Diversity of 16S ribosomal DNA-defined bacterial population in acid rock drainage from Japanese pyrite mine

Extremely Acidic Eukaryotic (Micro) Organisms: Life in Acid Mine Drainage Polluted Environments-Mini-Review

Acid Mine Drainage (AMD) results from sulfide oxidation, which incorporates hydrogen ions, sulfate, and metals/metalloids into the aquatic environment, allowing fixation, bioaccumulation and biomagnification of pollutants in the aquatic food chain. Acidic leachates from waste rock dams from pyritic and (to a lesser extent) coal mining are the main foci of Acid Mine Drainage (AMD) production. When AMD is incorporated into rivers, notable changes in water hydro-geochemistry and biota are observed. There is a high interest in the biodiversity of this type of extreme environments for several reasons. Studies indicate that extreme acid environments may reflect early Earth conditions, and are thus, suitable for astrobiological experiments as acidophilic microorganisms survive on the sulfates and iron oxides in AMD-contaminated waters/sediments, an analogous environment to Mars; other reasons are related to the biotechnological potential of extremophiles. In addition, AMD is responsible for decreasing the diversity and abundance of different taxa, as well as for selecting the most well-adapted species to these toxic conditions. Acidophilic and acidotolerant eukaryotic microorganisms are mostly composed by algae (diatoms and unicellular and filamentous algae), protozoa, fungi and fungi-like protists, and unsegmented pseudocoelomata animals such as Rotifera and micro-macroinvertebrates. In this work, a literature review summarizing the most recent studies on eukaryotic organisms and micro-organisms in Acid Mine Drainage-affected environments is elaborated.

Changes induced by heavy metals in the plant-associated microbiome of Miscanthus x giganteus

Miscanthus x giganteus is a high biomass producing plant with tolerance to heavy metals. This makes Miscanthus interesting to be used for phytoremediation of heavy metal contaminated areas coupled with energy production. Since plant performance in metal polluted areas is impaired, their growth and phytoremediation effect can be improved with bacterial assistance. To identify positive and negative responders of M. x giganteus associated microbiome influenced by Cd, Pb and Zn stress compared to non-contaminated controls, we designed a greenhouse experiment. Structure of the bacterial community in three rhizocompartments, namely rhizosphere, rhizoplane and root endosphere was analysed using an isolation independent molecular approach based on 16S rRNA gene barcoding. Furthermore, quantitative PCR (qPCR) was used for bacterial biomass estimation. Our results indicated that biomass and total bacterial diversity in rhizosphere, rhizoplane and root endosphere did not significantly change despite of substantial root uptake of heavy metals. Overall, we detected 6621 OTUs, from which 171 were affected by metal addition. Whereas Streptomyces and Amycolatopsis taxa were negatively affected by the heavy metal treatment in endosphere, taxa assigned to Luteolibacter in rhizosphere and rhizoplane (log₂ fold change 1.9-4.1) and Micromonospora in endosphere (log₂ fold change 10.2) were found to be significantly enriched and highly abundant (0.1-3.7% relative abundance) under heavy metal stress. Those taxa might be of key importance for M. x giganteus performance under heavy metal pollution and might be interesting candidates for the development of new bioinocula in the future to promote plant growth and phytoremediation in heavy metal contaminated soils.

A meta-taxonomic investigation of the prokaryotic diversity of water bodies impacted by acid mine drainage from the São Domingos mine in southern Portugal

The prokaryotic communities of water bodies contaminated by acid mine drainage from the São Domingos mining area in southern Portugal were analyzed using a meta-taxonomics approach with 16S rRNA gene sequences. Samples were collected in two seasonal sampling campaigns (summer and winter of 2017) from the most contaminated sites from where the water flows downstream to the freshwater reservoir of the river Chança. The physicochemical data indicate a trend of decreasing acid mine drainage contamination downstream of the mining area to the Chança's reservoir. The most contaminated sites (pH = 2.3-3.1) are distinguished by prokaryotic diversity with high abundances of operational taxonomics units related to acidophiles (genera Metallibacterium, Acidibacter, Leptospirillum, Acidobacterium, Thiomonas, Acidicapsa, Acidocella, Acidiphilium; family Acidobacteriaceae, order CPla-3 termite group). Likewise, in the transition zone in the mouth of the contaminated water flow into the Chança´s reservoir (pH = 6.4), a specific prokaryotic flora exists with some acidophiles, but notably with a cyanobacteria bloom and a high abundance of the genus Sediminibacterium (family I; order Subsection III). Moreover, the strong correlation between the abundance of acidophiles and characteristic physiochemical parameters (metals, acidity, and sulfate) confirm their potential as biomarkers of acid mine drainage pollution.

Microalgae-bacteria biofilms: a sustainable synergistic approach in remediation of acid mine drainage

Microalgae and bacteria offer a huge potential in delving interest to study and explore various mechanisms under extreme environments. Acid mine drainage (AMD) is one such environment which is extremely acidic containing copious amounts of heavy metals and poses a major threat to the ecosystem. Despite its extreme conditions, AMD is the habitat for several microbes and their activities. The use of various chemicals in prevention of AMD formation and conventional treatment in a larger scale is not feasible under different geological conditions. It implies that microbe-mediated approach is a viable and sustainable alternative technology for AMD remediation. Microalgae in biofilms play a pivotal role in such bioremediation as they maintain mutualism with heterotrophic bacteria. Synergistic approach of using microalgae-bacteria biofilms provides supportive metabolites from algal biomass for growth of bacteria and mediates remediation of AMD. However, by virtue of their physiology and capabilities of metal removal, non-acidophilic microalgae can be acclimated for use in AMD remediation. A combination of selective acidophilic and non-acidophilic microalgae together with bacteria, all in the form of biofilms, may be very effective for bioremediation of metal-contaminated waters. The present review critically examines the nature of mutualistic interactions established between microalgae and bacteria in biofilms and their role in removal of metals from AMDs, and consequent biomass production for the yield of biofuel. Integration of microalgal-bacterial consortia in fuel cells would be an attractive emerging approach of microbial biotechnology for AMD remediation.

Microalgae-bacteria biofilms: a sustainable synergistic approach in remediation of acid mine drainage

Microalgae and bacteria offer a huge potential in delving interest to study and explore various mechanisms under extreme environments. Acid mine drainage (AMD) is one such environment which is extremely acidic containing copious amounts of heavy metals and poses a major threat to the ecosystem. Despite its extreme conditions, AMD is the habitat for several microbes and their activities. The use of various chemicals in prevention of AMD formation and conventional treatment in a larger scale is not feasible under different geological conditions. It implies that microbe-mediated approach is a viable and sustainable alternative technology for AMD remediation. Microalgae in biofilms play a pivotal role in such bioremediation as they maintain mutualism with heterotrophic bacteria. Synergistic approach of using microalgae-bacteria biofilms provides supportive metabolites from algal biomass for growth of bacteria and mediates remediation of AMD. However, by virtue of their physiology and capabilities of metal removal, non-acidophilic microalgae can be acclimated for use in AMD remediation. A combination of selective acidophilic and non-acidophilic microalgae together with bacteria, all in the form of biofilms, may be very effective for bioremediation of metal-contaminated waters. The present review critically examines the nature of mutualistic interactions established between microalgae and bacteria in biofilms and their role in removal of metals from AMDs, and consequent biomass production for the yield of biofuel. Integration of microalgal-bacterial consortia in fuel cells would be an attractive emerging approach of microbial biotechnology for AMD remediation.

Isolation of Novel Bacteria Including Rarely Cultivated Phyla, Acidobacteria and Verrucomicrobia, from the Roots of Emergent Plants by Simple Culturing Method

A number of novel bacteria including members of rarely cultivated phyla, Acidobacteria and Verrucomicrobia, were successfully isolated from the roots of two emergent plants, Iris pseudacorus and Scirpus juncoides, by a simple culturing method. A total of 47.1% (66 strains) for I. pseudacorus and 42.1% (59 strains) for S. juncoides of all isolates (140 strains from each sample) were phylogenetically novel. Furthermore, Acidobacteria and Verrucomicrobia occupied 10.7% (15 strains) and 2.9% (4 strains) of I. pseudacorus isolates, and 2.1% (3 strains) and 3.6% (5 strains) of S. juncoides isolates, respectively, indicating that plant roots are attractive sources for isolating rarely cultivated microbes.

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.

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.

Community level physiological profiles of bacterial communities inhabiting uranium mining impacted sites

Bacterial activity and physiological diversity were characterized in mining and milling impacted soils collected from three abandoned uranium mine sites, Senokos, Buhovo and Sliven, using bacterial dehydrogenase activity and Biolog (EcoPlate) tests. The elemental composition of soils revealed high levels of uranium and heavy metals (sum of technogenic coefficients of contamination; TCC(sum) pollution as follows: Sliven (uranium - 374 mg/kg; TCC(sum) - 23.40) >Buhovo (uranium - 139.20mg/kg; TCC(sum) - 3.93) >Senokos (uranium - 23.01 mg/kg; TCC(sum) - 0.86). The physiological profiles of the bacterial community level were site specific, and indicated intensive utilization of polyols, carbohydrates and carboxylic acids in low and medium polluted environments, and i-erithrytol and 2-hydroxy-benzoic acid in the highly polluted environment of Sliven waste pile. Enzymes which take part in the biodegradation of recalcitrant substances were more resistant to pollution than these from the pathways of the easily degradable carbon sources. The Shannon index indicated that the physiological diversity of bacteria was site specific but not in line with the levels of pollution. A general tendency of increasing the importance of the number of utilizable substrates to bacterial physiological diversity was observed at less polluted sites, whereas in highly polluted sites the evenness of substrate utilization rate was more significant. Dehydrogenase activity was highest in Senokos upper soil layer and positively correlated (p<0.01) with the soil organic matter content. The bacterial activity (EcoPlate) and physiological diversity (Shannon index) correlated significantly and negatively with As, Cu, Zn, Pb and U, and Co, Cr, Ni and Mn, respectively. We concluded that the observed site specific shifts in bacterial communities were complex due to both the environmental peculiarities and the bacterial tolerance to the relevant level of pollution, rather than a strong indication of uranium and heavy metals toxicity.

Detection of WWE2-related Lentisphaerae by 16S rRNA gene sequencing and fluorescence in situ hybridization in landfill leachate

We collected samples of anaerobic landfill leachate from municipal solid waste landfill (Vert-le-Grand, France) and constructed 16S rRNA clone libraries using primers targeting Planctomycetes and relatives (Pla46F and 1390R). Analyses of 16S rRNA gene sequences resulted in the abundant representation of WWE2-related Lentisphaerae, members of the phylum Lentisphaerae, in the clone library (98% of the retrieved sequences). Although the sequences that are phylogenetically affiliated with the cultured isolate Victivallis vadensis were identified (WWE2 subgroup II), the majority of the sequences were affiliated with an uncultured Lentisphaerae lineage (WWE2 subgroup I). We designed oligonucleotides probes targeting the specific 16S rRNA gene regions of those 2 subgroups. Fluorescence in situ hybridization confirmed the abundance of the uncultivated WWE2 subgroup I in our leachate samples.

Microbiological polyphasic approach for soil health evaluation in an Italian polluted site

The use of microorganisms as bioindicators of soil health is quite a new feature, rarely considered for the soil health evaluation in chronically-polluted industrial sites, and still suffering of the bias related to the technique applied. In this work we applied a microbiological polyphasic approach, relying on soil indigenous microorganisms as bioindicators and combining culture-dependent and -independent methods, in order to evaluate soil health of four sites (1a, 1b, 2a and 2b) inside a chemical factory with a centenary activity. Functional as well as structural aspects were comprehensively considered. Results were related to the kind of pollutants found in each site. Heavy metal pollution was recorded in sites 1b and 2b, while both organic and inorganic substances were detected in sites 1a and 2a. Based on the chemical and physical properties of the four soils, site 1b and 2b grouped together, while 1a and 2a were separated from the others. The density of the culturable bacteria was very low in site 2a, where only gram-positive were found. According to the identification of culturable bacteria, site 2a showed the lowest similarity with the other sites. Microbial activity was detected only in sites 1b and 2b. PCR-DGGE (Denaturing Gradient Gel Electrophoresis), was performed on the culturable, total and active microbial communities. Consistently with the identification of culturable bacterial strains, the molecular profile of the culturable fraction of site 2a, was clearly separated from the molecular profiles of other sites in cluster analysis. Molecular fingerprintings of the whole and active bacterial communities differed among the sites, but clustered according to the pollutants present in each site. The presence of possible key species in each site has been discussed according to the whole and active species. Since the results obtained by microbiological analysis are consistent with the chemical data, we suggest that the use of this microbiological polyphasic approach and of microorganisms as intrinsic bioindicators, can be suitable for the evaluation of soil health.

Bacterial diversity in a mine water treatment plant

We investigated the microbial community in a pilot plant for treatment of acid mine water by biological ferrous iron oxidation using clone library analysis and calculated statistical parameters for further characterization. The microbial community in the plant was conspicuously dominated by a group of Betaproteobacteria affiliated with "Ferribacter polymyxa".

A novel acidophile community populating waste ore deposits at an acid mine drainage site

Waste ore samples (pH 3.0) were collected at an acid mine drainage (AMD) site in Anhui, China. The present acidophilic microbial community in the waste ore was studied with 16S rRNA gene clone library and denaturing gradient gel electrophoresis (DGGE). Eighteen different clones were identified and affiliated with Actinobacteria, low G + C Gram-positives, Thermomicrobia, Acidobacteria, Proteobacteria, candidate division TM7, and Planctomycetes. Phylogenetic analysis of 16S rRNA gene sequences revealed a diversity of acidophiles in the samples that were mostly novel. It is unexpected that the moderately thermophilic acidophiles were abundant in the acidic ecosystem and may play a great role in the generation of AMD. The result of DGGE was consistent with that of clone library analysis. These findings help in the better understanding of the generation mechanism of AMD and in developing a more efficient method to control AMD.

The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance

In the rRNA-based tree of life four bacterial phyla, comprising the Planctomycetes, Verrucomicrobia, Chlamydiae and Lentisphaerae, form together with the candidate phyla Poribacteria and OP3 a monophyletic group referred to as the PVC superphylum. This assemblage contains organisms that possess dramatically different lifestyles and which colonize sharply contrasting habitats. Some members of this group are among the most successful human pathogens, others are abundant soil microbes, and others still are of major importance for the marine nitrogen cycle and hold much promise for sustainable wastewater treatment. Recent comparative genomic and metagenomic analyses of a few representatives of this group revealed many unusual features and generated unexpected hypotheses regarding their physiology, some of which have already been confirmed experimentally. Furthermore, the availability of these genome sequences offered new insights into the evolutionary history of this peculiar group of microbes with major medical, ecological and biotechnological relevance.