Temporal evolution of bacterial communities associated with the in situ wetland-based remediation of a marine shore porphyry copper tailings deposit

Diaby, Nouhou; Dold, Bernhard; Rohrbach, E.; Holliger, Christof; Rossi, Pierre

doi:10.1016/j.scitotenv.2015.06.076

Cited by 19 publications

(14 citation statements)

References 56 publications

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“…However, taxa known to be involved in iron oxidation or sulfate reduction were not dominant within the near-surface sediment wetland samples analyzed here, suggesting that they are more abundant in other locations of the AMD ecosystem, such as deep anaerobic sediments, biofilms, or AMD mine water. For example, examination of a constructed wetland during its evolution over 225 days showed accumulation of sulfate reducing bacteria and aerobic bacteria in the water column over time ( Diaby et al, 2015 ). Likewise, samples previously taken within the southern Afon Goch wetland at the sediment–water interface identified taxa that grouped phylogenetically with sulfate reducing and oxidizing bacteria ( Dean et al, 2013 ).…”

Section: Resultsmentioning

confidence: 99%

“…Microbial community structures have been examined in mine tailings, AMD water and sediment, and biofilms from mine sites ( Huang et al, 2016 ). However, very few previous AMD studies have used large-scale sequencing approaches to examine bacteria associated with wetland plant rhizosphere sediments ( Diaby et al, 2015 ), and to our knowledge, none have characterized AMD-exposed natural wetlands in direct comparison to river sediment without wetland plants. Wetlands can show substantial resilience to highly metal-rich and acidic waters over very long periods of time; for example, natural wetlands that have been studied in Ireland, United Kingdom, and United States have been found to tolerate very high acidity (sometimes pH < 3), high dissolved metal concentrations (such as >200 mg L -1 of Fe) over many decades, indicating long-term adaptation to AMD stress ( Beining and Otte, 1996 ; August et al, 2002 ; Dean et al, 2013 ).…”

Section: Introductionmentioning

confidence: 99%

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Microbial Community Shifts in Response to Acid Mine Drainage Pollution Within a Natural Wetland Ecosystem

et al. 2018

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Natural wetlands are known to play an important role in pollutant remediation, such as remediating acid mine drainage (AMD) from abandoned mine sites. However, many aspects of the microbiological mechanisms underlying AMD remediation within wetlands are poorly understood, including the role and composition of associated microbial communities. We have utilized an AMD-polluted river-wetland system to perform rRNA sequence analysis of microbial communities that play a role in biogeochemical activities that are linked to water quality improvement. Next-generation sequencing of bacterial 16S rRNA gene amplicons from river and wetland sediment samples identified variation in bacterial community structure and diversity on the basis of dissolved and particulate metal concentrations, sediment metal concentrations and other water chemistry parameters (pH and conductivity), and wetland plant presence. Metabolic reconstruction analysis allowed prediction of relative abundance of microbial metabolic pathways and revealed differences between samples that cluster on the basis of the severity of AMD pollution. Global metabolic activity was predicted to be significantly higher in unpolluted and wetland sediments in contrast to polluted river sediments, indicating a metabolic stress response to AMD pollution. This is one of the first studies to explore microbial community structure dynamics within a natural wetland exposed to AMD and our findings indicate that wetland ecosystems play critical roles in maintaining diversity and metabolic structure of sediment microbial communities subject to high levels of acidity and metal pollution. Moreover, these microbial communities are predicted to be important for the remediation action of the wetland.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Microbial Community Shifts in Response to Acid Mine Drainage Pollution Within a Natural Wetland Ecosystem

et al. 2018

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“…Library preparation was carried out as shown in Diaby et al (2015). Briefly, PCR amplification of the 16S rRNA hypervariable regions V1-V3 was carried out using bacterial HPLC-purified bacterial primers 28f and 519rm (5′-GAGTTTGATCNTGGCTCAG-3′ and 5′-GTNTTACNGCGGCKGCTG-3′ respectively) and archaeal primers 109f and 915r (5′-ACKGCTCAGTAACACGT-3′ and 5′-GTGCTCCCCCGCCAATTCC respectively), with 0.1 ng/μl of template DNA (final concentration).…”

Section: Next-generation Library Preparationmentioning

confidence: 99%

“…Next-generation sequencing was conducted on an Ion Torrent Personal Genome Machine as shown in Diaby et al, 2015. Emulsion PCR was carried out applying the Ion XPress Plus Template Kit (Life Technologies) as described by the manufacturer.…”

Section: Semiconductor Sequencingmentioning

confidence: 99%

Microbial communities associated with uranium in-situ recovery mining process are related to acid mine drainage assemblages

Coral

Descostes

Boissezon

et al. 2018

Science of The Total Environment

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A large fraction (47%) of the world's uranium is mined by a technique called "In Situ Recovery" (ISR). This mining technique involves the injection of a leaching fluid (acidic or alkaline) into a uranium-bearing aquifer and the pumping of the resulting solution through cation exchange columns for the recovery of dissolved uranium. The present study reports the in-depth alterations brought to autochthonous microbial communities during acidic ISR activities. Water samples were collected from a uranium roll-front deposit that is part of an ISR mine in operation (Tortkuduk, Kazakhstan). Water samples were obtained at a depth of ca 500 m below ground level from several zones of the Uyuk aquifer following the natural redox zonation inherited from the roll front deposit, including the native mineralized orebody and both upstream and downstream adjacent locations. Samples were collected equally from both the entrance and the exit of the uranium concentration plant. Next-generation sequencing data showed that the redox gradient shaped the community structures, within the anaerobic, reduced, and oligotrophic habitats of the native aquifer zones. Acid injection induced drastic changes in the structures of these communities, with a large decrease in both cell numbers and diversity. Communities present in the acidified (pH values < 2) mining areas exhibited similarities to those present in acid mine drainage, with the dominance of Sulfobacillus sp., Leptospirillum sp. and Acidithiobacillus sp., as well as the archaean Ferroplasma sp. Communities located up- and downstream of the mineralized zone under ISR and affected by acidic fluids were blended with additional facultative anaerobic and acidophilic microorganisms. These mixed biomes may be suitable communities for the natural attenuation of ISR mining-affected subsurface through the reduction of metals and sulfate. Assessing the effect of acidification on the microbial community is critical to evaluating the potential for natural attenuation or active bioremediation strategies.

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“…Amplicons were sequenced on a Roche GS-FLX+ instrument (Roche, Switzerland) by Research and Testing Laboratory (USA). Sff files were processed using Mothur (Schloss et al, 2009 ) on a Biolinux 7 platform as described in Diaby et al ( 2015 ), providing between 1193 (original sample M1) and 6282 final reads (SFM7).…”

Section: Methodsmentioning

confidence: 99%

Indirect Evidence Link PCB Dehalogenation with Geobacteraceae in Anaerobic Sediment-Free Microcosms

et al. 2016

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Although polychlorinated biphenyls (PCBs) production was brought to a halt 30 years ago, recalcitrance to degradation makes them a major environmental pollutant at a global scale. Previous studies confirmed that organohalide-respiring bacteria (OHRB) were capable of utilizing chlorinated congeners as electron acceptor. OHRB belonging to the Phyla Chloroflexi and Firmicutes are nowadays considered as the main PCB-dechlorinating organisms. In this study, we aimed at exploring the involvement of other taxa in PCB dechlorination using sediment-free microcosms (SFMs) and the Delor PCB mixture. High rates of congener dehalogenation (up to 96%) were attained in long-term incubations of up to 692 days. Bacterial communities were dominated by Chloroflexi, Proteobacteria, and Firmicutes, among strictly simplified community structures composed of 12 major phyla only. In a first batch of SFMs, Dehalococcoides mccartyi closely affiliated with strains CG4 and CBDB1 was considered as the main actor associated with congener dehalogenation. Addition of 2-bromoethanesulfonate (BES), a known inhibitor of methanogenic activity in a second batch of SFMs had an adverse effect on the abundance of Dehalococcoides sp. Only two sequences affiliated to this Genus could be detected in two (out of six) BES-treated SFMs, contributing to a mere 0.04% of the communities. BES-treated SFMs showed very different community structures, especially in the contributions of organisms involved in fermentation and syntrophic activities. Indirect evidence provided by both statistical and phylogenetic analysis validated the implication of a new cluster of actors, distantly affiliated with the Family Geobacteraceae (Phylum δ-Proteobacteria), in the dehalogenation of low chlorinated PCB congeners. Members of this Family are known already for their dehalogenation capacity of chlorinated solvents. As a result, the present study widens the knowledge for the phylogenetic reservoir of indigenous PCB dechlorinating taxa.

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Temporal evolution of bacterial communities associated with the in situ wetland-based remediation of a marine shore porphyry copper tailings deposit

Cited by 19 publications

References 56 publications

Microbial Community Shifts in Response to Acid Mine Drainage Pollution Within a Natural Wetland Ecosystem

Microbial Community Shifts in Response to Acid Mine Drainage Pollution Within a Natural Wetland Ecosystem

Microbial communities associated with uranium in-situ recovery mining process are related to acid mine drainage assemblages

Indirect Evidence Link PCB Dehalogenation with Geobacteraceae in Anaerobic Sediment-Free Microcosms

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