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Twible LE, Whaley-Martin K, Chen LX, Colenbrander Nelson T, Arrey JL, Jarolimek CV, King JJ, Ramilo L, Sonnenberg H, Banfield JF, Apte SC, Warren LA. pH and thiosulfate dependent microbial sulfur oxidation strategies across diverse environments. Front Microbiol 2024; 15:1426584. [PMID: 39101034 PMCID: PMC11294248 DOI: 10.3389/fmicb.2024.1426584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 06/18/2024] [Indexed: 08/06/2024] Open
Abstract
Sulfur oxidizing bacteria (SOB) play a key role in sulfur cycling in mine tailings impoundment (TI) waters, where sulfur concentrations are typically high. However, our understanding of SOB sulfur cycling via potential S oxidation pathways (sox, rdsr, and S4I) in these globally ubiquitous contexts, remains limited. Here, we identified TI water column SOB community composition, metagenomics derived metabolic repertoires, physicochemistry, and aqueous sulfur concentration and speciation in four Canadian base metal mine, circumneutral-alkaline TIs over four years (2016 - 2019). Identification and examination of genomes from nine SOB genera occurring in these TI waters revealed two pH partitioned, metabolically distinct groups, which differentially influenced acid generation and sulfur speciation. Complete sox (csox) dominant SOB (e.g., Halothiobacillus spp., Thiomonas spp.) drove acidity generation and S2O3 2- consumption via the csox pathway at lower pH (pH ~5 to ~6.5). At circumneutral pH conditions (pH ~6.5 to ~8.5), the presence of non-csox dominant SOB (hosting the incomplete sox, rdsr, and/or other S oxidation reactions; e.g. Thiobacillus spp., Sulfuriferula spp.) were associated with higher [S2O3 2-] and limited acidity generation. The S4I pathway part 1 (tsdA; S2O3 2- to S4O6 2-), was not constrained by pH, while S4I pathway part 2 (S4O6 2- disproportionation via tetH) was limited to Thiobacillus spp. and thus circumneutral pH values. Comparative analysis of low, natural (e.g., hydrothermal vents and sulfur hot springs) and high (e.g., Zn, Cu, Pb/Zn, and Ni tailings) sulfur systems literature data with these TI results, reveals a distinct TI SOB mining microbiome, characterized by elevated abundances of csox dominant SOB, likely sustained by continuous replenishment of sulfur species through tailings or mining impacted water additions. Our results indicate that under the primarily oxic conditions in these systems, S2O3 2- availability plays a key role in determining the dominant sulfur oxidation pathways and associated geochemical and physicochemical outcomes, highlighting the potential for biological management of mining impacted waters via pH and [S2O3 2-] manipulation.
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Affiliation(s)
- Lauren E. Twible
- Department of Civil and Mineral Engineering, University of Toronto, Toronto, ON, Canada
| | - Kelly Whaley-Martin
- Department of Civil and Mineral Engineering, University of Toronto, Toronto, ON, Canada
| | - Lin-Xing Chen
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, United States
| | | | - James L.S. Arrey
- Department of Civil and Mineral Engineering, University of Toronto, Toronto, ON, Canada
| | - Chad V. Jarolimek
- School of Mathematical and Physical Sciences, University of Technology Sydney, Ultimo, NSW, Australia
| | - Josh J. King
- Commonwealth Scientific Industrial and Research Organization, Black Mountain, ACT, Australia
| | | | | | - Jillian F. Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, United States
| | - Simon C. Apte
- Commonwealth Scientific Industrial and Research Organization, Clayton, VIC, Australia
| | - Lesley A. Warren
- Department of Civil and Mineral Engineering, University of Toronto, Toronto, ON, Canada
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2
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Wei X, Chen H, Zhu F, Li J. Microbial community structure in an uranium-rich acid mine drainage site: implication for the biogeochemical release of uranium. Front Microbiol 2024; 15:1412599. [PMID: 38993490 PMCID: PMC11238263 DOI: 10.3389/fmicb.2024.1412599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 06/13/2024] [Indexed: 07/13/2024] Open
Abstract
The generation of acid mine drainage (AMD) characterized by high acidity and elevated levels of toxic metals primarily results from the oxidation and dissolution of sulfide minerals facilitated by microbial catalysis. Although there has been significant research on microbial diversity and community composition in AMD, as well as the relationship between microbes and heavy metals, there remains a gap in understanding the microbial community structure in uranium-enriched AMD sites. In this paper, water samples with varying levels of uranium pollution were collected from an abandoned stone coal mine in Jiangxi Province, China during summer and winter, respectively. Geochemical and high-throughput sequencing analyses were conducted to characterize spatiotemporal variations in bacterial diversity and community composition along pollution groups. The results indicated that uranium was predominantly concentrated in the AMD of new pits with strong acid production capacity, reaching a peak concentration of 9,370 μg/L. This was accompanied by elevated acidity and concentrations of iron and total phosphorus, which were identified as significant drivers shaping the composition of bacterial communities, rather than fluctuations in seasonal conditions. In an extremely polluted environment (pH < 3), bacterial diversity was lowest, with a predominant presence of acidophilic iron-oxidizing bacteria (such as Ferrovum), and a portion of acidophilic heterotrophic bacteria synergistically coexisting. As pollution levels decreased, the microbial community gradually evolved to cohabitation of various pH-neutral heterotrophic species, ultimately reverting back to background level. The pH was the dominant factor determining biogeochemical release of uranium in AMD. Acidophilic and uranium-tolerant bacteria, including Ferrovum, Leptospirillum, Acidiphilium, and Metallibacterium, were identified as playing key roles in this process through mechanisms such as enhancing acid production rate and facilitating organic matter biodegradation.
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Affiliation(s)
- Xinxiang Wei
- School of Water Resources and Environmental Engineering, East China University of Technology, Nanchang, Jiangxi, China
- Department of Hydraulic Engineering, Jiangxi Water Resource Institute, Nanchang, Jiangxi, China
| | - Hongliang Chen
- School of Water Resources and Environmental Engineering, East China University of Technology, Nanchang, Jiangxi, China
| | - Fangfang Zhu
- College of Nursing Health Sciences, Yunnan Open University, Kunming, Yunnan, China
| | - Jiang Li
- State Key Laboratory of Nuclear Resources and Environment, East China University of Technology, Nanchang, Jiangxi, China
- Teachers’ College, East China University of Technology, Nanchang, Jiangxi, China
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Chen M, Grégoire DS, Bain JG, Blowes DW, Hug LA. Legacy copper/nickel mine tailings potentially harbor novel iron/sulfur cycling microorganisms within highly variable communities. Appl Environ Microbiol 2024; 90:e0014324. [PMID: 38814057 PMCID: PMC11218620 DOI: 10.1128/aem.00143-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 05/07/2024] [Indexed: 05/31/2024] Open
Abstract
The oxidation of sulfide-bearing mine tailings catalyzed by acidophilic iron and sulfur-oxidizing bacteria releases toxic metals and other contaminants into soil and groundwater as acid mine drainage. Understanding the environmental variables that control the community structure and metabolic activity of microbes indigenous to tailings (especially the abiotic stressors of low pH and high dissolved metal content) is crucial to developing sustainable bioremediation strategies. We determined the microbial community composition along two continuous vertical gradients of Cu/Ni mine tailings at each of two tailings impoundments near Sudbury, Ontario. 16S rRNA amplicon data showed high variability in community diversity and composition between locations, as well as at different depths within each location. A temporal comparison for one tailings location showed low fluctuation in microbial communities across 2 years. Differences in community composition correlated most strongly with pore-water pH, Eh, alkalinity, salinity, and the concentration of several dissolved metals (including iron, but not copper or nickel). The relative abundances of individual genera differed in their degrees of correlation with geochemical factors. Several abundant lineages present at these locations have not previously been associated with mine tailings environments, including novel species predicted to be involved in iron and sulfur cycling.IMPORTANCEMine tailings represent a significant threat to North American freshwater, with legacy tailings areas generating acid mine drainage (AMD) that contaminates rivers, lakes, and aquifers. Microbial activity accelerates AMD formation through oxidative metabolic processes but may also ameliorate acidic tailings by promoting secondary mineral precipitation and immobilizing dissolved metals. Tailings exhibit high geochemical variation within and between mine sites and may harbor many novel extremophiles adapted to high concentrations of toxic metals. Characterizing the unique microbiomes associated with tailing environments is key to identifying consortia that may be used as the foundation for innovative mine-waste bioremediation strategies. We provide an in-depth analysis of microbial diversity at four copper/nickel mine tailings impoundments, describe how communities (and individual lineages) differ based on geochemical gradients, predict organisms involved in AMD transformations, and identify taxonomically novel groups present that have not previously been observed in mine tailings.
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Affiliation(s)
- Molly Chen
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Daniel S. Grégoire
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
- Department of Chemistry, Carleton University, Ottawa, Ontario, Canada
| | - Jeffrey G. Bain
- Department of Earth and Environmental Sciences, University of Waterloo, Waterloo, Ontario, Canada
| | - David W. Blowes
- Department of Earth and Environmental Sciences, University of Waterloo, Waterloo, Ontario, Canada
| | - Laura A. Hug
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
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4
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Cebekhulu S, Gómez-Arias A, Matu A, Alom J, Valverde A, Caraballo MA, Ololade O, Schneider P, Castillo J. Role of indigenous microbial communities in the mobilization of potentially toxic elements and rare-earth elements from alkaline mine waste. JOURNAL OF HAZARDOUS MATERIALS 2024; 466:133504. [PMID: 38310848 DOI: 10.1016/j.jhazmat.2024.133504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/05/2023] [Accepted: 01/09/2024] [Indexed: 02/06/2024]
Abstract
This study aims to evaluate the role of indigenous microorganisms in the mobilization of potentially toxic elements (PTE) and rare-earth elements (REE), the influence of the bioavailability of carbon sources that might boost microbial leaching, and the generation of neutral/alkaline mine drainage from alkaline tailings. These tailings, with significant concentrations of total organic carbon (TOC), were mainly colonized by bacteria belonging to the genera Sphingomonas, Novosphingobium and Solirubrobacter, and fungi of the genera Alternaria, Sarocladium and Aspergillus. Functionality analysis suggests the capability of these microorganisms to leach PTE and REE. Bio-/leaching tests confirmed the generation of neutral mine drainage, the influence of organic substrate, and the leaching of higher concentrations of PTE and REE due to the production of organic acids and siderophores by indigenous microorganisms. In addition, this study offers some insights into a sustainable alternative for reprocessing PMC alkaline tailings to recover REE.
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Affiliation(s)
- S Cebekhulu
- Centre for Environmental Management, University of the Free State, Bloemfontein, Republic of South Africa
| | - A Gómez-Arias
- Department of Chemistry, University of the Free State, Bloemfontein, Republic of South Africa
| | - A Matu
- Department of Microbiology and Biochemistry, University of the Free State, Bloemfontein, Republic of South Africa
| | - J Alom
- Department of Microbiology and Biochemistry, University of the Free State, Bloemfontein, Republic of South Africa
| | - A Valverde
- Instituto de Recursos Naturales y Agrobiologıa de Salamanca (IRNASA, CSIC), Salamanca, Spain
| | - M A Caraballo
- Department of Mining, Mechanic, Energetic and Construction Engineering, Higher Technical School of Engineering, University of Huelva, Huelva, Spain; Department of Water, Mining and Environment, Scientific and Technological Center of Huelva, University of Huelva, Huelva, Spain
| | - O Ololade
- Centre for Environmental Management, University of the Free State, Bloemfontein, Republic of South Africa
| | - P Schneider
- Department for Water, Environment, Civil Engineering and Safety, University of Applied Sciences Magdeburg-Stendal, Magdeburg, Germany
| | - J Castillo
- Department of Microbiology and Biochemistry, University of the Free State, Bloemfontein, Republic of South Africa.
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Pakostova E, Hilger DM, Blowes DW, Ptacek CJ. Microbial processes with the potential to mobilize As from a circumneutral-pH mixture of flotation and roaster tailings. Sci Rep 2023; 13:23048. [PMID: 38155250 PMCID: PMC10754864 DOI: 10.1038/s41598-023-50435-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 12/19/2023] [Indexed: 12/30/2023] Open
Abstract
The Northwest Tailings Containment Area at the inactive Giant Mine (Canada) contains a complex mixture of arsenic-containing substances, including flotation tailings (84.8 wt%; with 0.4 wt% residual S), roaster calcine wastes (14.4 wt% Fe oxides), and arsenic trioxide (0.8 wt%) derived from an electrostatic precipitator as well as As-containing water (21.3 ± 4.1 mg L-1 As) derived from the underground mine workings. In the vadose zone the tailings pore water has a pH of 7.6 and contains elevated metal(loid)s (2.37 ± 5.90 mg L-1 As); mineral oxidizers account for 2.5% of total 16S rRNA reads in solid samples. In the underlying saturated tailings, dissolved Fe and As concentrations increase with depth (up to 72 and 20 mg L-1, respectively), and the mean relative abundance of Fe(III)-reducers is 0.54% of total reads. The potential for As mobilization via both reductive and oxidative (bio)processes should be considered in Giant Mine remediation activities. The current remediation plan includes installation of an engineered cover that incorporates a geosynthetic barrier layer.
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Affiliation(s)
- Eva Pakostova
- Department of Earth and Environmental Sciences, University of Waterloo, Waterloo, Canada.
- Centre for Manufacturing and Materials, Coventry University, Coventry, UK.
| | - David M Hilger
- Department of Earth and Environmental Sciences, University of Waterloo, Waterloo, Canada
| | - David W Blowes
- Department of Earth and Environmental Sciences, University of Waterloo, Waterloo, Canada
| | - Carol J Ptacek
- Department of Earth and Environmental Sciences, University of Waterloo, Waterloo, Canada
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Hobart KK, Greensky Z, Hernandez K, Feinberg JM, Bailey JV, Jones DS. Microbial communities from weathered outcrops of a sulfide-rich ultramafic intrusion, and implications for mine waste management. Environ Microbiol 2023; 25:3512-3526. [PMID: 37667903 DOI: 10.1111/1462-2920.16489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 07/20/2023] [Indexed: 09/06/2023]
Abstract
The Duluth Complex (DC) contains sulfide-rich magmatic intrusions that represent one of the largest known economic deposits of copper, nickel, and platinum group elements. Previous work showed that microbial communities associated with experimentally-weathered DC waste rock and tailings were dominated by uncultivated taxa and organisms not typically associated with mine waste. However, those experiments were designed for kinetic testing and do not necessarily represent the conditions expected for long-term environmental weathering. We used 16S rRNA gene methods to characterize the microbial communities present on the surfaces of naturally-weathered and historically disturbed outcrops of DC material. Rock surfaces were dominated by diverse uncultured Ktedonobacteria, Acetobacteria, and Actinobacteria, with abundant algae and other phototrophs. These communities were distinct from microbial assemblages from experimentally-weathered DC rocks, suggesting different energy and nutrient resources in environmental samples. Sulfide mineral incubations performed with and without algae showed that photosynthetic microorganisms could have an inhibitory effect on autotrophic populations, resulting in slightly lower sulfate release and differences in dominant microorganisms. The microbial assemblages from these weathered outcrops show how communities develop during weathering of sulfide-rich DC rocks and represent baseline data that could evaluate the effectiveness of future reclamation of waste produced by large-scale mining operations.
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Affiliation(s)
- Kathryn K Hobart
- Department of Earth & Environmental Sciences, University of Minnesota, Minneapolis, Minnesota, USA
- Institute for Rock Magnetism, University of Minnesota, Minneapolis, Minnesota, USA
| | - ZhaaZhaawaanong Greensky
- Department of Earth & Environmental Sciences, University of Minnesota, Minneapolis, Minnesota, USA
| | - Kimberly Hernandez
- Department of Earth & Environmental Sciences, University of Minnesota, Minneapolis, Minnesota, USA
| | - Joshua M Feinberg
- Department of Earth & Environmental Sciences, University of Minnesota, Minneapolis, Minnesota, USA
- Institute for Rock Magnetism, University of Minnesota, Minneapolis, Minnesota, USA
| | - Jake V Bailey
- Department of Earth & Environmental Sciences, University of Minnesota, Minneapolis, Minnesota, USA
| | - Daniel S Jones
- Department of Earth & Environmental Sciences, University of Minnesota, Minneapolis, Minnesota, USA
- Department of Earth and Environmental Science, New Mexico Institute of Mining and Technology, Socorro, New Mexico, USA
- National Cave and Karst Research Institute, Carlsbad, New Mexico, USA
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7
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Zhu Q, Ruan M, Hu Z, Miao K, Ye C. The Relationship between Acid Production and the Microbial Community of Newly Produced Coal Gangue in the Early Oxidation Stage. Microorganisms 2023; 11:2626. [PMID: 38004638 PMCID: PMC10673393 DOI: 10.3390/microorganisms11112626] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/20/2023] [Accepted: 10/22/2023] [Indexed: 11/26/2023] Open
Abstract
Coal gangue is a solid waste formed during coal production, and the acid mine drainage it generates during open-pit storage severely pollutes the ecological environment of mining areas. Microorganisms play a crucial catalytic role in acidification, and their species and gene functions change during the oxidation process of coal gangue. In this study, the changes in microbial community structure were investigated during the initial acidification process for newly produced gangue exposed to moisture by monitoring the changes in pH, EC, sulfate ion concentration, and the iron oxidation rate of gangue leaching solutions. Moreover, the composition and functional abundance of microbial communities on the surface of the gangue were analyzed with rainfall simulation experiments and 16S rRNA sequencing. The study yielded the following findings: (1) The critical period for newly produced gangue oxidation spanned from 0~15 d after its exposure to water; the pH of leaching solutions decreased from 4.65 to 4.09 during this time, and the concentration and oxidation rate of iron in the leaching solutions remained at low levels, indicating that iron oxidation was not the main driver for acidification during this stage. (2) When the gangue was kept dry, Burkholderia spp. dominated the gangue microbial community. When the gangue was exposed to moisture, the rate of acidification accelerated, and Pseudomonas replaced Burkholderia as the dominant genus in the community. (3) In terms of gene function, the microbial community of the acidified gangue had stronger nitrogen cycling functions, and an increase in the abundance of microorganisms related to the sulfur cycle occurred after day 15 of the experiment. The microbial community in the acidified gangue had more stress resistance than the community of the newly formed gangue, but its potential to decompose environmental pollutants decreased.
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Affiliation(s)
- Qi Zhu
- Chinese Research Academy of Environmental Sciences, National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, State Environmental Protection Key Laboratory for Lake Pollution Control, Beijing 100012, China; (K.M.); (C.Y.)
| | - Mengying Ruan
- Institute of Land Reclamation and Ecological Restoration, China University of Mining and Technology-Beijing, Beijing 100083, China;
| | - Zhenqi Hu
- Institute of Land Reclamation and Ecological Restoration, China University of Mining and Technology-Beijing, Beijing 100083, China;
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, Xuzhou 221116, China
| | - Kexin Miao
- Chinese Research Academy of Environmental Sciences, National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, State Environmental Protection Key Laboratory for Lake Pollution Control, Beijing 100012, China; (K.M.); (C.Y.)
| | - Chun Ye
- Chinese Research Academy of Environmental Sciences, National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, State Environmental Protection Key Laboratory for Lake Pollution Control, Beijing 100012, China; (K.M.); (C.Y.)
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Interesting Halophilic Sulphur-Oxidising Bacteria with Bioleaching Potential: Implications for Pollutant Mobilisation from Mine Waste. Microorganisms 2023; 11:microorganisms11010222. [PMID: 36677514 PMCID: PMC9866277 DOI: 10.3390/microorganisms11010222] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/05/2023] [Accepted: 01/11/2023] [Indexed: 01/19/2023] Open
Abstract
For many years, research on the microbial-dissolution of metals from ores or waste materials mainly focussed on the study of acidophilic organisms. However, most acidophilic bioleaching microorganisms have limited tolerance to high chloride concentrations, thereby requiring fresh water for bioleaching operations. There is a growing interest in the use of seawater for leaching purposes, especially in regions with less access to fresh water. Consequently, there is a need to find halophilic organisms with bioleaching potentials. This study investigated the bioleaching potentials of four moderately halophilic sulphur-oxidising bacteria: Thiomicrospira cyclica, Thiohalobacter thiocyanaticus, Thioclava electrotropha and Thioclava pacifica. Results revealed T. electrotropha and T. pacifica as the most promising for bioleaching. Pure cultures of the two Thioclava strains liberated about 30% Co, and between 8-17% Cu, Pb, Zn, K, Cd, and Mn from a mine waste rock sample from the Neves Corvo mine, Portugal. Microwave roasting of the waste rock at 400 and 500 °C improved the bioleaching efficiency of T. electrotropha for Pb (13.7 to 45.7%), Ag (5.3 to 36%) and In (0 to 27.4%). Mineralogical analysis of the bioleached residues using SEM/MLA-GXMAP showed no major difference in the mineral compositions before or after bioleaching by the Thioclava spp. Generally, the bioleaching rates of the Thioclava spp. are quite low compared to that of the conventional acidophilic bioleaching bacteria. Nevertheless, their ability to liberate potential pollutants (metal(loid)s) into solution from mine waste raises environmental concerns. This is due to their relevance in the biogeochemistry of mine waste dumps, as similar neutrophile halophilic sulphur-oxidising organisms (e.g., Halothiobacillus spp.) have been isolated from mine wastes. On the other hand, the use of competent halophilic microorganisms could be the future of bioleaching due to their high tolerance to Cl- ions and their potential to catalyse mineral dissolution in seawater media, instead of fresh water.
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Li B, Wang X, Liu G, Zheng L, Cheng C. Microbial diversity response to geochemical gradient characteristics on AMD from abandoned Dashu pyrite mine in Southwest China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:74983-74997. [PMID: 35648344 DOI: 10.1007/s11356-022-21031-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
The formation and release of acid mine drainage (AMD) have caused extremely serious pollution in the environment around many mining areas. The biological oxidation of metal sulfide minerals causes the production and release of AMD. To understand the interaction mechanism between microbial and AMD, the study uses Southwest Dashu pyrite as an example to investigate the geochemical gradient characteristics and microbial diversity response on AMD from abandoned mine. Through collecting and testing the water samples, the geochemical parameters such as physical and chemical indexes, main ion composition and microbial community composition of seven mine drainage points were obtained. The results showed that the geochemical and microbial community structure the decrease of AMD pollution in the study area with the decrease of altitude has obvious gradient characteristics. Although AMD has the distribution of acid-resistant iron and sulfur bacteria oxidizing bacteria, the microbial community diversity has obvious gradient characteristics. The categories with a relative abundance of > 5% include Proteobacteria, Actinobacteriota, Firmicutes, WPS-2, Chloroflexi, Bacteroidota, and Acidobacteriota. Actinobacteriota, which was common in the AMD, was distributed throughout the samples. The correlation analysis between water quality parameters and microbial community showed that the microbial community structure was affected by environmental factors. With the increase of acidity and metal ion content, the diversity of microbial community decreased, and the content of acid-resistant iron and sulfur oxidizing bacteria increased. The results showed that pH, dissolved oxygen (Do), the total iron (Fe) content (TFe), SO42-, and Al3+ were the five parameters that most affected microbiological diversity and interaction. Hydrogeochemistry and major ions analysis revealed that AMD in the study area mainly comes from the biological oxidation of metal sulfides and the dissolution and cation exchange of other minerals around the deposit. The degree of AMD pollution is related to the hydrogeochemical conditions in the mine. The higher the mine's water level, the lower the pollutants, and the less AMD is produced and released. The findings confirmed that geochemical gradients significantly changed the biota of the mine water and enriched the related microbial diversity adapted to different environmental factors. Therefore, the findings provide strong support for mine containment to inhibit oxidation and lay the foundation for prevention and control strategies of AMD pollution sources.
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Affiliation(s)
- Bo Li
- Southwest University of Science and Technology, School of Environment and Resourse, Mianyang, 621010, China.
- State Key Laboratory of Geohazard Prevention and Geoenvironment Protection, Chengdu, 610059, China.
- State Environmental Protection Key Laboratory of Synergetic Control and Joint Remediation for Soil & Water Pollution, Chengdu, 610059, China.
| | - Xuemei Wang
- State Key Laboratory of Geohazard Prevention and Geoenvironment Protection, Chengdu, 610059, China
- State Environmental Protection Key Laboratory of Synergetic Control and Joint Remediation for Soil & Water Pollution, Chengdu, 610059, China
| | - Guo Liu
- State Key Laboratory of Geohazard Prevention and Geoenvironment Protection, Chengdu, 610059, China
- State Environmental Protection Key Laboratory of Synergetic Control and Joint Remediation for Soil & Water Pollution, Chengdu, 610059, China
| | - Linfeng Zheng
- Southwest University of Science and Technology, School of Environment and Resourse, Mianyang, 621010, China
- State Key Laboratory of Geohazard Prevention and Geoenvironment Protection, Chengdu, 610059, China
- State Environmental Protection Key Laboratory of Synergetic Control and Joint Remediation for Soil & Water Pollution, Chengdu, 610059, China
| | - Chen Cheng
- State Key Laboratory of Geohazard Prevention and Geoenvironment Protection, Chengdu, 610059, China
- State Environmental Protection Key Laboratory of Synergetic Control and Joint Remediation for Soil & Water Pollution, Chengdu, 610059, China
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10
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Sánchez-Andrea I, van der Graaf CM, Hornung B, Bale NJ, Jarzembowska M, Sousa DZ, Rijpstra WIC, Sinninghe Damsté JS, Stams AJM. Acetate Degradation at Low pH by the Moderately Acidophilic Sulfate Reducer Acididesulfobacillus acetoxydans gen. nov. sp. nov. Front Microbiol 2022; 13:816605. [PMID: 35391737 PMCID: PMC8982180 DOI: 10.3389/fmicb.2022.816605] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 01/31/2022] [Indexed: 11/19/2022] Open
Abstract
In acid drainage environments, biosulfidogenesis by sulfate-reducing bacteria (SRB) attenuates the extreme conditions by enabling the precipitation of metals as their sulfides, and the neutralization of acidity through proton consumption. So far, only a handful of moderately acidophilic SRB species have been described, most of which are merely acidotolerant. Here, a novel species within a novel genus of moderately acidophilic SRB is described, Acididesulfobacillus acetoxydans gen. nov. sp. nov. strain INE, able to grow at pH 3.8. Bioreactor studies with strain INE at optimum (5.0) and low (3.9) pH for growth showed that strain INE alkalinized its environment, and that this was more pronounced at lower pH. These studies also showed the capacity of strain INE to completely oxidize organic acids to CO2, which is uncommon among acidophilic SRB. Since organic acids are mainly in their protonated form at low pH, which increases their toxicity, their complete oxidation may be an acid stress resistance mechanism. Comparative proteogenomic and membrane lipid analysis further indicated that the presence of saturated ether-bound lipids in the membrane, and their relative increase at lower pH, was a protection mechanism against acid stress. Interestingly, other canonical acid stress resistance mechanisms, such as a Donnan potential and increased active charge transport, did not appear to be active.
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Affiliation(s)
- Irene Sánchez-Andrea
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
- *Correspondence: Irene Sánchez-Andrea,
| | | | - Bastian Hornung
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, Netherlands
| | - Nicole J. Bale
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Netherlands
| | - Monika Jarzembowska
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Diana Z. Sousa
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - W. Irene C. Rijpstra
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Netherlands
| | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
| | - Alfons J. M. Stams
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
- Centre of Biological Engineering, University of Minho, Braga, Portugal
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11
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Napieralski SA, Fang Y, Marcon V, Forsythe B, Brantley SL, Xu H, Roden EE. Microbial chemolithotrophic oxidation of pyrite in a subsurface shale weathering environment: Geologic considerations and potential mechanisms. GEOBIOLOGY 2022; 20:271-291. [PMID: 34633148 DOI: 10.1111/gbi.12474] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 09/02/2021] [Accepted: 09/27/2021] [Indexed: 06/13/2023]
Abstract
Oxidative weathering of pyrite plays an important role in the biogeochemical cycling of Fe and S in terrestrial environments. While the mechanism and occurrence of biologically accelerated pyrite oxidation under acidic conditions are well established, much less is known about microbially mediated pyrite oxidation at circumneutral pH. Recent work (Percak-Dennett et al., 2017, Geobiology, 15, 690) has demonstrated the ability of aerobic chemolithotrophic microorganisms to accelerate pyrite oxidation at circumneutral pH and proposed two mechanistic models by which this phenomenon might occur. Here, we assess the potential relevance of aerobic microbially catalyzed circumneutral pH pyrite oxidation in relation to subsurface shale weathering at Susquehanna Shale Hills Critical Zone Observatory (SSHCZO) in Pennsylvania, USA. Specimen pyrite mixed with native shale was incubated in groundwater for 3 months at the inferred depth of in situ pyrite oxidation. The colonized materials were used as an inoculum for pyrite-oxidizing enrichment cultures. Microbial activity accelerated the release of sulfate across all conditions. 16S rRNA gene sequencing and metagenomic analysis revealed the dominance of a putative chemolithoautotrophic sulfur-oxidizing bacterium from the genus Thiobacillus in the enrichment cultures. Previously proposed models for aerobic microbial pyrite oxidation were assessed in terms of physical constraints, enrichment culture geochemistry, and metagenomic analysis. Although we conclude that subsurface pyrite oxidation at SSCHZO is largely abiotic, this work nonetheless yields new insight into the potential pathways by which aerobic microorganisms may accelerate pyrite oxidation at circumneutral pH. We propose a new "direct sulfur oxidation" pathway, whereby sulfhydryl-bearing outer membrane proteins mediate oxidation of pyrite surfaces through a persulfide intermediate, analogous to previously proposed mechanisms for direct microbial oxidation of elemental sulfur. The action of this and other direct microbial pyrite oxidation pathways have major implications for controls on pyrite weathering rates in circumneutral pH sedimentary environments where pore throat sizes permit widespread access of microorganisms to pyrite surfaces.
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Affiliation(s)
| | - Yihang Fang
- Department of Geoscience, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Virginia Marcon
- Earth and Environmental Systems Institute, University Park, Pennsylvania, USA
- The Department of Geosciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Brandon Forsythe
- Earth and Environmental Systems Institute, University Park, Pennsylvania, USA
| | - Susan L Brantley
- Earth and Environmental Systems Institute, University Park, Pennsylvania, USA
- The Department of Geosciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Huifang Xu
- Department of Geoscience, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Eric E Roden
- Department of Geoscience, University of Wisconsin-Madison, Madison, Wisconsin, USA
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12
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Zhou YH, Wang C, Liu HC, Xue Z, Nie ZY, Liu Y, Wan JL, Yang Y, Shu WS, Xia JL. Correlation Between Fe/S/As Speciation Transformation and Depth Distribution of Acidithiobacillus ferrooxidans and Acidiphilium acidophilum in Simulated Acidic Water Column. Front Microbiol 2022; 12:819804. [PMID: 35222314 PMCID: PMC8863614 DOI: 10.3389/fmicb.2021.819804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 12/21/2021] [Indexed: 11/21/2022] Open
Abstract
It is well known that speciation transformations of As(III) vs. As(V) in acid mine drainage (AMD) are mainly driven by microbially mediated redox reactions of Fe and S. However, these processes are rarely investigated. In this study, columns containing mine water were inoculated with two typical acidophilic Fe/S-oxidizing/reducing bacteria [the chemoautotrophic Acidithiobacillus (At.) ferrooxidans and the heterotrophic Acidiphilium (Aph.) acidophilum], and three typical energy substrates (Fe2+, S0, and glucose) and two concentrations of As(III) (2.0 and 4.5 mM) were added. The correlation between Fe/S/As speciation transformation and bacterial depth distribution at three different depths, i.e., 15, 55, and 105 cm from the top of the columns, was comparatively investigated. The results show that the cell growth at the top and in the middle of the columns was much more significantly inhibited by the additions of As(III) than at the bottom, where the cell growth was promoted even on days 24–44. At. ferrooxidans dominated over Aph. acidophilum in most samples collected from the three depths, but the elevated proportions of Aph. acidophilum were observed in the top and bottom column samples when 4.5 mM As(III) was added. Fe2+ bio-oxidation and Fe3+ reduction coupled to As(III) oxidation occurred for all three column depths. At the column top surfaces, jarosites were formed, and the addition of As(III) could lead to the formation of the amorphous FeAsO4⋅2H2O. Furthermore, the higher As(III) concentration could inhibit Fe2+ bio-oxidation and the formation of FeAsO4⋅2H2O and jarosites. S oxidation coupled to Fe3+ reduction occurred at the bottom of the columns, with the formations of FeAsO4⋅2H2O precipitate and S intermediates. The formed FeAsO4⋅2H2O and jarosites at the top and bottom of the columns could adsorb to and coprecipitate with As(III) and As(V), resulting in the transfer of As from solution to solid phases, thus further affecting As speciation transformation. The distribution difference of Fe/S energy substrates could apparently affect Fe/S/As speciation transformation and bacterial depth distribution between the top and bottom of the water columns. These findings are valuable for elucidating As fate and toxicity mediated by microbially driven Fe/S redox in AMD environments.
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Affiliation(s)
- Yu-Hang Zhou
- Key Lab of Biometallurgy of Ministry of Education of China, School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Can Wang
- Key Lab of Biometallurgy of Ministry of Education of China, School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Hong-Chang Liu
- Key Lab of Biometallurgy of Ministry of Education of China, School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Zhen Xue
- Key Lab of Biometallurgy of Ministry of Education of China, School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Zhen-Yuan Nie
- Key Lab of Biometallurgy of Ministry of Education of China, School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Yue Liu
- Key Lab of Biometallurgy of Ministry of Education of China, School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Jiao-Li Wan
- Key Lab of Biometallurgy of Ministry of Education of China, School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Yu Yang
- Key Lab of Biometallurgy of Ministry of Education of China, School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou, China
| | - Jin-Lan Xia
- Key Lab of Biometallurgy of Ministry of Education of China, School of Minerals Processing and Bioengineering, Central South University, Changsha, China
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13
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Dev S, Galey M, Chun CL, Novotny C, Ghosh T, Aggarwal S. Enrichment of psychrophilic and acidophilic sulfate-reducing bacterial consortia - a solution toward acid mine drainage treatment in cold regions. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2021; 23:2007-2020. [PMID: 34821889 DOI: 10.1039/d1em00256b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Failure of sulfate-reducing bacteria (SRB)-mediated treatment of acid mine drainage (AMD) in cold regions due to inhibition of bacteria by acidic pH and low temperature can be overcome by enriching psychrophilic and acidophilic microbial consortia from local metal-rich sediments. In this study, we enriched microbial consortia from Arctic mine sediments at varying pH (3-7) and temperatures (15-37 °C) under anaerobic conditions with repeated sub-culturing in three successive stages, and analyzed the microbial community using 16S rRNA gene sequencing. The enriched SRB genera resulted in high sulfate reduction (85-88%), and significant metal removal (49-99.9%) during the initial stages (stage 1 and 2). Subsequently, sub-culturing the inoculum at pH 3-4.5 resulted in lower sulfate reduction (9-34%) due to the inhibition of SRB by accumulated acetic acid (0.3-9 mM). The microbial metabolic interactions for successful sulfate and metal removal involved initial glycerol co-fermentation to acetic acid at acidic pH (by Desulfosporosinus, Desulfotomaculum, Desulfurospora, and fermentative bacteria including Cellulomonas and Anaerovorax), followed by acetic acid oxidation to CO2 and H2 (by Desulfitobacterium) at neutral pH, and subsequent H2 utilization (by Desulfosporosinus). The results, including the structural and functional properties of enriched microbial consortia, can inform the development of effective biological treatment strategies for AMD in cold regions.
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Affiliation(s)
- Subhabrata Dev
- Water and Environmental Research Center, University of Alaska Fairbanks, 1760 Tanana Loop, Fairbanks, AK 99775, USA.
- Mineral Industry Research Laboratory, University of Alaska Fairbanks, Fairbanks, AK 99775, USA
| | - Miranda Galey
- Natural Resources Research Institute, University of Minnesota Duluth, Duluth, MN 55812, USA
| | - Chan Lan Chun
- Natural Resources Research Institute, University of Minnesota Duluth, Duluth, MN 55812, USA
- Department of Civil Engineering, University of Minnesota Duluth, Duluth, MN 55812, USA
| | - Chad Novotny
- Teck Resources Limited, Vancouver, BC V6C 0B3, Canada
| | - Tathagata Ghosh
- Mineral Industry Research Laboratory, University of Alaska Fairbanks, Fairbanks, AK 99775, USA
| | - Srijan Aggarwal
- Water and Environmental Research Center, University of Alaska Fairbanks, 1760 Tanana Loop, Fairbanks, AK 99775, USA.
- Department of Civil, Geological and Environmental Engineering, University of Alaska Fairbanks, Fairbanks, Alaska, 99775, USA
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14
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Abstract
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.
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15
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Piervandi Z, Khodadadi Darban A, Mousavi SM, Abdollahy M, Asadollahfardi G, Funari V, Dinelli E, Webster RD, Sillanpää M. Effect of biogenic jarosite on the bio-immobilization of toxic elements from sulfide tailings. CHEMOSPHERE 2020; 258:127288. [PMID: 32947659 DOI: 10.1016/j.chemosphere.2020.127288] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 05/29/2020] [Accepted: 06/01/2020] [Indexed: 06/11/2023]
Abstract
The discharge of toxic elements from tailings soils in the aquatic environments occurs chiefly in the presence of indigenous bacteria. The biotic components may interact in the opposite direction, leading to the formation of a passivation layer, which can inhibit the solubility of the elements. In this work, the influence of jarosite on the bio-immobilization of toxic elements was studied by native bacteria. In batch experiments, the bio-immobilization of heavy metals by an inhibitory layer was examined in the different aquatic media using pure cultures of Acidithiobacillus ferrooxidans and Acidithiobacillus thiooxidans. A variety of analyses also investigated the mechanisms of metals bio-immobilization. Among different tests, the highest metal solubility yielded 99% Mn, 91% Cr, 95% Fe, and 78% Cu using A. ferrooxidans in 9KFe medium after ten days. After 22 days, these percentages decreased down to 30% Mn and about 20% Cr, Fe, and Cu, likely due to metal immobilization by biogenic jarosite. The formation of jarosite was confirmed by an electron probe micro-analyzer (EPMA), X-ray diffraction (XRD), and scanning electron microscope (SEM). The mechanisms of metal bio-immobilization by biogenic jarosite from tailings soil confirmed three main steps: 1) the dissolution of metal sulfides in the presence of Acidithiobacillus bacteria; 2) the nucleation of jarosite on the surface of sulfide minerals; 3) the co-precipitation of dissolved elements with jarosite during the bio-immobilization process, demonstrated by a structural study for jarosite. Covering the surface of soils by the jarosite provided a stable compound in the acidic environment of mine-waste.
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Affiliation(s)
- Zeinab Piervandi
- Mineral Processing Group, Department of Mining Engineering, Tarbiat Modarres University, Tehran, Iran
| | - Ahmad Khodadadi Darban
- Mineral Processing Group, Department of Mining Engineering, Tarbiat Modarres University, Tehran, Iran.
| | - Seyyed Mohammad Mousavi
- Biotechnology Group, Department of Chemical Engineering, Tarbiat Modarres University, Tehran, Iran.
| | - Mahmoud Abdollahy
- Mineral Processing Group, Department of Mining Engineering, Tarbiat Modarres University, Tehran, Iran
| | | | - Valerio Funari
- Department of Earth System Science and Environmental Technologies, National Research Council ISMAR-CNR Bologna Research Area, Bologna, Italy
| | - Enrico Dinelli
- Department of Biological Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Richard David Webster
- Nanyang Environment and Water Research Institute, Nanyang Technological University, Singapore
| | - Mika Sillanpää
- School of Civil Engineering and Surveying, Faculty of Health, Engineering and Sciences, University of Southern Queensland, West Street, Toowoomba, 4350, QLD, Australia; Institute of Research and Development, Duy Tan University, Da Nang 550000, Vietnam; Faculty of Environment and Chemical Engineering, Duy Tan University, Da Nang 550000, Vietnam; Department of Chemical Engineering, School of Mining, Metallurgy and Chemical Engineering, University of Johannesburg, P. O. Box 17011, Doornfontein 2028, South Africa
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16
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Abstract
Mismanagement of mine waste rock can mobilize acidity, metal (loid)s, and other contaminants, and thereby negatively affect downstream environments. Hence, strategic long-term planning is required to prevent and mitigate deleterious environmental impacts. Technical frameworks to support waste-rock management have existed for decades and typically combine static and kinetic testing, field-scale experiments, and sometimes reactive-transport models. Yet, the design and implementation of robust long-term solutions remains challenging to date, due to site-specificity in the generated waste rock and local weathering conditions, physicochemical heterogeneity in large-scale systems, and the intricate coupling between chemical kinetics and mass- and heat-transfer processes. This work reviews recent advances in our understanding of the hydrogeochemical behavior of mine waste rock, including improved laboratory testing procedures, innovative analytical techniques, multi-scale field investigations, and reactive-transport modeling. Remaining knowledge-gaps pertaining to the processes involved in mine waste weathering and their parameterization are identified. Practical and sustainable waste-rock management decisions can to a large extent be informed by evidence-based simplification of complex waste-rock systems and through targeted quantification of a limited number of physicochemical parameters. Future research on the key (bio)geochemical processes and transport dynamics in waste-rock piles is essential to further optimize management and minimize potential negative environmental impacts.
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17
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Ogbughalu OT, Vasileiadis S, Schumann RC, Gerson AR, Li J, Smart RSC, Short MD. Role of microbial diversity for sustainable pyrite oxidation control in acid and metalliferous drainage prevention. JOURNAL OF HAZARDOUS MATERIALS 2020; 393:122338. [PMID: 32120208 DOI: 10.1016/j.jhazmat.2020.122338] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 02/13/2020] [Accepted: 02/15/2020] [Indexed: 06/10/2023]
Abstract
Acid and metalliferous drainage (AMD) remains a challenging issue for the mining sector. AMD management strategies have attempted to shift from treatment of acid leachates post-generation to more sustainable at-source prevention. Here, the efficacy of microbial-geochemical at-source control approach was investigated over a period of 84 weeks. Diverse microbial communities were stimulated using organic carbon amendment in a simulated silicate-containing sulfidic mine waste rock environment. Mineral waste in the unamended leach system generated AMD quickly and throughout the study, with known lithotrophic iron- and sulfur-oxidising microbes dominating column communities. The organic-amended mineral waste column showed suppressed metal dissolution and AMD generation. Molecular DNA-based next generation sequencing confirmed a less diverse lithotrophic community in the acid-producing control, with a more diverse microbial community under organic amendment comprising organotrophic iron/sulfur-reducers, autotrophs, hydrogenotrophs and heterotrophs. Time-series multivariate statistical analyses displayed distinct ecological patterns in microbial diversity between AMD- and non-AMD-environments. Focused ion beam-TEM micrographs and elemental mapping showed that silicate-stabilised passivation layers were successfully established across pyrite surfaces in organic-amended treatments, with these layers absent in unamended controls. Organic amendment and resulting increases in microbial abundance and diversity played an important role in sustaining these passivating layers in the long-term.
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Affiliation(s)
- Omy T Ogbughalu
- School of Natural and Built Environments, University of South Australia, Mawson Lakes, SA, 5095, Australia.
| | - Sotirios Vasileiadis
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, 41500, Greece
| | - Russell C Schumann
- School of Natural and Built Environments, University of South Australia, Mawson Lakes, SA, 5095, Australia; Levay and Co. Environmental Services, Edinburgh, SA, 5111, Australia
| | - Andrea R Gerson
- Blue Minerals Consultancy, Wattle Grove, TAS 7109, Australia
| | - Jun Li
- School of Natural and Built Environments, University of South Australia, Mawson Lakes, SA, 5095, Australia
| | | | - Michael D Short
- School of Natural and Built Environments, University of South Australia, Mawson Lakes, SA, 5095, Australia; Future Industries Institute, University of South Australia, Mawson Lakes, SA, 5095, Australia
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18
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Performance of a Geosynthetic-Clay-Liner Cover System at a Cu/Zn Mine Tailings Impoundment. Appl Environ Microbiol 2020; 86:AEM.02846-19. [PMID: 32033946 DOI: 10.1128/aem.02846-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 01/29/2020] [Indexed: 12/18/2022] Open
Abstract
The abandoned Kam Kotia Mine (Canada) is undergoing remediation. A geosynthetic-clay-liner (GCL) cover system was installed in the Northern Impounded Tailings (NIT) area in 2008 to isolate acid-generating tailings from water and oxygen and to mitigate sulfide oxidation. The cover system includes a vegetated uppermost soil layer underlain by a granular protective layer (sand), a clay moisture-retaining layer, a GCL, a granular capillary-break material (cushion sand), and a crushed waste rock-capillary break layer installed above the tailings. The goal of this study was to characterize the microbiology of the covered tailings to assess the performance of the cover system for mitigating sulfide bio-oxidation. Tailings beneath the GCL were characterized by high sulfur and low carbon content. The bulk pH of the tailings pore water was circumneutral (∼5.5 to 7.3). Total genomic DNA was extracted from 36 samples recovered from the constituent layers of the cover system and the underlying tailings and was analyzed in triplicates using high-throughput amplicon sequencing of 16S rRNA genes. Iron-oxidizing, sulfur-oxidizing, sulfate-reducing, and aerobic heterotrophic microorganisms were enumerated by use of most probable number enumeration, which identified heterotrophs as the most numerous group of culturable microorganisms throughout the depth profile. Low relative abundances and viable counts of microorganisms that catalyze transformations of iron and sulfur in the covered tailings, compared to previous studies on unreclaimed tailings, indicate that sulfide oxidation rates have decreased due to the presence of the GCL. Characterization of the microbial community can provide a sensitive indicator for assessing the performance of remediation systems.IMPORTANCE Mining activities are accompanied by significant environmental and financial liabilities, including the release of acid mine drainage (AMD). AMD is caused by accelerated chemical and biological oxidation of sulfide minerals in mine wastes and is characterized by low pH and high concentrations of sulfate and metal(loid)s. Microorganisms assume important roles in the catalysis of redox reactions. Our research elucidates linkages among the biogeochemistry of mine wastes and remediation systems and microbial community and activity. This study assesses the performance and utility of geosynthetic-clay-liner cover systems for management of acid-generating mine wastes. Analyses of the microbial communities in tailings isolated beneath an engineered cover system provide a better understanding of the complex biogeochemical processes involved in the redox cycling of key elements, contribute to the remediation of mine wastes, and provide a valuable tool for assessment of the effectiveness of the remediation system.
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19
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Park JH, Han HJ. Effect of tungsten-resistant bacteria on uptake of tungsten by lettuce and tungsten speciation in plants. JOURNAL OF HAZARDOUS MATERIALS 2019; 379:120825. [PMID: 31279307 DOI: 10.1016/j.jhazmat.2019.120825] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 06/07/2019] [Accepted: 06/25/2019] [Indexed: 06/09/2023]
Abstract
Tungsten is an emerging contaminant because of its potential toxicity to humans. However, tungsten-plant-microbe interactions remains unknown. The objective of the study was to evaluate the effect of tungsten-resistant bacteria on tungsten species in plants and microbial community structure in soil. Although bacterial inoculation did not affect lettuce (Lactuca sativa L.) growth or tungsten uptake via root, tungsten-resistant bacteria increased translocation of tungsten from root to shoot. Bacterial inoculation slightly oxidized tungsten in lettuce based on tungsten L3 x-ray absorption near-edge structure (XANES). Tungsten in lettuce roots and shoots grown in tungsten(VI)-spiked soil existed as a mixture of tungsten(IV) and tungsten(VI). Tungsten accumulated as polytungstate in the root and monotungstate in the shoot. Inoculation with tungsten-resistant bacteria and plant growth increased microbial diversity in tungsten-contaminated soil. In tungsten-spiked soils without plants, metal-resistant or reducing bacteria were found while bacteria growing in rhizosphere were detected in soils supporting plant growth. These results indicate a role of the bacteria and plants in phytoremediation of tungsten-contaminated soil.
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Affiliation(s)
- Jin Hee Park
- Department of Environmental & Biological Chemistry, Chungbuk National University, Cheongju, Chungbuk 28644, Republic of Korea.
| | - Hyeop-Jo Han
- Department of Energy and Resources Engineering, Chonnam National University, Gwangju 61186, Republic of Korea
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20
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Lin J, He F, Su B, Sun M, Owens G, Chen Z. The stabilizing mechanism of cadmium in contaminated soil using green synthesized iron oxide nanoparticles under long-term incubation. JOURNAL OF HAZARDOUS MATERIALS 2019; 379:120832. [PMID: 31276925 DOI: 10.1016/j.jhazmat.2019.120832] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 04/08/2019] [Accepted: 06/26/2019] [Indexed: 05/02/2023]
Abstract
Despite numerous studies having been conducted on the stabilization of heavy metal contaminated soil, our understanding of the mechanisms involved remains limited. Here green synthesized iron oxide nanoparticles (GION) were applied to stabilize cadmium (Cd) in a contaminated soil. GION not only stabilized soil Cd, but also improved soil properties within one year of incubation. After GION application both the exchangeable and carbonate bound Cd fractions decreased by 14.2-83.5% and 18.3-85.8% respectively, and most of the Cd was translocated to the residual Cd fraction. The application of GION also strongly altered soil bacterial communities. In GION treatments, the abundance of Gemmatimonadetes, Proteobacteria, and Saccharibacteria increased which led to a shift in the dominant bacterial genera from Bacillus to Candidatus koribacter. The variation in bacteria confirmed the restoration of the contaminated soil. The most abundant bacterial genus and species found in GION treatments were related to (i) plant derived biomass decomposition; (ii) ammoxidation and denitrification; and (iii) Fe oxidation. GION application may enhance the formation of larger soil aggregates with anaerobic centers and coprecipitation coupled Fe (II) oxidization, ammoxidation and nitrite reduction followed by Fe mineral ripening may be involved in Cd stabilization. The predominant stabilization mechanism was thus coprecipitation-ripening-stabilization.
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Affiliation(s)
- Jiajiang Lin
- Fujian Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Fujian Normal University, Fuzhou 350007, China
| | - Fengxin He
- Fujian Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Fujian Normal University, Fuzhou 350007, China
| | - Binglin Su
- Fujian Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Fujian Normal University, Fuzhou 350007, China
| | - Mengqiang Sun
- Fujian Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Fujian Normal University, Fuzhou 350007, China
| | - Gary Owens
- Environmental Contaminants Group, Future Industries Institute, University of South Australia, Mawson Lakes, SA, 5095, Australia
| | - Zuliang Chen
- Fujian Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Fujian Normal University, Fuzhou 350007, China; Environmental Contaminants Group, Future Industries Institute, University of South Australia, Mawson Lakes, SA, 5095, Australia.
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21
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Henne A, Craw D, Gagen EJ, Southam G. Bacterial influence on storage and mobilisation of metals in iron-rich mine tailings from the Salobo mine, Brazil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 680:91-104. [PMID: 31100671 DOI: 10.1016/j.scitotenv.2019.04.448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/30/2019] [Accepted: 04/30/2019] [Indexed: 06/09/2023]
Abstract
In this study we investigated the potential effects of promoting bacterial activity on tailings from the Salobo iron-oxide copper‑gold (IOCG) mine, Brazil. In particular we focussed on (1) the potential for mobilising additional Cu and (2) the effects of long-term storage on other metals. Unlike typical sulphide-ore tailings, the pH of the Salobo tailings is circumneutral and these tailings are dominated by Fe-bearing silicates and magnetite, with minor micrometre-scale encapsulated Cu-bearing sulphides. While these tailings do not produce acid mine drainage, an endemic strain of Acidithiobacillus ferrooxidans was isolated from the mine site. These bacteria were used in laboratory column leaching experiments of tailings material, which ran for up to 395 days, without the addition of ferrous iron. Bacteria-tailings interactions were typically maintained at a pH > 5, due to silicate-mediated pH buffering. This was eventually overcome after ~200 days by regular addition of acidic (pH 2.2) nutrient solution, as well as growth and acid generation by bacteria. Copper dissolution was not significantly enhanced by bacterial activity compared to abiotic control experiments while pH was >5. However, as the experiments were progressively acidified, additional Cu was mobilised in the biotic systems. The mineral alteration reactions produced abundant ferrihydrite precipitates within the tailings, which was enhanced by bacterial activity as the pH decreased. Adsorption of metal cations to these precipitates ensured that effluent solutions had only low levels (<0.5 mg/l) of dissolved trace metals such as As, Co, Pb, Zn, Se, Ni and Cr. These adsorption processes will strongly inhibit metal leaching from the tailings during long-term storage, as long as the iron oxidising bacteria are producing the requisite excess of ferrihydrite and the pH is >5. This case study shows that bacterially-mediated silicate weathering, in Fe(II)-bearing silicate rich tailings with only minor sulphides and Acidithiobacillus ferrooxidans can enhance the environmental stability of the tailings.
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Affiliation(s)
- A Henne
- School of Earth and Environmental Sciences, The University of Queensland, St Lucia, QLD 4072, Australia.
| | - D Craw
- Department of Geology, The University of Otago, North Dunedin, Dunedin 9016, New Zealand
| | - E J Gagen
- School of Earth and Environmental Sciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - G Southam
- School of Earth and Environmental Sciences, The University of Queensland, St Lucia, QLD 4072, Australia
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Köhler JM, Kalensee F, Cao J, Günther PM. Hadesarchaea and other extremophile bacteria from ancient mining areas of the East Harz region (Germany) suggest an ecological long-term memory of soil. SN APPLIED SCIENCES 2019. [DOI: 10.1007/s42452-019-0874-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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Metataxonomics of Tunisian phosphogypsum based on five bioinformatics pipelines: Insights for bioremediation. Genomics 2019; 112:981-989. [PMID: 31220587 DOI: 10.1016/j.ygeno.2019.06.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 06/15/2019] [Indexed: 11/23/2022]
Abstract
Phosphogypsum (PG) is an acidic by-product from the phosphate fertilizer industry and it is characterized by a low nutrient availability and the presence of radionuclides and heavy metals which pose a serious problem in its management. Here, we have applied Illumina MiSeq sequencing technology and five bioinformatics pipelines to explore the phylogenetic communities in Tunisian PG. Taking One Codex as a reference method, we present the results of 16S-rDNA-gene-based metataxonomics abundances with four other alternative bioinformatics pipelines (MetaGenome Rapid Annotation using Subsystem Technology (MG-RAST), mothur, MICrobial Community Analysis (MICCA) and Quantitative Insights into Microbial Ecology (QIIME)), when analyzing the Tunisian PG. Importantly, based on 16S rDNA datasets, the functional capabilities of microbial communities of PG were deciphered. They suggested the presence of PG autochthonous bacteria valorizable into (1) removal of radioactive elements and toxic heavy metals, (2) promotion of plant growth, (3) oxidation and (4) reduction of sulfate. These bacteria can be explored further for applications in the bioremediation of by-products, like PG, by different processes.
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24
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He J, Li W, Liu J, Chen S, Frost RL. Investigation of mineralogical and bacteria diversity in Nanxi River affected by acid mine drainage from the closed coal mine: Implications for characterizing natural attenuation process. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 217:263-270. [PMID: 30947135 DOI: 10.1016/j.saa.2019.03.069] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 03/16/2019] [Accepted: 03/18/2019] [Indexed: 06/09/2023]
Abstract
Due to the supply-side reform and environmental protection in China, many small coal mines have been closed since 2015. However, acid mine drainage from these coal mines are continuously discharging into many rural creeks, which requires the systematical investigation on the variations of geochemical and environmental biological aspects in these water systems. In this study, from a classic acid mine drainage (AMD) from a closed coal mine of Hunan, China, various sediments and water samples in different sections were collected and analyzed. According to the corresponding Mineralogical and simple bacterial characteristics analysis (16S rRNA gene sequencing), the main findings were: 1) Secondary iron-containing minerals gradually transited from Gr(CO32-) (green rust), Sh (schwertmannite) to Akg (Akaganeite) and more stable Gt (Goethite); 2) compared to the pristine sediment, these minerals decreased the acid-neutralizing capacity and cation exchange capacity (CEC) of sediments; 3) Proteobacteria and Firmicutes were the dominant phyla and the obvious variation of Firmicutes species was observed in the creek affected by AMD, which probably could been a biological index to diagnose the natural attenuation of AMD. These results could be greatly significant to understand typical variations of creek attenuation and bacterial community in the presence of high metal and sulfate concentration.
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Affiliation(s)
- Jianwen He
- The Key Laboratory of Solid Waste Treatment and Resource Recycle, Ministry of Education, Southwest University of Science and Technology, Mianyang, Sichuan 621010, PR China
| | - Wenxu Li
- The Key Laboratory of Solid Waste Treatment and Resource Recycle, Ministry of Education, Southwest University of Science and Technology, Mianyang, Sichuan 621010, PR China
| | - Jing Liu
- The School of Resource and Environment, Southwest University, Chongqing 400715, PR China.
| | - Shu Chen
- The Key Laboratory of Solid Waste Treatment and Resource Recycle, Ministry of Education, Southwest University of Science and Technology, Mianyang, Sichuan 621010, PR China
| | - Ray L Frost
- School of Chemistry, Physics and Mechanical Engineering, Science and Engineering Faculty, Queensland University of Technology, 2 George Street, GPO Box 2434, Brisbane, Queensland 4001, Australia.
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Hottenstein JD, Neilson JW, Gil-Loaiza J, Root RA, White SA, Chorover J, Maier RM. Soil Microbiome Dynamics During Pyritic Mine Tailing Phytostabilization: Understanding Microbial Bioindicators of Soil Acidification. Front Microbiol 2019; 10:1211. [PMID: 31275251 PMCID: PMC6593306 DOI: 10.3389/fmicb.2019.01211] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 05/13/2019] [Indexed: 11/17/2022] Open
Abstract
Challenges to the reclamation of pyritic mine tailings arise from in situ acid generation that severely constrains the growth of natural revegetation. While acid mine drainage (AMD) microbial communities are well-studied under highly acidic conditions, fewer studies document the dynamics of microbial communities that generate acid from pyritic material under less acidic conditions that can allow establishment and support of plant growth. This research characterizes the taxonomic composition dynamics of microbial communities present during a 6-year compost-assisted phytostabilization field study in extremely acidic pyritic mine tailings. A complementary microcosm experiment was performed to identify successional community populations that enable the acidification process across a pH gradient. Taxonomic profiles of the microbial populations in both the field study and microcosms reveal shifts in microbial communities that play pivotal roles in facilitating acidification during the transition between moderately and highly acidic conditions. The potential co-occurrence of organoheterotrophic and lithoautotrophic energy metabolisms during acid generation suggests the importance of both groups in facilitating acidification. Taken together, this research suggests that key microbial populations associated with pH transitions could be used as bioindicators for either sustained future plant growth or for acid generation conditions that inhibit further plant growth.
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Affiliation(s)
- John D Hottenstein
- Department of Soil, Water and Environmental Science, The University of Arizona, Tucson, AZ, United States
| | - Julie W Neilson
- Department of Soil, Water and Environmental Science, The University of Arizona, Tucson, AZ, United States
| | - Juliana Gil-Loaiza
- Department of Soil, Water and Environmental Science, The University of Arizona, Tucson, AZ, United States
| | - Robert A Root
- Department of Soil, Water and Environmental Science, The University of Arizona, Tucson, AZ, United States
| | - Scott A White
- Department of Soil, Water and Environmental Science, The University of Arizona, Tucson, AZ, United States
| | - Jon Chorover
- Department of Soil, Water and Environmental Science, The University of Arizona, Tucson, AZ, United States
| | - Raina M Maier
- Department of Soil, Water and Environmental Science, The University of Arizona, Tucson, AZ, United States
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26
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Gao P, Sun X, Xiao E, Xu Z, Li B, Sun W. Characterization of iron-metabolizing communities in soils contaminated by acid mine drainage from an abandoned coal mine in Southwest China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:9585-9598. [PMID: 30726542 DOI: 10.1007/s11356-019-04336-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 01/22/2019] [Indexed: 06/09/2023]
Abstract
Acid mine discharge (AMD) has been demonstrated to have significant impacts on microbial community composition in the surrounding soil environment. However, their effect on adjacent soil has not been extensively studied. In this study, microbial community composition of 20 AMD-contaminated soil samples collected from an abandoned coal mine along an AMD creek was characterized using high-throughput sequencing. All samples were characterized as extremely low in pH (< 3) and relatively enriched in HCl-extractable Fe species. The dominant phylotypes were belonging to genera Ochrobactrum, Acidiphilium, Staphylococcus, Brevibacterium, and Corynebacterium. Canonical correspondence analysis results revealed that the HCl-extractable Fe(III) had a strong impact on the soil microbial assemblage. Co-occurrence network analysis revealed that Aquicella, Acidobacteriaceae, Ochrobactrum, Enhydrobacter, Sphingomonas, and Legionellales were actively correlated with other taxa. As expected, most of the abundant taxa have been reported as acidophilic Fe-metabolizing bacteria. Hence, a co-occurring sub-network and a phylogenetic tree related to microbial taxa responsible for Fe metabolism were constructed and described. The biotic interaction showed that Dechloromonas exhibited densely connections with Fe(III)-reducing bacteria of Comamonas, Burkholderia, Shewanella, Stenotrophomonas, Acidithiobacillus, and Pseudomonas. These results demonstrated that Fe-metabolizing bacteria could have an important role in the Fe biogeochemical cycling.
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Affiliation(s)
- Pin Gao
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-Environmental Science and Technology, 808 Tianyuan Road, Guangzhou, 510650, Guangdong, China
- College of Environmental Science and Engineering, Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, Donghua University, Shanghai, 201620, China
| | - Xiaoxu Sun
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-Environmental Science and Technology, 808 Tianyuan Road, Guangzhou, 510650, Guangdong, China
| | - Enzong Xiao
- Innovation Center and Key Laboratory of Waters Safety and Protection in the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China
| | - Zhixian Xu
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-Environmental Science and Technology, 808 Tianyuan Road, Guangzhou, 510650, Guangdong, China
| | - Baoqin Li
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-Environmental Science and Technology, 808 Tianyuan Road, Guangzhou, 510650, Guangdong, China
| | - Weimin Sun
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-Environmental Science and Technology, 808 Tianyuan Road, Guangzhou, 510650, Guangdong, China.
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27
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Whaley-Martin K, Jessen GL, Nelson TC, Mori JF, Apte S, Jarolimek C, Warren LA. The Potential Role of Halothiobacillus spp. in Sulfur Oxidation and Acid Generation in Circum-Neutral Mine Tailings Reservoirs. Front Microbiol 2019; 10:297. [PMID: 30906283 PMCID: PMC6418380 DOI: 10.3389/fmicb.2019.00297] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 02/04/2019] [Indexed: 11/13/2022] Open
Abstract
The biogeochemistry of acid mine drainage (AMD) derived from waste rock associated sulfide mineral oxidation is relatively well-characterized and linked to Acidithiobacillus spp.. However, little is understood about the microbial communities and sulfur cycling before AMD develops, a key component of its prevention. This study aimed to examine circum-neutral mining impacted water (MIW) communities and its laboratory enrichments for sulfur oxidizing bacteria (SoxBac). MIW in situ microbial communities differed in diversity, structure and relative abundance consistent with site specific variations in total aqueous sulfur concentrations (TotS; ~2-17 mM), pH (3.67-7.34), and oxygen (22-93% saturation). However, the sulfur oxidizer, Halothiobacillus spp. dominated seven of the nine total SoxBac enrichment communities (~76-100% relative abundance), spanning three of the four mines. The presence and relative abundance of the identified sixteen known and five unclassified Halothiobacillus spp. here, were the important clustering determinants across parent MIW and enrichment communities. Further, the presence of Halothiobacillus spp. was associated with driving the pH <4 in enrichment experiments, and the combination of specific Halothiobacillus spp. in the enrichments affected the observed acid to sulfate ratios indicating differential sulfur cycling. Halothiobacillus spp. also dominated the parent communities of the two acidic MIWs providing corroborating evidence for its active role in net acid generation within these waters. These results identify a putative indicator organism specific to mine tailings reservoirs and highlight the need for further study of tailings associated sulfur cycling for better mine management and environmental stewardship.
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Affiliation(s)
- Kelly Whaley-Martin
- Civil and Mineral Engineering Department, University of Toronto, Toronto, ON, Canada
| | - Gerdhard L Jessen
- Civil and Mineral Engineering Department, University of Toronto, Toronto, ON, Canada
| | | | - Jiro F Mori
- Civil and Mineral Engineering Department, University of Toronto, Toronto, ON, Canada
| | - Simon Apte
- Commonwealth Scientific Industry and Research Organization, Clayton, VIC, Australia
| | - Chad Jarolimek
- Commonwealth Scientific Industry and Research Organization, Clayton, VIC, Australia
| | - Lesley A Warren
- Civil and Mineral Engineering Department, University of Toronto, Toronto, ON, Canada
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28
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He G, Wang X, Liu X, Xiao X, Huang S, Wu J. Nutrients Availability Shapes Fungal Community Composition and Diversity in the Rare Earth Mine Tailings of Southern Jiangxi, China. RUSS J ECOL+ 2019. [DOI: 10.1134/s1067413618660037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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29
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Margaryan A, Panosyan H, Mamimin C, Trchounian A, Birkeland NK. Insights into the Bacterial Diversity of the Acidic Akhtala Mine Tailing in Armenia Using Molecular Approaches. Curr Microbiol 2019; 76:462-469. [DOI: 10.1007/s00284-019-01640-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 01/24/2019] [Indexed: 11/30/2022]
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30
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Blackmore S, Vriens B, Sorensen M, Power IM, Smith L, Hallam SJ, Mayer KU, Beckie RD. Microbial and geochemical controls on waste rock weathering and drainage quality. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 640-641:1004-1014. [PMID: 30021267 DOI: 10.1016/j.scitotenv.2018.05.374] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 05/30/2018] [Accepted: 05/30/2018] [Indexed: 06/08/2023]
Abstract
Bacteria can adversely affect the quality of drainage released from mine waste by catalyzing the oxidation of sulfide minerals and thereby accelerating the release of acidity and metals. However, the microbiological and geochemical controls on drainage quality from unsaturated and geochemically heterogeneous waste rock remain poorly understood. Here, we identified coexisting neutrophilic and acidophilic bacteria in different types of waste rock, indicating that robust endemic consortia are sustained within pore-scale microenvironments. Subsequently, natural weathering was simulated in laboratory column experiments with waste rock that contained either in-situ microbial consortia or suppressed populations with up to 1000 times smaller abundance and reduced phenotypic diversity after heating and drying. Drainage from waste rock with in-situ populations was up to two pH units lower and contained up to 16 times more sulfate and heavy metals compared to drainage from waste rock bearing treated populations, indicating significantly higher sulfide-oxidation rates. The drainage chemistry was further affected by sorption and formation of secondary-mineral phases (e.g., gypsum and hydroxy-carbonates). This study provides direct evidence for the existence of diverse microbial communities in waste rock and their important catalytic role on weathering rates, and illustrates the mutual controls of microbiology and geochemistry on waste-rock drainage quality.
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Affiliation(s)
- Sharon Blackmore
- Department of Earth, Ocean and Atmospheric Sciences, The University of British Columbia, 2020-2207 Main Mall, Vancouver V6T 1Z4, Canada; BGC Engineering Inc., 1718 Argyle Street, Suite 630, Halifax B3J 3N6, Canada
| | - Bas Vriens
- Department of Earth, Ocean and Atmospheric Sciences, The University of British Columbia, 2020-2207 Main Mall, Vancouver V6T 1Z4, Canada.
| | - Melanie Sorensen
- Department of Microbiology and Immunology, The University of British Columbia, 1365 - 2350 Health Sciences Mall, Vancouver V6T 1Z3, Canada; Department of Genome Sciences, University of Washington, 3720 15th Avenue NE, Seattle 98195-5065, United States
| | - Ian M Power
- School of the Environment, Trent University, 1600 West Bank Drive, Peterborough K9L 0G2, Canada
| | - Leslie Smith
- Department of Earth, Ocean and Atmospheric Sciences, The University of British Columbia, 2020-2207 Main Mall, Vancouver V6T 1Z4, Canada
| | - Steven J Hallam
- Department of Microbiology and Immunology, The University of British Columbia, 1365 - 2350 Health Sciences Mall, Vancouver V6T 1Z3, Canada
| | - K Ulrich Mayer
- Department of Earth, Ocean and Atmospheric Sciences, The University of British Columbia, 2020-2207 Main Mall, Vancouver V6T 1Z4, Canada
| | - Roger D Beckie
- Department of Earth, Ocean and Atmospheric Sciences, The University of British Columbia, 2020-2207 Main Mall, Vancouver V6T 1Z4, Canada
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31
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Sun X, Zhou Y, Tan Y, Wu Z, Lu P, Zhang G, Yu F. Restoration with pioneer plants changes soil properties and remodels the diversity and structure of bacterial communities in rhizosphere and bulk soil of copper mine tailings in Jiangxi Province, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:22106-22119. [PMID: 29802615 DOI: 10.1007/s11356-018-2244-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 05/06/2018] [Indexed: 06/08/2023]
Abstract
To unravel the ecological function played by pioneer plants in the practical restoration of mine tailings, it is vital to explore changes of soil characteristics and microbial communities in rhizosphere and bulk soil following the adaptation and survival of plants. In the present study, the diversity and structure of rhizospheric bacterial communities of three pioneer plants in copper mine tailings were investigated by Illumina MiSeq sequencing, and the effects of pioneer plants on soil properties were also evaluated. Significant soil improvement was detected in rhizospheric samples, and Alnus cremastogyne showed higher total organic matter, total nitrogen, and available phosphorus than two other herbaceous plants. Microbial diversity indices in rhizosphere and bulk soil of reclaimed tailings were significantly higher than bare tailings, even the soil properties of bulk soil in reclaimed tailings were not significantly different from those of bare tailings. A detailed taxonomic composition analysis demonstrated that Alphaproteobacteria and Deltaproteobacteria, Chloroflexi, Acidobacteria, and Gemmatimonadetes showed significantly higher relative abundance in rhizosphere and bulk soil. In contrast, Gammaproteobacteria and Firmicutes were abundant in bare tailings, in which Bacillus, Pseudomonas, and Lactococcus made up the majority of the bacterial community (63.04%). Many species within known heavy metal resistance and nutrient regulatory microorganism were identified in reclaimed tailings, and were more abundant among rhizospheric microbes. Hierarchical clustering and principal coordinate analysis (PCoA) analysis demonstrated that the bacterial profiles in the rhizosphere clustered strictly together according to plant types, and were distinguishable from bulk soil. However, we also identified a large shared OTUs that occurred repeatedly and was unaffected by highly diverse soil properties in rhizosphere and bulk samples. Redundancy analysis indicated that water content and Cu and As concentrations were the main environmental regulators of microbial composition. These results suggest that the interactive effect of pioneer plants and harsh soil environmental conditions remodel the specific bacterial communities in rhizosphere and bulk soil in mine tailings. And A. cremastogyne might be approximate candidate for phytoremediation of mine tailings for better soil amelioration effect and relative higher diversity of bacterial community in rhizosphere.
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Affiliation(s)
- Xiaoyan Sun
- Jiangxi Engineering and Technology Research Center for Ecological Remediation of Heavy Metal Pollution, Institute of Biology and Resources, Jiangxi Academy of Sciences, Nanchang, 330096, People's Republic of China.
| | - Yanling Zhou
- Jiangxi Engineering and Technology Research Center for Ecological Remediation of Heavy Metal Pollution, Institute of Biology and Resources, Jiangxi Academy of Sciences, Nanchang, 330096, People's Republic of China
| | - Yinjing Tan
- Jiangxi Engineering and Technology Research Center for Ecological Remediation of Heavy Metal Pollution, Institute of Biology and Resources, Jiangxi Academy of Sciences, Nanchang, 330096, People's Republic of China
| | - Zhaoxiang Wu
- Jiangxi Engineering and Technology Research Center for Ecological Remediation of Heavy Metal Pollution, Institute of Biology and Resources, Jiangxi Academy of Sciences, Nanchang, 330096, People's Republic of China
| | - Ping Lu
- Jiangxi Engineering and Technology Research Center for Ecological Remediation of Heavy Metal Pollution, Institute of Biology and Resources, Jiangxi Academy of Sciences, Nanchang, 330096, People's Republic of China
| | - Guohua Zhang
- Jiangxi Engineering and Technology Research Center for Ecological Remediation of Heavy Metal Pollution, Institute of Biology and Resources, Jiangxi Academy of Sciences, Nanchang, 330096, People's Republic of China
| | - Faxin Yu
- Jiangxi Engineering and Technology Research Center for Ecological Remediation of Heavy Metal Pollution, Institute of Biology and Resources, Jiangxi Academy of Sciences, Nanchang, 330096, People's Republic of China
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32
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Zhang X, Liu X, Yang F, Chen L. Pan-Genome Analysis Links the Hereditary Variation of Leptospirillum ferriphilum With Its Evolutionary Adaptation. Front Microbiol 2018; 9:577. [PMID: 29636744 PMCID: PMC5880901 DOI: 10.3389/fmicb.2018.00577] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 03/13/2018] [Indexed: 01/16/2023] Open
Abstract
Niche adaptation has long been recognized to drive intra-species differentiation and speciation, yet knowledge about its relatedness with hereditary variation of microbial genomes is relatively limited. Using Leptospirillum ferriphilum species as a case study, we present a detailed analysis of genomic features of five recognized strains. Genome-to-genome distance calculation preliminarily determined the roles of spatial distance and environmental heterogeneity that potentially contribute to intra-species variation within L. ferriphilum species at the genome level. Mathematical models were further constructed to extrapolate the expansion of L. ferriphilum genomes (an 'open' pan-genome), indicating the emergence of novel genes with new sequenced genomes. The identification of diverse mobile genetic elements (MGEs) (such as transposases, integrases, and phage-associated genes) revealed the prevalence of horizontal gene transfer events, which is an important evolutionary mechanism that provides avenues for the recruitment of novel functionalities and further for the genetic divergence of microbial genomes. Comprehensive analysis also demonstrated that the genome reduction by gene loss in a broad sense might contribute to the observed diversification. We thus inferred a plausible explanation to address this observation: the community-dependent adaptation that potentially economizes the limiting resources of the entire community. Now that the introduction of new genes is accompanied by a parallel abandonment of some other ones, our results provide snapshots on the biological fitness cost of environmental adaptation within the L. ferriphilum genomes. In short, our genome-wide analyses bridge the relation between genetic variation of L. ferriphilum with its evolutionary adaptation.
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Affiliation(s)
- Xian Zhang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Fei Yang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China
| | - Lv Chen
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China
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33
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Valentín-Vargas A, Neilson JW, Root RA, Chorover J, Maier RM. Treatment impacts on temporal microbial community dynamics during phytostabilization of acid-generating mine tailings in semiarid regions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 618:357-368. [PMID: 29132003 PMCID: PMC5773348 DOI: 10.1016/j.scitotenv.2017.11.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Revised: 09/28/2017] [Accepted: 11/01/2017] [Indexed: 05/27/2023]
Abstract
Direct revegetation, or phytostabilization, is a containment strategy for contaminant metals associated with mine tailings in semiarid regions. The weathering of sulfide ore-derived tailings frequently drives acidification that inhibits plant establishment resulting in materials prone to wind and water dispersal. The specific objective of this study was to associate pyritic mine waste acidification, characterized through pore-water chemistry analysis, with dynamic changes in microbial community diversity and phylogenetic composition, and to evaluate the influence of different treatment strategies on the control of acidification dynamics. Samples were collected from a highly instrumented one-year mesocosm study that included the following treatments: 1) unamended tailings control; 2) tailings amended with 15% compost; and 3) the 15% compost-amended tailings planted with Atriplex lentiformis. Tailings samples were collected at 0, 3, 6 and 12months and pore water chemistry was monitored as an indicator of acidification and weathering processes. Results confirmed that the acidification process for pyritic mine tailings is associated with a temporal progression of bacterial and archaeal phylotypes from pH sensitive Thiobacillus and Thiomonas to communities dominated by Leptospirillum and Ferroplasma. Pore-water chemistry indicated that weathering rates were highest when Leptospirillum was most abundant. The planted treatment was most successful in disrupting the successional evolution of the Fe/S-oxidizing community. Plant establishment stimulated growth of plant-growth-promoting heterotrophic phylotypes and controlled the proliferation of lithoautotrophic Fe/S-oxidizers. The results suggest the potential for eco-engineering a microbial inoculum to stimulate plant establishment and inhibit proliferation of the most efficient Fe/S-oxidizing phylotypes.
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Affiliation(s)
- Alexis Valentín-Vargas
- Department of Soil, Water and Environmental Science, 429 Shantz Bldg. #38, 1177 E. Fourth Street, University of Arizona, Tucson, AZ 85721-0038, USA
| | - Julia W Neilson
- Department of Soil, Water and Environmental Science, 429 Shantz Bldg. #38, 1177 E. Fourth Street, University of Arizona, Tucson, AZ 85721-0038, USA.
| | - Robert A Root
- Department of Soil, Water and Environmental Science, 429 Shantz Bldg. #38, 1177 E. Fourth Street, University of Arizona, Tucson, AZ 85721-0038, USA
| | - Jon Chorover
- Department of Soil, Water and Environmental Science, 429 Shantz Bldg. #38, 1177 E. Fourth Street, University of Arizona, Tucson, AZ 85721-0038, USA
| | - Raina M Maier
- Department of Soil, Water and Environmental Science, 429 Shantz Bldg. #38, 1177 E. Fourth Street, University of Arizona, Tucson, AZ 85721-0038, USA
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34
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Percak-Dennett E, He S, Converse B, Konishi H, Xu H, Corcoran A, Noguera D, Chan C, Bhattacharyya A, Borch T, Boyd E, Roden EE. Microbial acceleration of aerobic pyrite oxidation at circumneutral pH. GEOBIOLOGY 2017; 15:690-703. [PMID: 28452176 DOI: 10.1111/gbi.12241] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Accepted: 03/22/2017] [Indexed: 06/07/2023]
Abstract
Pyrite (FeS2 ) is the most abundant sulfide mineral on Earth and represents a significant reservoir of reduced iron and sulfur both today and in the geologic past. In modern environments, oxidative transformations of pyrite and other metal sulfides play a key role in terrestrial element partitioning with broad impacts to contaminant mobility and the formation of acid mine drainage systems. Although the role of aerobic micro-organisms in pyrite oxidation under acidic-pH conditions is well known, to date there is very little known about the capacity for aerobic micro-organisms to oxidize pyrite at circumneutral pH. Here, we describe two enrichment cultures, obtained from pyrite-bearing subsurface sediments, that were capable of sustained cell growth linked to pyrite oxidation and sulfate generation at neutral pH. The cultures were dominated by two Rhizobiales species (Bradyrhizobium sp. and Mesorhizobium sp.) and a Ralstonia species. Shotgun metagenomic sequencing and genome reconstruction indicated the presence of Fe and S oxidation pathways in these organisms, and the presence of a complete Calvin-Benson-Bassham CO2 fixation system in the Bradyrhizobium sp. Oxidation of pyrite resulted in thin (30-50 nm) coatings of amorphous Fe(III) oxide on the pyrite surface, with no other secondary Fe or S phases detected by electron microscopy or X-ray absorption spectroscopy. Rates of microbial pyrite oxidation were approximately one order of magnitude higher than abiotic rates. These results demonstrate the ability of aerobic microbial activity to accelerate pyrite oxidation and expand the potential contribution of micro-organisms to continental sulfide mineral weathering around the time of the Great Oxidation Event to include neutral-pH environments. In addition, our findings have direct implications for the geochemistry of modern sedimentary environments, including stimulation of the early stages of acid mine drainage formation and mobilization of pyrite-associated metals.
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Affiliation(s)
- E Percak-Dennett
- Department of Geoscience, NASA Astrobiology Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - S He
- Department of Geoscience, NASA Astrobiology Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - B Converse
- Department of Geoscience, NASA Astrobiology Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - H Konishi
- Department of Geoscience, NASA Astrobiology Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - H Xu
- Department of Geoscience, NASA Astrobiology Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - A Corcoran
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - D Noguera
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - C Chan
- Department of Geological Sciences, University of Delaware, Newark, DE, USA
| | - A Bhattacharyya
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - T Borch
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - E Boyd
- Department of Microbiology & Immunology, Montana State University, Bozeman, MT, USA
| | - E E Roden
- Department of Geoscience, NASA Astrobiology Institute, University of Wisconsin-Madison, Madison, WI, USA
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Novel Microbial Assemblages Dominate Weathered Sulfide-Bearing Rock from Copper-Nickel Deposits in the Duluth Complex, Minnesota, USA. Appl Environ Microbiol 2017; 83:AEM.00909-17. [PMID: 28600313 DOI: 10.1128/aem.00909-17] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 06/02/2017] [Indexed: 11/20/2022] Open
Abstract
The Duluth Complex in northeastern Minnesota hosts economically significant deposits of copper, nickel, and platinum group elements (PGEs). The primary sulfide mineralogy of these deposits includes the minerals pyrrhotite, chalcopyrite, pentlandite, and cubanite, and weathering experiments show that most sulfide-bearing rock from the Duluth Complex generates moderately acidic leachate (pH 4 to 6). Microorganisms are important catalysts for metal sulfide oxidation and could influence the quality of water from mines in the Duluth Complex. Nevertheless, compared with that of extremely acidic environments, much less is known about the microbial ecology of moderately acidic sulfide-bearing mine waste, and so existing information may have little relevance to those microorganisms catalyzing oxidation reactions in the Duluth Complex. Here, we characterized the microbial communities in decade-long weathering experiments (kinetic tests) conducted on crushed rock and tailings from the Duluth Complex. Analyses of 16S rRNA genes and transcripts showed that differences among microbial communities correspond to pH, rock type, and experimental treatment. Moreover, microbial communities from the weathered Duluth Complex rock were dominated by taxa that are not typically associated with acidic mine waste. The most abundant operational taxonomic units (OTUs) were from the genera Meiothermus and Sulfuriferula, as well as from diverse clades of uncultivated Chloroflexi, Acidobacteria, and Betaproteobacteria Specific taxa, including putative sulfur-oxidizing Sulfuriferula spp., appeared to be primarily associated with Duluth Complex rock, but not pyrite-bearing rocks subjected to the same experimental treatment. We discuss the implications of these results for the microbial ecology of moderately acidic mine waste with low sulfide content, as well as for kinetic testing of mine waste.IMPORTANCE Economic sulfide mineral deposits in the Duluth Complex may represent the largest undeveloped source of copper and nickel on Earth. Microorganisms are important catalysts for sulfide mineral oxidation, and research on extreme acidophiles has improved our ability to manage and remediate mine wastes. We found that the microbial assemblages associated with weathered rock from the Duluth Complex are dominated by organisms not widely associated with mine waste or mining-impacted environments, and we describe geochemical and experimental influences on community composition. This report will be a useful foundation for understanding the microbial biogeochemistry of moderately acidic mine waste from these and similar deposits.
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Microbial Diversity and Community Assembly across Environmental Gradients in Acid Mine Drainage. MINERALS 2017. [DOI: 10.3390/min7060106] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Microorganisms play an important role in weathering sulfide minerals worldwide and thrive in metal-rich and extremely acidic environments in acid mine drainage (AMD). Advanced molecular methods provide in-depth information on the microbial diversity and community dynamics in the AMD-generating environment. Although the diversity is relatively low and in general inversely correlated with the acidity, a considerable number of microbial species have been detected and described in AMD ecosystems. The acidophilic microbial communities dominated by iron/sulfur-oxidizing microbes vary widely in their composition and structure across diverse environmental gradients. Environmental conditions affect the microbial community assembly via direct and indirect interactions with microbes, resulting in an environmentally dependent biogeographic pattern. This article summarizes the latest studies to provide a better understanding of the microbial biodiversity and community assembly in AMD environments.
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Wegner CE, Liesack W. Unexpected Dominance of Elusive Acidobacteria in Early Industrial Soft Coal Slags. Front Microbiol 2017; 8:1023. [PMID: 28642744 PMCID: PMC5462947 DOI: 10.3389/fmicb.2017.01023] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 05/22/2017] [Indexed: 11/19/2022] Open
Abstract
Acid mine drainage (AMD) and mine tailing environments are well-characterized ecosystems known to be dominated by organisms involved in iron- and sulfur-cycling. Here we examined the microbiology of industrial soft coal slags that originate from alum leaching, an ecosystem distantly related to AMD environments. Our study involved geochemical analyses, bacterial community profiling, and shotgun metagenomics. The slags still contained high amounts of alum constituents (aluminum, sulfur), which mediated direct and indirect effects on bacterial community structure. Bacterial groups typically found in AMD systems and mine tailings were not present. Instead, the soft coal slags were dominated by uncharacterized groups of Acidobacteria (DA052 [subdivision 2], KF-JG30-18 [subdivision 13]), Actinobacteria (TM214), Alphaproteobacteria (DA111), and Chloroflexi (JG37-AG-4), which have previously been detected primarily in peatlands and uranium waste piles. Shotgun metagenomics allowed us to reconstruct 13 high-quality Acidobacteria draft genomes, of which two genomes could be directly linked to dominating groups (DA052, KF-JG30-18) by recovered 16S rRNA gene sequences. Comparative genomics revealed broad carbon utilization capabilities for these two groups of elusive Acidobacteria, including polysaccharide breakdown (cellulose, xylan) and the competence to metabolize C1 compounds (ribulose monophosphate pathway) and lignin derivatives (dye-decolorizing peroxidases). Equipped with a broad range of efflux systems for metal cations and xenobiotics, DA052 and KF-JG30-18 may have a competitive advantage over other bacterial groups in this unique habitat.
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Affiliation(s)
- Carl-Eric Wegner
- Department of Biogeochemistry, Max Planck Institute for Terrestrial MicrobiologyMarburg, Germany
- Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University JenaJena, Germany
| | - Werner Liesack
- Department of Biogeochemistry, Max Planck Institute for Terrestrial MicrobiologyMarburg, Germany
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Bruneel O, Mghazli N, Hakkou R, Dahmani I, Filali Maltouf A, Sbabou L. In-depth characterization of bacterial and archaeal communities present in the abandoned Kettara pyrrhotite mine tailings (Morocco). Extremophiles 2017; 21:671-685. [PMID: 28447266 DOI: 10.1007/s00792-017-0933-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 04/17/2017] [Indexed: 01/28/2023]
Abstract
In Morocco, pollution caused by closed mines continues to be a serious threat to the environment, like the generation of acid mine drainage. Mine drainage is produced by environmental and microbial oxidation of sulfur minerals originating from mine wastes. The fundamental role of microbial communities is well known, like implication of Fe-oxidizing and to a lesser extent S-oxidizing microorganism in bioleaching. However, the structure of the microbial communities varies a lot from one site to another, like diversity depends on many factors such as mineralogy, concentration of metals and metalloids or pH, etc. In this study, prokaryotic communities in the pyrrhotite-rich tailings of Kettara mine were characterized using the Illumina sequencing. In-depth phylogenetic analysis revealed a total of 12 phyla of bacteria and 1 phyla of Archaea. The majority of sequences belonged to the phylum of Proteobacteria and Firmicutes with a predominance of Bacillus, Pseudomonas or Corynebacterium genera. Many microbial populations are implicated in the iron, sulfur and arsenic cycles, like Acidiferrobacter, Leptospirillum, or Alicyclobacillus in Fe; Acidiferrobacter and Sulfobacillus in S; and Bacillus or Pseudomonas in As. This is one of the first description of prokaryotic communities in pyrrhotite-rich mine tailings using high-throughput sequencing.
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Affiliation(s)
- Odile Bruneel
- Laboratoire de Microbiologie et Biologie Moléculaire, LMBM, Faculté des Sciences, Université Mohammed V, Av Ibn Batouta, BP1014, Rabat, Morocco.
- Laboratoire HydroSciences Montpellier, UMR5569 (CNRS/IRD/UM), Université de Montpellier, CC0057 (MSE), 16, rue Auguste Broussonet, 34090, Montpellier, France.
| | - N Mghazli
- Laboratoire de Microbiologie et Biologie Moléculaire, LMBM, Faculté des Sciences, Université Mohammed V, Av Ibn Batouta, BP1014, Rabat, Morocco
| | - R Hakkou
- Laboratoire de Chimie des Matériaux et de l'Environnement (LCME), Faculté des Sciences et Technique Guéliz, Université de Cadi Ayyad, Avenue Abdelkarim Elkhattabi, Gueliz, P.O. Box 549, Marrakech, Morocco
| | - I Dahmani
- Laboratoire de Microbiologie et Biologie Moléculaire, LMBM, Faculté des Sciences, Université Mohammed V, Av Ibn Batouta, BP1014, Rabat, Morocco
| | - A Filali Maltouf
- Laboratoire de Microbiologie et Biologie Moléculaire, LMBM, Faculté des Sciences, Université Mohammed V, Av Ibn Batouta, BP1014, Rabat, Morocco
| | - L Sbabou
- Laboratoire de Microbiologie et Biologie Moléculaire, LMBM, Faculté des Sciences, Université Mohammed V, Av Ibn Batouta, BP1014, Rabat, Morocco
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Jie S, Li M, Gan M, Zhu J, Yin H, Liu X. Microbial functional genes enriched in the Xiangjiang River sediments with heavy metal contamination. BMC Microbiol 2016; 16:179. [PMID: 27502206 PMCID: PMC4976514 DOI: 10.1186/s12866-016-0800-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 08/04/2016] [Indexed: 11/10/2022] Open
Abstract
Background Xiangjiang River (Hunan, China) has been contaminated with heavy metal for several decades by surrounding factories. However, little is known about the influence of a gradient of heavy metal contamination on the diversity, structure of microbial functional gene in sediment. To deeply understand the impact of heavy metal contamination on microbial community, a comprehensive functional gene array (GeoChip 5.0) has been used to study the functional genes structure, composition, diversity and metabolic potential of microbial community from three heavy metal polluted sites of Xiangjiang River. Results A total of 25595 functional genes involved in different biogeochemical processes have been detected in three sites, and different diversities and structures of microbial functional genes were observed. The analysis of gene overlapping, unique genes, and various diversity indices indicated a significant correlation between the level of heavy metal contamination and the functional diversity. Plentiful resistant genes related to various metal were detected, such as copper, arsenic, chromium and mercury. The results indicated a significantly higher abundance of genes involved in metal resistance including sulfate reduction genes (dsr) in studied site with most serious heavy metal contamination, such as cueo, mer, metc, merb, tehb and terc gene. With regard to the relationship between the environmental variables and microbial functional structure, S, Cu, Cd, Hg and Cr were the dominating factor shaping the microbial distribution pattern in three sites. Conclusions This study suggests that high level of heavy metal contamination resulted in higher functional diversity and the abundance of metal resistant genes. These variation therefore significantly contribute to the resistance, resilience and stability of the microbial community subjected to the gradient of heavy metals contaminant in Xiangjiang River. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0800-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shiqi Jie
- School of Minerals Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Mingming Li
- School of Minerals Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Min Gan
- School of Minerals Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Jianyu Zhu
- School of Minerals Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410083, China.
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410083, China. .,Department of Botany and Microbiology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA.
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
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Kocaman AT, Cemek M, Edwards KJ. Kinetics of pyrite, pyrrhotite, and chalcopyrite dissolution byAcidithiobacillus ferrooxidans. Can J Microbiol 2016; 62:629-42. [DOI: 10.1139/cjm-2016-0085] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The main objective of this study was to investigate the dissolution kinetics of pyrite, pyrrhotite, and chalcopyrite. Crushed minerals were reacted with Acidithiobacillus ferrooxidans (25 °C). The kinetics of dissolution was investigated by monitoring pH and Fe2+and Fe3+ion concentrations in the leaching solutions. Pyrite, pyrrhotite, and chalcopyrite dissolution by A. ferrooxidans was found to be a chemically controlled process. With bacteria, the dissolution rates of the minerals increased in the order of pyrrhotite, pyrite, and chalcopyrite. The number of cells attached to mineral surfaces increased in the same order. Acidithiobacillus ferrooxidans was found to enhance the dissolution rates of the minerals. The acid-insoluble trait of pyrite and acid-soluble trait of the other 2 minerals affected the pH changes in the leaching solutions.
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Affiliation(s)
- Ayse Tuba Kocaman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
- Faculty of Chemical and Metallurgical Engineering, Department of Bioengineering, Yildiz Technical University, 34210 Esenler, Istanbul, Turkey
| | - Mustafa Cemek
- Faculty of Chemical and Metallurgical Engineering, Department of Bioengineering, Yildiz Technical University, 34210 Esenler, Istanbul, Turkey
| | - Katrina Jane Edwards
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
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Li Y, Jia Z, Sun Q, Zhan J, Yang Y, Wang D. Ecological restoration alters microbial communities in mine tailings profiles. Sci Rep 2016; 6:25193. [PMID: 27126064 PMCID: PMC4850430 DOI: 10.1038/srep25193] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 04/12/2016] [Indexed: 11/16/2022] Open
Abstract
Ecological restoration of mine tailings have impact on soil physiochemical properties and microbial communities. The surface soil has been a primary concern in the past decades, however it remains poorly understood about the adaptive response of microbial communities along the profile during ecological restoration of the tailings. In this study, microbial communities along a 60-cm profile were investigated in a mine tailing pond during ecological restoration of the bare waste tailings (BW) with two vegetated soils of Imperata cylindrica (IC) and Chrysopogon zizanioides (CZ) plants. Revegetation of both IC and CZ could retard soil degradation of mine tailing by stimulation of soil pH at 0-30 cm soils and altered the bacterial communities at 0-20 cm depths of the mine tailings. Significant differences existed in the relative abundance of the phyla Alphaproteobacteria, Deltaproteobacteria, Acidobacteria, Firmicutes and Nitrospira. Slight difference of bacterial communities were found at 30-60 cm depths of mine tailings. Abundance and activity analysis of nifH genes also explained the elevated soil nitrogen contents at the surface 0-20 cm of the vegetated soils. These results suggest that microbial succession occurred primarily at surface tailings and vegetation of pioneering plants might have promoted ecological restoration of mine tailings.
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Affiliation(s)
- Yang Li
- School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui Province, China
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, Jiangsu Province, China
| | - Qingye Sun
- School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui Province, China
| | - Jing Zhan
- School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui Province, China
| | - Yang Yang
- School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui Province, China
| | - Dan Wang
- School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui Province, China
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42
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Huang LN, Kuang JL, Shu WS. Microbial Ecology and Evolution in the Acid Mine Drainage Model System. Trends Microbiol 2016; 24:581-593. [PMID: 27050827 DOI: 10.1016/j.tim.2016.03.004] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 02/19/2016] [Accepted: 03/08/2016] [Indexed: 10/22/2022]
Abstract
Acid mine drainage (AMD) is a unique ecological niche for acid- and toxic-metals-adapted microorganisms. These low-complexity systems offer a special opportunity for the ecological and evolutionary analyses of natural microbial assemblages. The last decade has witnessed an unprecedented interest in the study of AMD communities using 16S rRNA high-throughput sequencing and community genomic and postgenomic methodologies, significantly advancing our understanding of microbial diversity, community function, and evolution in acidic environments. This review describes new data on AMD microbial ecology and evolution, especially dynamics of microbial diversity, community functions, and population genomes, and further identifies gaps in our current knowledge that future research, with integrated applications of meta-omics technologies, will fill.
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Affiliation(s)
- Li-Nan Huang
- College of Ecology and Evolution, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Jia-Liang Kuang
- College of Ecology and Evolution, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Wen-Sheng Shu
- College of Ecology and Evolution, Sun Yat-sen University, Guangzhou 510275, PR China.
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Diaby N, Dold B, Rohrbach E, Holliger C, Rossi P. Temporal evolution of bacterial communities associated with the in situ wetland-based remediation of a marine shore porphyry copper tailings deposit. THE SCIENCE OF THE TOTAL ENVIRONMENT 2015; 533:110-121. [PMID: 26151655 DOI: 10.1016/j.scitotenv.2015.06.076] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 06/18/2015] [Accepted: 06/19/2015] [Indexed: 06/04/2023]
Abstract
Mine tailings are a serious threat to the environment and public health. Remediation of these residues can be carried out effectively by the activation of specific microbial processes. This article presents detailed information about temporal changes in bacterial community composition during the remediation of a section of porphyry copper tailings deposited on the Bahía de Ite shoreline (Peru). An experimental remediation cell was flooded and transformed into a wetland in order to prevent oxidation processes, immobilizing metals. Initially, the top oxidation zone of the tailings deposit displayed a low pH (3.1) and high concentrations of metals, sulfate, and chloride, in a sandy grain size geological matrix. This habitat was dominated by sulfur- and iron-oxidizing bacteria, such as Leptospirillum spp., Acidithiobacillus spp., and Sulfobacillus spp., in a microbial community which structure resembled acid mine drainage environments. After wetland implementation, the cell was water-saturated, the acidity was consumed and metals dropped to a fraction of their initial respective concentrations. Bacterial communities analyzed by massive sequencing showed time-dependent changes both in composition and cell numbers. The final remediation stage was characterized by the highest bacterial diversity and evenness. Aside from classical sulfate reducers from the phyla δ-Proteobacteria and Firmicutes, community structure comprised taxa derived from very diverse habitats. The community was also characterized by an elevated proportion of rare phyla and unaffiliated sequences. Numerical ecology analysis confirmed that the temporal population evolution was driven by pH, redox, and K. Results of this study demonstrated the usefulness of a detailed follow-up of the remediation process, not only for the elucidation of the communities gradually switching from autotrophic, oxidizing to heterotrophic and reducing living conditions, but also for the long term management of the remediation wetlands.
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Affiliation(s)
- N Diaby
- University of Lausanne, Institute of Mineralogy and Geochemistry, Anthropole, Lausanne, Switzerland
| | - B Dold
- University of Lausanne, Institute of Mineralogy and Geochemistry, Anthropole, Lausanne, Switzerland
| | - E Rohrbach
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Architecture, Civil and Environmental Engineering, Laboratory for Environmental Biotechnology, Lausanne, Switzerland
| | - C Holliger
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Architecture, Civil and Environmental Engineering, Laboratory for Environmental Biotechnology, Lausanne, Switzerland
| | - P Rossi
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Architecture, Civil and Environmental Engineering, Central Environmental Laboratory, Lausanne, Switzerland.
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Novel and Unexpected Microbial Diversity in Acid Mine Drainage in Svalbard (78° N), Revealed by Culture-Independent Approaches. Microorganisms 2015; 3:667-94. [PMID: 27682111 PMCID: PMC5023264 DOI: 10.3390/microorganisms3040667] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 09/02/2015] [Accepted: 09/29/2015] [Indexed: 11/17/2022] Open
Abstract
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.
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