and in the environment: geobiotechnological urban mining

This chapter explains the manifold geobiotechnological possibilities to separate industrial valuable metals from various industrial residues and stored waste products of the past. In addition to an overview of the different microbially catalyzed chemical reactions applicable for a separation of metals and details of published studies, results of many individual investigations from various research projects are described. These concern the separation of rare earth elements from phosphorous production slags, the attempts of tin leaching from mining flotation residues, the separation of metals from spent catalysts, or the treatment of ashes as valuable metal-containing material. The residues of environmental technologies are integrated into this overview as well. The description of the different known microbial processes offers starting points for suitable and new technologies. In addition to the application of chemolithoautotrophic microorganisms the use of heterotrophic microorganisms is explained.

New clusters of arsenite oxidase and unusual bacterial groups in enrichments from arsenic-contaminated soil

In the present study cultivation-dependent and molecular methods were applied in combination to investigate the arsenite-oxidizing communities in enrichment cultures from arsenic and lead smelter-impacted soils with respect to both 16S rRNA and arsenite oxidase gene diversity. Enrichments with arsenite as the only electron donor resulted in completely different communities than enrichments with yeast extract and the simultaneous presence of arsenite. The lithoautotrophic community appeared to be dominated by Ferrimicrobium-related Actinobacteria, unusual Acidobacteria, Myxobacteria, and α-Proteobacteria but the heterotrophic community comprised many Dokdonella-related γ-Proteobacteria. Gene sequences of clones encoding arsenite oxidase from the enrichment for lithoautotrophs belonged to three major clusters with sequences from non-cultivated microorganisms. So, primers used to detect arsenite oxidase genes could amplify the genes from many α-, β- and γ-Proteobacteria, but not from various strains of the other phyla present in the enrichment for lithotrophs. This was also observed for the isolates where arsenite oxidase genes from new proteobacterial isolates of the genera Burkholderia, Bosea, Alcaligenes, Bradyrhizobium and Methylobacterium could be amplified but the genes of the new Rhodococcus isolate S43 could not. The results indicate that the ability to oxidize arsenite is widespread in various unusual taxa, and molecular methods for their detection require further improvement.

A modular continuous flow reactor system for the selective bio-oxidation of iron and precipitation of schwertmannite from mine-impacted waters

A novel modular bioremediation system which facilitates the selective removal of soluble iron from extremely acidic (pH ∼2) metal-rich wastewaters by ferrous iron oxidation and selective precipitation of the ferric iron produced is described. In the first of the three modules, rapid ferrous iron oxidation was mediated by the recently-characterized iron-oxidizing autotrophic acidophile, "Ferrovum myxofaciens", which grew as long "streamers" within the reactor. Over 90% of the iron present in influent test liquors containing 280mg/L iron was oxidized at a dilution rate of 0.41h(-1), in a proton-consuming reaction. The ferric iron-rich solutions produced were pumped into a second reactor where controlled addition of sodium hydroxide caused the water pH to increase to 3.5 and ferric iron to precipitate as the mineral schwertmannite. Addition of a flocculating agent promoted rapid aggregation and settling of the fine-grain schwertmannite particles. A third passive module (a packed-bed bioreactor, also inoculated with "Fv. myxofaciens") acted as a polishing reactor, lowering soluble iron concentrations in the processed water to <1mg/L. The system was highly effective in selectively removing iron from a synthetic acidic (pH 2.1) mine water that contained soluble aluminum, copper, manganese and zinc in addition to iron. Schwertmannite was again produced, with little or no co-precipitation of other metals.

Organic matter in sediments of an acidic mining lake as assessed by lipid analysis. Part I: fatty acids

Fatty acid (FA) patterns of sediments collected from the bottom of an acidic mine pit lake (AML) at different depths (surface sediment: 0 to 1cm; deep sediment: 4 to 5 cm) were studied to characterize microbial communities and the sources of sedimentary organic matter (SOM). Studies were performed on the molecular level utilizing source-specific, diagnostic FA biomarkers. The biomarker-based approach has been used widely in marine sediment studies, but has not been applied for sediments from AMLs so far. Combined FA concentrations in the surface sediment were higher compared to those in the deep sediment (497 vs. 127 μg g(-1)d.w., respectively). This was related to deposition of autochthonous biomass and higher terrestrial plants onto the surface sediment, as well as--to lesser extent--with higher bacterial activity on the sediment-water interface. The FA distribution in both sediments was characterized by a strong even-over-odd preference and was bimodal in nature: there was a cluster at nC(14)-nC(18) characteristic of chiefly autochthonous (algal and bacterial) SOM production, and another cluster at nC(22-28) related to input from higher plants. The FA distribution in the surface sediment pointed to higher terrestrial input compared to autochthonous contribution to SOM (67%:33%) as an estimate. Fingerprinting of viable bacteria was accomplished through signature FA markers including branched C(15) and C(17) surrogates, cyclopropanoic acids, 3-hydroxy (OH) acids and monounsaturated surrogates with unusual double bond localization. The abundance of Gram-negative bacteria was higher in the surface sediment as evidenced by total diagnostic 3-OH-fatty acids (37 μg g(-1) versus 25 μg g(-1)). Potential source taxa in both sediment layers included acidophilic iron- and sulfur-oxidizing bacteria including Acidithiobacillus ferrooxidans. High abundances of terminally branched C(15) and C(17) surrogates in both sediments pointed to sulfate- and iron-reducing bacteria. Signature FAs characteristic of methanotrophs were virtually lacking in both sediments.

Schwertmannite formation adjacent to bacterial cells in a mine water treatment plant and in pure cultures of Ferrovum myxofaciens

Schwertmannite has previously been found in iron- and sulfate-rich mine waters at pH 2.8-4.5. In the present study, schwertmannite (Fe(8)O(8)(OH)(6)SO(4)) was shown to be the major mineral in a mine water treatment plant at pH 3, in which ferrous iron is mainly oxidized by bacteria belonging to the species Ferrovum myxofaciens. Strain EHS6, which is closely related to the type strain of Fv. myxofaciens, was isolated from the pilot plant and characterized as an acidophilic, iron-oxidizing bacterium. In contrast to the pilot plant, the mineral phase formed by a pure culture of Fv. myxofaciens EHS6 was a mixture of schwertmannite and jarosite (KFe(3)(SO(4))(2)(OH)(6)). In contrast to other reports of neutrophilic, iron-oxidizing bacteria, acidophilic microorganisms in the pilot plant and cultures of strain EHS6 did not show encrustation of the cell surface or deposition of minerals inside the cell, though a few cells appeared to be in contact with jarosite crystals. It was concluded that no direct biomineralization occurred in the pilot plant or in laboratory cultures. The lack of encrustation of bacterial cells in the pilot plant is considered advantageous since the cells are still able to get in contact with ferrous iron and the iron oxidation process in the mine water treatment plant can proceed.

Selective removal of transition metals from acidic mine waters by novel consortia of acidophilic sulfidogenic bacteria

Two continuous‐flow bench‐scale bioreactor systems populated by mixed communities of acidophilic sulfate‐reducing bacteria were constructed and tested for their abilities to promote the selective precipitation of transition metals (as sulfides) present in synthetic mine waters, using glycerol as electron donor. The objective with the first system (selective precipitation of copper from acidic mine water containing a variety of soluble metals) was achieved by maintaining a bioreactor pH of ∼2.2–2.5. The second system was fed with acidic (pH 2.5) synthetic mine water containing 3 mM of both zinc and ferrous iron, and varying concentrations (0.5–30 mM) of aluminium. Selective precipitation of zinc sulfide was possible by operating the bioreactor at pH 4.0 and supplementing the synthetic mine water with 4 mM glycerol. Analysis of the microbial populations in the bioreactors showed that they changed with varying operational parameters, and novel acidophilic bacteria (including one sulfidogen) were isolated from the bioreactors. The acidophilic sulfidogenic bioreactors provided ‘proof of principle’ that segregation of metals present in mine waters is possible using simple online systems within which controlled pH conditions are maintained. The modular units are versatile and robust, and involve minimum engineering complexity.

Distribution and diversity of Gallionella-like neutrophilic iron oxidizers in a tidal freshwater marsh

Microbial iron oxidation is an integral part of the iron redox cycle in wetlands. Nonetheless, relatively little is known about the composition and ecology of iron-oxidizing communities in the soils and sediments of wetlands. In this study, sediment cores were collected across a freshwater tidal marsh in order to characterize the iron-oxidizing bacteria (FeOB) and to link their distributions to the geochemical properties of the sediments. We applied recently designed 16S rRNA primers targeting Gallionella-related FeOB by using a nested PCR-denaturing gradient gel electrophoresis (DGGE) approach combined with a novel quantitative PCR (qPCR) assay. Gallionella-related FeOB were detected in most of the samples. The diversity and abundance of the putative FeOB were generally higher in the upper 5 to 12 cm of sediment than in deeper sediment and higher in samples collected in April than in those collected in July and October. Oxygen supply by macrofauna appears to be a major force in controlling the spatial and temporal variations in FeOB communities. The higher abundance of Gallionella-related FeOB in April coincided with elevated concentrations of extractable Fe(III) in the sediments. Despite this coincidence, the distributions of FeOB did not exhibit a simple relationship to the redox zonation inferred from the geochemical depth profiles.