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Ciraula DA, Kleine-Marshall BI, Galeczka IM, Lévy L. Advanced Monitoring of H 2S Injection through the Coupling of Reactive Transport Models and Geophysical Responses. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:11128-11139. [PMID: 38857430 PMCID: PMC11210474 DOI: 10.1021/acs.est.3c10139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 05/21/2024] [Accepted: 05/22/2024] [Indexed: 06/12/2024]
Abstract
Hydrogen sulfide (H2S), an environmentally harmful pollutant, is a byproduct of geothermal energy production. To reduce the H2S emissions, H2S-charged water is injected into the basaltic subsurface, where it mineralizes to iron sulfides. Here, we couple geophysical induced polarization (IP) measurements in H2S injection wells and geochemical reactive transport models (RTM) to monitor the H2S storage efforts in the subsurface of Nesjavellir, one of Iceland's most productive geothermal fields. An increase in the IP response after 40 days of injection indicates iron-sulfide formation near the injection well. Likewise, the RTM shows that iron sulfides readily form at circumneutral to alkaline pH conditions, and the iron supply from basalt dissolution limits its formation. Agreement in the trends of the magnitude and distribution of iron-sulfide formation between IP and RTM suggests that coupling the methods can improve the monitoring of H2S mineralization by providing insight into the parameters influencing iron-sulfide formation. In particular, accurate fluid flow parameters in RTMs are critical to validate the predictions of the spatial distribution of subsurface iron-sulfide formation over time obtained through IP observations. This work establishes a foundation for expanding H2S sequestration monitoring efforts and a framework for coupling geophysical and geochemical site evaluations in environmental studies.
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Affiliation(s)
- Daniel A. Ciraula
- Nordic
Volcanological Center, Institute of Earth Sciences, University of Iceland, Reykjavík 101, Iceland
| | - Barbara I. Kleine-Marshall
- GeoZentrum
Nordbayern, Friedrich-Alexander-Universität, Schlossgarten 5, Erlangen-Nuremberg 91054, Germany
| | - Iwona M. Galeczka
- ÍSOR-Iceland
Geosurvey, UrĐarhvarf 8, Kópavogur 203, Iceland
- Carbfix, HöfĐabakki
9D, Reykjavík 110, Iceland
| | - Léa Lévy
- ÍSOR-Iceland
Geosurvey, UrĐarhvarf 8, Kópavogur 203, Iceland
- Engineering
Geology, Lund University, Lund Box 117 SE-221 00, Sweden
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2
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Visser AN, Martin JD, Osenbrück K, Rügner H, Grathwohl P, Kappler A. In situ incubation of iron(II)-bearing minerals and Fe(0) reveals insights into metabolic flexibility of chemolithotrophic bacteria in a nitrate polluted karst aquifer. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:172062. [PMID: 38554974 DOI: 10.1016/j.scitotenv.2024.172062] [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: 12/04/2023] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/02/2024]
Abstract
Groundwater nitrate pollution is a major reason for deteriorating water quality and threatens human and animal health. Yet, mitigating groundwater contamination naturally is often complicated since most aquifers are limited in bioavailable carbon. Since metabolically flexible microbes might have advantages for survival, this study presents a detailed description and first results on our modification of the BacTrap© method, aiming to determine the prevailing microbial community's potential to utilize chemolithotrophic pathways. Our microbial trapping devices (MTDs) were amended with four different iron sources and incubated in seven groundwater monitoring wells for ∼3 months to promote growth of nitrate-reducing Fe(II)-oxidizing bacteria (NRFeOxB) in a nitrate-contaminated karst aquifer. Phylogenetic analysis based on 16S rRNA gene sequences implies that the identity of the iron source influenced the microbial community's composition. In addition, high throughput amplicon sequencing revealed increased relative 16S rRNA gene abundances of OTUs affiliated to genera such as Thiobacillus, Rhodobacter, Pseudomonas, Albidiferax, and Sideroxydans. MTD-derived enrichments set up with Fe(II)/nitrate/acetate to isolate potential NRFeOxB, were dominated by e.g., Acidovorax spp., Paracoccus spp. and Propionivibrio spp. MTDs are a cost-effective approach for investigating microorganisms in groundwater and our data not only solidifies the MTD's capacity to provide insights into the metabolic flexibility of the aquifer's microbial community, but also substantiates its metabolic potential for anaerobic Fe(II) oxidation.
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Affiliation(s)
- Anna-Neva Visser
- GeoZentrum Nordbayern, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Germany; Department of Geosciences, University of Tübingen, Germany.
| | - Joseph D Martin
- Department of Biology, Terrestrial Ecology, University of Copenhagen, Denmark
| | - Karsten Osenbrück
- Department of Geosciences, University of Tübingen, Germany; Federal Institute for Geosciences and Natural Resources (BGR), Hannover, Germany
| | - Hermann Rügner
- Department of Geosciences, University of Tübingen, Germany
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3
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Yang Y, Kong Z, Ma H, Shao Z, Wang X, Shen Y, Chai H. Insights into the transport and bio-degradation of dissolved inorganic nitrogen in the biochar-pyrite amended stormwater biofilter using dynamic modeling. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 347:119152. [PMID: 37774660 DOI: 10.1016/j.jenvman.2023.119152] [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: 07/03/2023] [Revised: 09/04/2023] [Accepted: 09/23/2023] [Indexed: 10/01/2023]
Abstract
The stormwater biofilter is a prevailing green infrastructure for urban stormwater management, but it is less effective in dissolved nitrogen removal, especially for nitrate. The mechanism that governs the nitrate leaching and performance stability of stormwater biofilters is poorly understood. In this study, a water quality model was developed to predict the ammonium and nitrate dynamics in a biochar-pyrite amended stormwater biofilter. The transport of dissolved nitrogen species was described by advection-dispersion models. The kinetics of adsorption and pyrite-based autotrophic denitrification are included in the model and simulated with a steady-state saturated flow. The model was calibrated and validated using eleven storm events. The modeling results reveal that the contribution of pyrite-based autotrophic denitrification to nitrate leaching alleviation improves with the increased drying duration. The nitrate removal efficiency was affected by a series of design parameters. Pyrite filling rate has a minor effect on nitrate removal promotion. Service area ratio and submerged zone depth are the key parameters to prevent nitrate leaching, as they influence the emergence and discharge time of nitrate breakthrough. The high inflow volume (high service area ratio) and small submerged zone can lead to earlier and increased discharge of peak nitrate otherwise the peak nitrate could be retained in the submerged zone and denitrified during the drying period. The developed mechanistic model provides a useful tool to evaluate the treatment ability of stormwater biofilters under varying conditions and offers a guideline for biofilter design optimization.
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Affiliation(s)
- Yan Yang
- National Research Base of Intelligent Manufacturing Service, Chongqing Technology and Business University, Chongqing, 400067, China; Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), College of Environment and Ecology, Chongqing University, Chongqing, 400045, China
| | - Zheng Kong
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), College of Environment and Ecology, Chongqing University, Chongqing, 400045, China; Australian Centre for Water and Environmental Biotechnology (ACWEB, Formerly AWMC), The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Haiyuan Ma
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), College of Environment and Ecology, Chongqing University, Chongqing, 400045, China
| | - Zhiyu Shao
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), College of Environment and Ecology, Chongqing University, Chongqing, 400045, China
| | - Xinyue Wang
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), College of Environment and Ecology, Chongqing University, Chongqing, 400045, China
| | - Yu Shen
- National Research Base of Intelligent Manufacturing Service, Chongqing Technology and Business University, Chongqing, 400067, China; Chongqing South-to-Thais Environmental Protection Technology Research Institute Co., Ltd., Chongqing, 400060, China
| | - Hongxiang Chai
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), College of Environment and Ecology, Chongqing University, Chongqing, 400045, China.
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4
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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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Richardson JB, Thrasher SA, Saccardi B, Clark EV. Sulfidic schist release of As, Cu, and Pb in laboratory experiments and across eleven watersheds in central Massachusetts, USA. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2023; 45:8223-8241. [PMID: 37566165 DOI: 10.1007/s10653-023-01718-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 07/28/2023] [Indexed: 08/12/2023]
Abstract
Sulfidic schists are important rock formations due to their trace metal and metalloid (TMM) content and carry the potential for pyrite and pyrrhotite to hydrate and oxidize leading to acid-enhanced chemical weathering. The objectives of this study were to compare TMMs in sulfidic schists to other co-occurring bedrock, evaluate conditions that optimize TMM rock weathering, and examine streamwater TMMs in relation to bedrock lithology and human development in eleven streams across central Massachusetts. Sulfidic schists samples had the highest As (72 ± 46 mg kg-1), Cu (63 ± 21 mg kg-1), and Pb (63 ± 33 mg kg-1) concentrations. Electron Probe Microanalysis (EPMA) images show As and Pb were widely distributed across silicate and sulfide minerals in both the mica schist and sulfidic schists, not exclusively hosted in sulfide minerals as hypothesized. Batch reactors had TMM dissolution rates an order of magnitude higher for sulfidic schists than granite and mica schists. Furthermore, TMM dissolution was greatest under pH 9 than pH 7 or pH 5 and dissolution rates were two times greater under anoxic conditions compared to oxic conditions. Streamwater concentrations of As (0.01 to 10.3 μg L-1), Cu (0.2 to 206 μg L-1), and Pb (0.001 to 8.3 μg L-1) were below Massachusetts Surface Water Quality Standards. Across the eleven watersheds, % sulfidic schists were positively correlated with mean streamwater S and Cu concentrations and area-normalized annual export. Streamwater As and Pb concentrations were significantly correlated with %Developed land and %Mica schist, which strongly covaried. Our study confirmed the elevated abundance of TMMs in sulfidic schists but laboratory experiments suggest the precipitation of amorphous Fe oxyhydroxide phases decreased dissolved TMMs during oxic weathering. Future work will need to incorporate groundwater and stable isotope systems to separate anthropogenic and geogenic analyses.
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Affiliation(s)
- Justin B Richardson
- Department of Geoscience, University of Massachusetts Amherst, 233 Morrill Science Center, Amherst, MA, 01003, USA.
- School of Earth and Sustainability, University of Massachusetts Amherst, Amherst, MA, 01003, USA.
| | - Stephanie A Thrasher
- Department of Geoscience, University of Massachusetts Amherst, 233 Morrill Science Center, Amherst, MA, 01003, USA
| | - Brian Saccardi
- Department of Geoscience, University of Massachusetts Amherst, 233 Morrill Science Center, Amherst, MA, 01003, USA
| | - Elyse V Clark
- Department of Earth and Geographic Sciences, Fitchburg State University, Fitchburg, MA, 01420, USA
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6
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Shen C, Su L, Zhao Y, Liu W, Liu R, Zhang F, Shi Y, Wang J, Tang Q, Yang Y, Bon Man Y, Zhang J. Plants boost pyrrhotite-driven nitrogen removal in constructed wetlands. BIORESOURCE TECHNOLOGY 2023; 367:128240. [PMID: 36332867 DOI: 10.1016/j.biortech.2022.128240] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/25/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
Pyrrhotite is a promising electron donor for autotrophic denitrification. Using pyrrhotite as the substrate in constructed wetlands (CWs) can enhance the nitrogen removal performance in carbon-limited wastewater treatment. However, the role of plants in pyrrhotite-integrated CW is under debate as the oxygen released from plant roots may destroy the anoxic condition for autotrophic denitrification. This study compared pyrrhotite-integrated CWs with and without plants and identified the effects of plants' presence in nitrogen removal, pyrrhotite oxidized dissolution, and microbial community. The results show that plants enhanced the TN removal significantly (from 41.6 ± 3.9 % to 97.1 ± 2.6 %). Plants can accelerate the PAD in CW through the strengthening of pyrrhotite dissolution. Enriched functional (Thiobacillus and Acidiferrobacter) and a more complex bacterial co-occurrence network has been found in CW with plants. This study identified the role of plants in PAD acceleration, providing an in-depth understanding of pyrrhotite in CW systems.
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Affiliation(s)
- Cheng Shen
- Zhejiang Province Key Laboratory of Recycling and Ecological Treatment of Waste Biomass, School of Environment and Natural Resources, Zhejiang University of Science & Technology, Hangzhou, Zhejiang 310023, China; Dooge Centre for Water Resources Research, School of Civil Engineering, University College Dublin, Belfield Dublin 4, Ireland
| | - Liti Su
- Zhejiang Province Key Laboratory of Recycling and Ecological Treatment of Waste Biomass, School of Environment and Natural Resources, Zhejiang University of Science & Technology, Hangzhou, Zhejiang 310023, China
| | - Yaqian Zhao
- Dooge Centre for Water Resources Research, School of Civil Engineering, University College Dublin, Belfield Dublin 4, Ireland; State Key Laboratory of Eco-Hydraulics in Northwest Arid Region, Xi'an University of Technology, Xi'an 710048, China
| | - Wenbo Liu
- Zhejiang Province Key Laboratory of Recycling and Ecological Treatment of Waste Biomass, School of Environment and Natural Resources, Zhejiang University of Science & Technology, Hangzhou, Zhejiang 310023, China
| | - Ranbin Liu
- Sino-Dutch R&D Centre for Future Wastewater Treatment Technologies/Beijing Advanced Innovation Center of Future Urban Design, Beijing University of Civil Engineering & Architecture, Beijing 100044, China; Dooge Centre for Water Resources Research, School of Civil Engineering, University College Dublin, Belfield Dublin 4, Ireland
| | - Fuhao Zhang
- Sino-Dutch R&D Centre for Future Wastewater Treatment Technologies/Beijing Advanced Innovation Center of Future Urban Design, Beijing University of Civil Engineering & Architecture, Beijing 100044, China; State Key Laboratory of Eco-Hydraulics in Northwest Arid Region, Xi'an University of Technology, Xi'an 710048, China
| | - Yun Shi
- Zhejiang Province Key Laboratory of Recycling and Ecological Treatment of Waste Biomass, School of Environment and Natural Resources, Zhejiang University of Science & Technology, Hangzhou, Zhejiang 310023, China
| | - Jie Wang
- Zhejiang Province Key Laboratory of Recycling and Ecological Treatment of Waste Biomass, School of Environment and Natural Resources, Zhejiang University of Science & Technology, Hangzhou, Zhejiang 310023, China
| | - Qiuqi Tang
- Zhejiang Province Key Laboratory of Recycling and Ecological Treatment of Waste Biomass, School of Environment and Natural Resources, Zhejiang University of Science & Technology, Hangzhou, Zhejiang 310023, China
| | - Yan Yang
- Sino-Dutch R&D Centre for Future Wastewater Treatment Technologies/Beijing Advanced Innovation Center of Future Urban Design, Beijing University of Civil Engineering & Architecture, Beijing 100044, China
| | - Yu Bon Man
- Consortium on Health, Environment, Education and Research (CHEER), Department of Science and Environmental Studies, The Education University of Hong Kong, 10 Lo Ping Road, Tai Po, Hong Kong SAR, China
| | - Jin Zhang
- Zhejiang Province Key Laboratory of Recycling and Ecological Treatment of Waste Biomass, School of Environment and Natural Resources, Zhejiang University of Science & Technology, Hangzhou, Zhejiang 310023, China.
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7
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Zhu Y, Di Capua F, Li D, Li H. Enhancement and mechanisms of micron-pyrite driven autotrophic denitrification with different pretreatments for treating organic-limited waters. CHEMOSPHERE 2022; 308:136306. [PMID: 36067811 DOI: 10.1016/j.chemosphere.2022.136306] [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: 05/09/2022] [Revised: 08/18/2022] [Accepted: 08/29/2022] [Indexed: 06/15/2023]
Abstract
Pyrite-driven autotrophic denitrification (PAD) represents a cheap and promising way for nitrogen removal from organic-limited wastewater, which has obtained increasing attention in recent years. However, the limited denitrification rate and unclear mechanism underlying the process have hindered the engineered application of PAD. This study aims to shed light on the impacts of different pretreatments (i.e., ultrasonication, acid-washing and calcination) on micron-pyrite surface characteristics, denitrification performance and biofilm formation during PAD in batch reactors. A series of solid-phase analyses revealed that all pretreatments could significantly promote biofilm attachment on pyrite granules, but impacted the proportion, distribution and chemical oxidation state of sulfur (S) and iron (Fe) at varying degrees. Batch tests showed that ultrasonication and acid-washing could enhance the total nitrogen reduction rate by 14% and 99%, and decrease the sulfate production rate by 51% and 42%, respectively, when compared with untreated pyrite. Microbial community analysis indicated that Thiobacillus and Rhodanobacter dominated in PAD systems. Two types of indirect mechanisms (i.e., contact and non-contact) for pyrite leaching may co-occur in PAD system, resulting in ferrous iron (Fe2+), thiosulfate (S2O32-) and sulfide (S2-) as the main electron donors for denitrification. A PAD mechanism model was proposed to describe the PAD electron transfer pathway with the aim to optimize the engineered application of PAD for nitrogen removal.
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Affiliation(s)
- Yingjie Zhu
- College of Environmental Science and Engineering, Tongji University, 200092, Shanghai, China
| | - Francesco Di Capua
- Department of Civil Environmental Land Construction and Chemistry (DICATECh), Polytechnic University of Bari, 70125, Bari, Italy
| | - Duanxin Li
- College of Environmental Science and Engineering, Tongji University, 200092, Shanghai, China
| | - Huaizheng Li
- College of Environmental Science and Engineering, Tongji University, 200092, Shanghai, China.
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Spietz RL, Payne D, Szilagyi R, Boyd ES. Reductive biomining of pyrite by methanogens. Trends Microbiol 2022; 30:1072-1083. [PMID: 35624031 DOI: 10.1016/j.tim.2022.05.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 01/13/2023]
Abstract
Pyrite (FeS2) is the most abundant iron sulfide mineral in Earth's crust. Until recently, FeS2 has been considered a sink for iron (Fe) and sulfur (S) at low temperature in the absence of oxygen or oxidative weathering, making these elements unavailable to biology. However, anaerobic methanogens can transfer electrons extracellularly to reduce FeS2 via direct contact with the mineral. Reduction of FeS2 occurs through a multistep process that generates aqueous sulfide (HS-) and FeS2-associated pyrrhotite (Fe1-xS). Subsequent dissolution of Fe1-xS provides Fe(II)(aq), but not HS-, that rapidly complexes with HS-(aq) generated from FeS2 reduction to form soluble iron sulfur clusters [nFeS(aq)]. Cells assimilate nFeS(aq) to meet Fe/S nutritional demands by mobilizing and hyperaccumulating Fe and S from FeS2. As such, reductive dissolution of FeS2 by methanogens has important implications for element cycling in anoxic habitats, both today and in the geologic past.
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Affiliation(s)
- Rachel L Spietz
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA
| | - Devon Payne
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA
| | - Robert Szilagyi
- Department of Chemistry, University of British Columbia - Okanagan, Kelowna, BC V1V 1V7, Canada
| | - Eric S Boyd
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA.
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Wei M, Zeng X, Han X, Shao Z, Xie Q, Dong C, Wang Y, Qiu Z. Potential autotrophic carbon-fixer and Fe(II)-oxidizer Alcanivorax sp. MM125-6 isolated from Wocan hydrothermal field. Front Microbiol 2022; 13:930601. [PMID: 36316996 PMCID: PMC9616709 DOI: 10.3389/fmicb.2022.930601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 09/09/2022] [Indexed: 12/02/2022] Open
Abstract
The genus Alcanivorax is common in various marine environments, including in hydrothermal fields. They were previously recognized as obligate hydrocarbonoclastic bacteria, but their potential for autotrophic carbon fixation and Fe(II)-oxidation remains largely elusive. In this study, an in situ enrichment experiment was performed using a hydrothermal massive sulfide slab deployed 300 m away from the Wocan hydrothermal vent. Furthermore, the biofilms on the surface of the slab were used as an inoculum, with hydrothermal massive sulfide powder from the same vent as an energy source, to enrich the potential iron oxidizer in the laboratory. Three dominant bacterial families, Alcanivoraceae, Pseudomonadaceae, and Rhizobiaceae, were enriched in the medium with hydrothermal massive sulfides. Subsequently, strain Alcanivorax sp. MM125-6 was isolated from the enrichment culture. It belongs to the genus Alcanivorax and is closely related to Alcanivorax profundimaris ST75FaO-1 T (98.9% sequence similarity) indicated by a phylogenetic analysis based on 16S rRNA gene sequences. Autotrophic growth experiments on strain MM125-6 revealed that the cell concentrations were increased from an initial 7.5 × 105 cells/ml to 3.13 × 108 cells/ml after 10 days, and that the δ13C VPDB in the cell biomass was also increased from 234.25‰ on day 2 to gradually 345.66 ‰ on day 10. The gradient tube incubation showed that bands of iron oxides and cells formed approximately 1 and 1.5 cm, respectively, below the air-agarose medium interface. In addition, the SEM-EDS data demonstrated that it can also secrete acidic exopolysaccharides and adhere to the surface of sulfide minerals to oxidize Fe(II) with NaHCO3 as the sole carbon source, which accelerates hydrothermal massive sulfide dissolution. These results support the conclusion that strain MM125-6 is capable of autotrophic carbon fixation and Fe(II) oxidization chemoautotrophically. This study expands our understanding of the metabolic versatility of the Alcanivorax genus as well as their important role(s) in coupling hydrothermal massive sulfide weathering and iron and carbon cycles in hydrothermal fields.
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Affiliation(s)
- Mingcong Wei
- Ocean College, Zhejiang University, Zhoushan, China
- Key Laboratory of Submarine Geosciences, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Xiang Zeng
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Xiqiu Han
- Ocean College, Zhejiang University, Zhoushan, China
- Key Laboratory of Submarine Geosciences, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Zongze Shao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Qian Xie
- Key Laboratory of Submarine Geosciences, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Chuanqi Dong
- Key Laboratory of Submarine Geosciences, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- College of Marine Geosciences, Ocean University of China, Qingdao, China
| | - Yejian Wang
- Key Laboratory of Submarine Geosciences, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Zhongyan Qiu
- Key Laboratory of Submarine Geosciences, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
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10
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Chen J, Liu Y, Diep P, Mahadevan R. Harnessing synthetic biology for sustainable biomining with Fe/S-oxidizing microbes. Front Bioeng Biotechnol 2022; 10:920639. [PMID: 36131722 PMCID: PMC9483119 DOI: 10.3389/fbioe.2022.920639] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
Biomining is a biotechnological approach where microorganisms are used to recover metals from ores and waste materials. While biomining applications are motivated by critical issues related to the climate crisis (e.g., habitat destruction due to mine effluent pollution, metal supply chains, increasing demands for cleantech-critical metals), its drawbacks hinder its widespread commercial applications: lengthy processing times, low recovery, and metal selectivity. Advances in synthetic biology provide an opportunity to engineer iron/sulfur-oxidizing microbes to address these limitations. In this forum, we review recent progress in synthetic biology-enhanced biomining with iron/sulfur-oxidizing microbes and delineate future research avenues.
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Affiliation(s)
- Jinjin Chen
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Yilan Liu
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Patrick Diep
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON, Canada
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11
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Spietz RL, Payne D, Kulkarni G, Metcalf WW, Roden EE, Boyd ES. Investigating Abiotic and Biotic Mechanisms of Pyrite Reduction. Front Microbiol 2022; 13:878387. [PMID: 35615515 PMCID: PMC9124975 DOI: 10.3389/fmicb.2022.878387] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 03/31/2022] [Indexed: 11/16/2022] Open
Abstract
Pyrite (FeS2) has a very low solubility and therefore has historically been considered a sink for iron (Fe) and sulfur (S) and unavailable to biology in the absence of oxygen and oxidative weathering. Anaerobic methanogens were recently shown to reduce FeS2 and assimilate Fe and S reduction products to meet nutrient demands. However, the mechanism of FeS2 mineral reduction and the forms of Fe and S assimilated by methanogens remained unclear. Thermodynamic calculations described herein indicate that H2 at aqueous concentrations as low as 10-10 M favors the reduction of FeS2, with sulfide (HS-) and pyrrhotite (Fe1- x S) as products; abiotic laboratory experiments confirmed the reduction of FeS2 with dissolved H2 concentrations greater than 1.98 × 10-4 M H2. Growth studies of Methanosarcina barkeri provided with FeS2 as the sole source of Fe and S resulted in H2 production but at concentrations too low to drive abiotic FeS2 reduction, based on abiotic laboratory experimental data. A strain of M. barkeri with deletions in all [NiFe]-hydrogenases maintained the ability to reduce FeS2 during growth, providing further evidence that extracellular electron transport (EET) to FeS2 does not involve H2 or [NiFe]-hydrogenases. Physical contact between cells and FeS2 was required for mineral reduction but was not required to obtain Fe and S from dissolution products. The addition of a synthetic electron shuttle, anthraquinone-2,6-disulfonate, allowed for biological reduction of FeS2 when physical contact between cells and FeS2 was prohibited, indicating that exogenous electron shuttles can mediate FeS2 reduction. Transcriptomics experiments revealed upregulation of several cytoplasmic oxidoreductases during growth of M. barkeri on FeS2, which may indicate involvement in provisioning low potential electrons for EET to FeS2. Collectively, the data presented herein indicate that reduction of insoluble FeS2 by M. barkeri occurred via electron transfer from the cell surface to the mineral surface resulting in the generation of soluble HS- and mineral-associated Fe1- x S. Solubilized Fe(II), but not HS-, from mineral-associated Fe1- x S reacts with aqueous HS- yielding aqueous iron sulfur clusters (FeS aq ) that likely serve as the Fe and S source for methanogen growth and activity. FeS aq nucleation and subsequent precipitation on the surface of cells may result in accelerated EET to FeS2, resulting in positive feedback between cell activity and FeS2 reduction.
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Affiliation(s)
- Rachel L. Spietz
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, United States
| | - Devon Payne
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, United States
| | - Gargi Kulkarni
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - William W. Metcalf
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Eric E. Roden
- Department of Geosciences, University of Wisconsin, Madison, WI, United States
| | - Eric S. Boyd
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, United States
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12
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He Y, Guo J, Song Y, Chen Z, Lu C, Han Y, Li H, Hou Y. Te(IV) bioreduction in the sulfur autotrophic reactor: Performance, kinetics and synergistic mechanism. WATER RESEARCH 2022; 214:118216. [PMID: 35228038 DOI: 10.1016/j.watres.2022.118216] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 02/12/2022] [Accepted: 02/18/2022] [Indexed: 06/14/2023]
Abstract
A laboratory-scale sulfur autotrophic reactor (SAR) was first constructed for treating tellurite [Te(IV)] wastewater. The SAR had excellent Te(IV) bioreduction efficiency (90-96%) at 5-30 mg/L and conformed to the First-order kinetic model. The Te(IV) bioreduction was elaborated deeply from extracellular polymeric substances (EPS) functions, microbial metabolic activity, key enzyme activity, microbial community succession and quorum sensing. Te(IV) stimulated the increase of redox substances in EPS and the improved cell membrane permeability led to the increase of electron transport system activity. Catalase and reduced nicotinamide adenine dinucleotide (NADH) alleviated the oxidative stress caused by Te(IV) toxicity to maintain metabolic activity. The increase of sulfur dioxygenase activity (SDO) suggested that more ATP produced by sulfur oxidation might provide energy for various physiological activities. Meanwhile, nitrate reductase (NAR), nitrite reductase (NIR) and sulfide: quinone oxidoreductase (SQR) played an active role in sulfur oxidation and Te(IV) bioreduction. Combined with the above results and dynamic succession of three functional microbial communities, a synergistic mechanism was proposed to explain the excellent performance of SAR. This work provided a promising strategy for Te(IV) wastewater treatment process and Te(IV) bioreduction mechanism.
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Affiliation(s)
- Yue He
- School of Environmental and Municipal Engineering, Tianjin Key Laboratory of Aquatic Science and Technology, Tianjin Chengjian University, Jinjing Road 26, Tianjin 300384, China
| | - Jianbo Guo
- School of Civil Engineering and Architecture, Taizhou University, Taizhou 318000, Zhejiang, China; School of Environmental and Municipal Engineering, Tianjin Key Laboratory of Aquatic Science and Technology, Tianjin Chengjian University, Jinjing Road 26, Tianjin 300384, China.
| | - Yuanyuan Song
- School of Environmental and Municipal Engineering, Tianjin Key Laboratory of Aquatic Science and Technology, Tianjin Chengjian University, Jinjing Road 26, Tianjin 300384, China
| | - Zhi Chen
- Department of Building, Civil, and Environmental Engineering, Concordia University, 1455 de Maisonneuve Blvd. W. Montreal, Quebec, Canada
| | - Caicai Lu
- School of Environmental and Municipal Engineering, Tianjin Key Laboratory of Aquatic Science and Technology, Tianjin Chengjian University, Jinjing Road 26, Tianjin 300384, China
| | - Yi Han
- School of Environmental and Municipal Engineering, Tianjin Key Laboratory of Aquatic Science and Technology, Tianjin Chengjian University, Jinjing Road 26, Tianjin 300384, China
| | - Haibo Li
- School of Environmental and Municipal Engineering, Tianjin Key Laboratory of Aquatic Science and Technology, Tianjin Chengjian University, Jinjing Road 26, Tianjin 300384, China
| | - Yanan Hou
- School of Environmental and Municipal Engineering, Tianjin Key Laboratory of Aquatic Science and Technology, Tianjin Chengjian University, Jinjing Road 26, Tianjin 300384, China
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13
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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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14
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Liu T, Hu Y, Chen N, Xue L, Feng C, Ye Y. Electrochemical investigation of the oxidation of pyrite in neutral solutions. Electrochim Acta 2021. [DOI: 10.1016/j.electacta.2021.139078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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15
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Liu T, Hu Y, Chen N, He Q, Feng C. High redox potential promotes oxidation of pyrite under neutral conditions: Implications for optimizing pyrite autotrophic denitrification. JOURNAL OF HAZARDOUS MATERIALS 2021; 416:125844. [PMID: 33878651 DOI: 10.1016/j.jhazmat.2021.125844] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 04/05/2021] [Accepted: 04/05/2021] [Indexed: 06/12/2023]
Abstract
Pyrite autotrophic denitrification (PAD) represents an important natural attenuation process of nitrate pollution and plays a pivotal role in linking nitrogen, sulfur, and iron cycles in a variety of anoxic environments. However, there are knowledge gaps about the oxidation mechanism of pyrite under anaerobic neutral conditions. This study explored the performance of PAD in the presence of EDTA and revealed the mechanism of anaerobic pyrite oxidation and microbial mineral transformation. It was demonstrated that ~200 mV was the electrochemical threshold for converting pyrite into bioavailable forms in PAD conditions, and accelerated pyrite oxidation by Fe3+-EDTA complexes can improve the performance of PAD effectively. Furthermore, genus related to sulfur and nitrogen cycle (Sulfurimonas, Denitrobacter) were found at higher abundances in cultures containing EDTA. The analysis of metagenomic binning showed that the microbial community in PAD culture with EDTA addition exhibited higher levels of functional diversity and redundancy. These results will further the understanding of the oxidation mechanism of pyrite under anaerobic neutral conditions and the corresponding microbial activities, and provide insights into the practical application of PAD.
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Affiliation(s)
- Tong Liu
- School of Water Resources and Environment, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), Beijing 100083, PR China
| | - Yutian Hu
- School of Water Resources and Environment, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), Beijing 100083, PR China
| | - Nan Chen
- School of Water Resources and Environment, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), Beijing 100083, PR China
| | - Qiaochong He
- School of Environmental Engineering, Henan University of Technology, Zhengzhou 450001, PR China
| | - Chuanping Feng
- School of Water Resources and Environment, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), Beijing 100083, PR China.
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16
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Nitrate Removal by a Novel Lithoautotrophic Nitrate-Reducing, Iron(II)-Oxidizing Culture Enriched from a Pyrite-Rich Limestone Aquifer. Appl Environ Microbiol 2021; 87:e0046021. [PMID: 34085863 DOI: 10.1128/aem.00460-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nitrate removal in oligotrophic environments is often limited by the availability of suitable organic electron donors. Chemolithoautotrophic bacteria may play a key role in denitrification in aquifers depleted in organic carbon. Under anoxic and circumneutral pH conditions, iron(II) was hypothesized to serve as an electron donor for microbially mediated nitrate reduction by Fe(II)-oxidizing (NRFeOx) microorganisms. However, lithoautotrophic NRFeOx cultures have never been enriched from any aquifer, and as such, there are no model cultures available to study the physiology and geochemistry of this potentially environmentally relevant process. Using iron(II) as an electron donor, we enriched a lithoautotrophic NRFeOx culture from nitrate-containing groundwater of a pyrite-rich limestone aquifer. In the enriched NRFeOx culture that does not require additional organic cosubstrates for growth, within 7 to 11 days, 0.3 to 0.5 mM nitrate was reduced and 1.3 to 2 mM iron(II) was oxidized, leading to a stoichiometric NO3-/Fe(II) ratio of 0.2, with N2 and N2O identified as the main nitrate reduction products. Short-range ordered Fe(III) (oxyhydr)oxides were the product of iron(II) oxidation. Microorganisms were observed to be closely associated with formed minerals, but only few cells were encrusted, suggesting that most of the bacteria were able to avoid mineral precipitation at their surface. Analysis of the microbial community by long-read 16S rRNA gene sequencing revealed that the culture is dominated by members of the Gallionellaceae family that are known as autotrophic, neutrophilic, and microaerophilic iron(II) oxidizers. In summary, our study suggests that NRFeOx mediated by lithoautotrophic bacteria can lead to nitrate removal in anthropogenically affected aquifers. IMPORTANCE Removal of nitrate by microbial denitrification in groundwater is often limited by low concentrations of organic carbon. In these carbon-poor ecosystems, nitrate-reducing bacteria that can use inorganic compounds such as Fe(II) (NRFeOx) as electron donors could play a major role in nitrate removal. However, no lithoautotrophic NRFeOx culture has been successfully isolated or enriched from this type of environment, and as such, there are no model cultures available to study the rate-limiting factors of this potentially important process. Here, we present the physiology and microbial community composition of a novel lithoautotrophic NRFeOx culture enriched from a fractured aquifer in southern Germany. The culture is dominated by a putative Fe(II) oxidizer affiliated with the Gallionellaceae family and performs nitrate reduction coupled to Fe(II) oxidation leading to N2O and N2 formation without the addition of organic substrates. Our analyses demonstrate that lithoautotrophic NRFeOx can potentially lead to nitrate removal in nitrate-contaminated aquifers.
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17
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Jakus N, Mellage A, Höschen C, Maisch M, Byrne JM, Mueller CW, Grathwohl P, Kappler A. Anaerobic Neutrophilic Pyrite Oxidation by a Chemolithoautotrophic Nitrate-Reducing Iron(II)-Oxidizing Culture Enriched from a Fractured Aquifer. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:9876-9884. [PMID: 34247483 DOI: 10.1021/acs.est.1c02049] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Neutrophilic microbial pyrite (FeS2) oxidation coupled to denitrification is thought to be an important natural nitrate attenuation pathway in nitrate-contaminated aquifers. However, the poor solubility of pyrite raises questions about its bioavailability and the mechanisms underlying its oxidation. Here, we investigated direct microbial pyrite oxidation by a neutrophilic chemolithoautotrophic nitrate-reducing Fe(II)-oxidizing culture enriched from a pyrite-rich aquifer. We used pyrite with natural abundance (NA) of Fe isotopes (NAFe-pyrite) and 57Fe-labeled siderite to evaluate whether the oxidation of the more soluble Fe(II)-carbonate (FeCO3) can indirectly drive abiotic pyrite oxidation. Our results showed that in setups where only pyrite was incubated with bacteria, direct microbial pyrite oxidation contributed ca. 26% to overall nitrate reduction. The rest was attributed to the oxidation of elemental sulfur (S0), present as a residue from pyrite synthesis. Pyrite oxidation was evidenced in the NAFe-pyrite/57Fe-siderite setups by maps of 56FeO and 32S obtained using a combination of SEM with nanoscale secondary ion MS (NanoSIMS), which showed the presence of 56Fe(III) (oxyhydr)oxides that could solely originate from 56FeS2. Based on the fit of a reaction model to the geochemical data and the Fe-isotope distributions from NanoSIMS, we conclude that anaerobic oxidation of pyrite by our neutrophilic enrichment culture was mainly driven by direct enzymatic activity of the cells. The contribution of abiotic pyrite oxidation by Fe3+ appeared to be negligible in our experimental setup.
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Affiliation(s)
- Natalia Jakus
- Geomicrobiology, Center for Applied Geoscience, University of Tuebingen, Tübingen D-72076, Germany
- Microbial Ecology, Center for Applied Geoscience, University of Tuebingen, Tübingen D-72076, Germany
| | - Adrian Mellage
- Hydrogeology, Center for Applied Geosciences, University of Tuebingen, Tübingen D-72076, Germany
| | - Carmen Höschen
- Soil Science, TUM School of Life Sciences, Technical University of Munich, Freising-Weihenstephan D-85354, Germany
| | - Markus Maisch
- Geomicrobiology, Center for Applied Geoscience, University of Tuebingen, Tübingen D-72076, Germany
| | - James M Byrne
- Geomicrobiology, Center for Applied Geoscience, University of Tuebingen, Tübingen D-72076, Germany
| | - Carsten W Mueller
- Soil Science, TUM School of Life Sciences, Technical University of Munich, Freising-Weihenstephan D-85354, Germany
| | - Peter Grathwohl
- Hydrogeochemistry, Center for Applied Geoscience, University of Tuebingen, D-72076 Tübingen, Germany
| | - Andreas Kappler
- Geomicrobiology, Center for Applied Geoscience, University of Tuebingen, Tübingen D-72076, Germany
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18
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Erickson ML, Swanner ED, Ziegler BA, Havig JR. Months-long spike in aqueous arsenic following domestic well installation and disinfection: Short- and long-term drinking water quality implications. JOURNAL OF HAZARDOUS MATERIALS 2021; 414:125409. [PMID: 33677323 DOI: 10.1016/j.jhazmat.2021.125409] [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: 06/30/2020] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
Exposure to high concentration geogenic arsenic via groundwater is a worldwide health concern. Well installation introduces oxic drilling fluids and hypochlorite (a strong oxidant) for disinfection, thus inducing geochemical disequilibrium. Well installation causes changes in geochemistry lasting 12 + months, as illustrated in a recent study of 250 new domestic wells in Minnesota, north-central United States. One study well had extremely high initial arsenic (1550 µg/L) that substantially decreased after 15 months (5.2 µg/L). The drilling and development of the study well were typical and ordinary; nothing observable indicated the very high initial arsenic concentration. We hypothesized that oxidation of arsenic-containing sulfides (which lowers pH) combined with low pH dissolution of arsenic-bearing Fe (oxyhydr)oxides caused the very high arsenic concentration. Geochemical equilibrium considerations and modeling supported our hypothesis. Groundwater equilibrium redox conditions are poised at the Fe(III)(s)/Fe(II)(aq) stability boundary, indicating arsenic-bearing Fe (oxyhydr)oxide mineral sensitivity to pH and redox changes. Changing groundwater geochemistry can have negative implications for home water treatment (e.g., reduced arsenic removal efficiency, iron fouling), which can lead to ongoing but unrecognized hazard of arsenic exposure from domestic well water. Our results may inform arsenic mobilization processes and geochemical sensitivity in similarly complex aquifers in Southeast Asia and elsewhere.
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Affiliation(s)
- Melinda L Erickson
- US Geological Survey, 2280 Woodale Drive, Mounds View, MN 55112, United States.
| | - Elizabeth D Swanner
- Department of Geological & Atmospheric Sciences, Iowa State University, 253 Science, Ames, IA 50011, United States.
| | - Brady A Ziegler
- Department of Geosciences, Trinity University, One Trinity Place, #45, San Antonio, TX 78212, United States.
| | - Jeff R Havig
- Department of Earth and Environmental Sciences, University of Minnesota, 116 Church Street SE., Minneapolis, MN 55455, United States.
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19
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Huang J, Jones A, Waite TD, Chen Y, Huang X, Rosso KM, Kappler A, Mansor M, Tratnyek PG, Zhang H. Fe(II) Redox Chemistry in the Environment. Chem Rev 2021; 121:8161-8233. [PMID: 34143612 DOI: 10.1021/acs.chemrev.0c01286] [Citation(s) in RCA: 166] [Impact Index Per Article: 55.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Iron (Fe) is the fourth most abundant element in the earth's crust and plays important roles in both biological and chemical processes. The redox reactivity of various Fe(II) forms has gained increasing attention over recent decades in the areas of (bio) geochemistry, environmental chemistry and engineering, and material sciences. The goal of this paper is to review these recent advances and the current state of knowledge of Fe(II) redox chemistry in the environment. Specifically, this comprehensive review focuses on the redox reactivity of four types of Fe(II) species including aqueous Fe(II), Fe(II) complexed with ligands, minerals bearing structural Fe(II), and sorbed Fe(II) on mineral oxide surfaces. The formation pathways, factors governing the reactivity, insights into potential mechanisms, reactivity comparison, and characterization techniques are discussed with reference to the most recent breakthroughs in this field where possible. We also cover the roles of these Fe(II) species in environmental applications of zerovalent iron, microbial processes, biogeochemical cycling of carbon and nutrients, and their abiotic oxidation related processes in natural and engineered systems.
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Affiliation(s)
- Jianzhi Huang
- Department of Civil and Environmental Engineering, Case Western Reserve University, 2104 Adelbert Road, Cleveland, Ohio 44106, United States
| | - Adele Jones
- UNSW Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - T David Waite
- UNSW Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Yiling Chen
- Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Xiaopeng Huang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Kevin M Rosso
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Andreas Kappler
- Geomicrobiology, Center for Applied Geosciences, University of Tuebingen, 72076 Tuebingen, Germany
| | - Muammar Mansor
- Geomicrobiology, Center for Applied Geosciences, University of Tuebingen, 72076 Tuebingen, Germany
| | - Paul G Tratnyek
- School of Public Health, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, United States
| | - Huichun Zhang
- Department of Civil and Environmental Engineering, Case Western Reserve University, 2104 Adelbert Road, Cleveland, Ohio 44106, United States
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20
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Ham B, Kwon JS, Boyanov MI, O'Loughlin EJ, Kemner KM, Kwon MJ. Geochemical and microbial characteristics of seepage water and mineral precipitates in a radwaste disposal facility impacted by seawater intrusion and high alkalinity. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 285:112087. [PMID: 33582476 DOI: 10.1016/j.jenvman.2021.112087] [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: 10/27/2020] [Revised: 01/27/2021] [Accepted: 01/28/2021] [Indexed: 06/12/2023]
Abstract
The construction of an underground facility can dramatically change the quality, flow direction, and level of groundwater. It may also impact subsurface microbial composition and activity. Groundwater quality was monitored over eight years in two observational wells near an underground disposal facility on the east coast of South Korea. The results showed dramatic increases in dissolved ions such as O2, Na, Ca, Mg, and SO4 during facility construction. Seepage water samples downgradient from the silos and tunnels, and precipitates deposited along the seepage water flow path were collected to determine the impact inside the disposal facility. X-ray analysis (powder X-ray diffraction (pXRD) and X-ray absorption fine structure (XAFS)) were used to characterize the mineral precipitates. Microbial community composition was determined by 16S rRNA gene sequencing. The seepage water composition was of two types: Ca-Cl and Ca-Na-HCO3. The ratio of Cl and δ18O showed that the Ca-Cl type seepage water was influenced by groundwater mixed with seawater ranging from 2.7% to 15.1%. Various sulfate-reducing bacteria were identified in the Ca-Cl type seepage water, exhibiting relatively high sulfate content from seawater intrusion. Samples from the Ca-Na-HCO3 type seepage water had an extremely high pH (>10) and abundance of Hydrogenophaga. The precipitates observed along the flow path of the seepage water included calcite, ferrihydrite, green rust, and siderite, depending on seepage water chemistry and microbial activity. This study suggests that the construction of underground structures creates distinct, localized geochemical conditions (e.g., high alkalinity, high salinity, and oxic conditions), which may impact microbial communities. These biogeochemical changes may have undesirable large-scale impacts such as water pump clogging. An understanding of the process and long-term monitoring are essential to assess the safety of underground facilities.
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Affiliation(s)
- Baknoon Ham
- KU-KIST Green School, Korea University, Seoul, 02841, South Korea
| | - Jang-Soon Kwon
- Korea Atomic Energy Research Institute, Daejeon, 34057, South Korea
| | - Maxim I Boyanov
- Institute of Chemical Engineering, Bulgarian Academy of Sciences, Sofia, 1113, Bulgaria; Biosciences Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | | | - Kenneth M Kemner
- Biosciences Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Man Jae Kwon
- Department of Earth and Environmental Sciences, Korea University, Seoul, 02841, South Korea.
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21
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Zhao M, Liu X, Li Z, Liang X, Wang Z, Zhang C, Liu W, Liu R, Zhao Y. Inhibition effect of sulfur on Cd activity in soil-rice system and its mechanism. JOURNAL OF HAZARDOUS MATERIALS 2021; 407:124647. [PMID: 33341579 DOI: 10.1016/j.jhazmat.2020.124647] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/04/2020] [Accepted: 11/19/2020] [Indexed: 06/12/2023]
Abstract
Sulfur (S) can regulate the mobility of cadmium (Cd) in soil and reduce Cd uptake by rice. However, the mechanism of how S affects soil properties and then regulates Cd mobility in rice growth through multiple factors is unclear. Diffusive gradients in thin films (DGT) and other in situ detection techniques, were innovatively used in this study. The effect of S on soil Cd mobility under flooded condition was analyzed in situ and the related mechanism was discussed. The results showed that the addition of S increased the level of dissolved organic oxygen (DOC), increased the concentration of Fe(Ⅱ) and S(-Ⅱ), and decreased the concentration of labile Cd in soil. Multiple regression analysis showed that Fe(Ⅱ), S(-Ⅱ), DOC were negatively correlated with labile Cd. S promoted the reduction of sulfate and iron and accelerated the formation of CdS and iron complexed Cd. The results of path analysis showed that the synergistic effect of S and Fe significantly inhibited the mobility of Cd. In particular, the mobility of Cd at tillering stage was greatly affected by S and Fe. Mercapto-palygorskite can effectively increase the concentration of Fe(Ⅱ),S(-Ⅱ) and DOC in soil, and reduce the harm of Cd to rice better than S0 and Na2SO4.
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Affiliation(s)
- Meng Zhao
- Key Laboratory for environmental factors control of Agro-product quality safety, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China; Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Xiaowei Liu
- Key Laboratory for environmental factors control of Agro-product quality safety, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China; Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Zhitao Li
- Technical Centre for Soil, Agriculture and Rural Ecology and Environment, Ministry of Ecology and Environment, Beijing 100012, China
| | - Xuefeng Liang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Zhen Wang
- Key Laboratory for environmental factors control of Agro-product quality safety, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China; Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Chuangchuang Zhang
- Key Laboratory for environmental factors control of Agro-product quality safety, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China; Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Wenjing Liu
- Key Laboratory for environmental factors control of Agro-product quality safety, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China; Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Rongle Liu
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China.
| | - Yujie Zhao
- Key Laboratory for environmental factors control of Agro-product quality safety, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China; Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China.
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Gu X, Heaney PJ, Reis FDAA, Brantley SL. Deep abiotic weathering of pyrite. Science 2020; 370:370/6515/eabb8092. [PMID: 33093082 DOI: 10.1126/science.abb8092] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 08/17/2020] [Indexed: 11/02/2022]
Abstract
Pyrite is a ubiquitous iron sulfide mineral that is oxidized by trace oxygen. The mineral has been largely absent from global sediments since the rise in oxygen concentration in Earth's early atmosphere. We analyzed weathering in shale, the most common rock exposed at Earth's surface, with chemical and microscopic analysis. By looking across scales from 10-9 to 102 meters, we determined the factors that control pyrite oxidation. Under the atmosphere today, pyrite oxidation is rate-limited by diffusion of oxygen to the grain surface and regulated by large-scale erosion and clast-scale fracturing. We determined that neither iron- nor sulfur-oxidizing microorganisms control global pyrite weathering fluxes despite their ability to catalyze the reaction. This multiscale picture emphasizes that fracturing and erosion are as important as atmospheric oxygen in limiting pyrite reactivity over Earth's history.
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Affiliation(s)
- Xin Gu
- Department of Geosciences, The Pennsylvania State University, University Park, PA 16802, USA.
| | - Peter J Heaney
- Department of Geosciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Fabio D A Aarão Reis
- Instituto de Física, Universidade Federal Fluminense, Avenida Litorânea s/n, 24210-340 Niterói, RJ, Brazil
| | - Susan L Brantley
- Department of Geosciences, The Pennsylvania State University, University Park, PA 16802, USA.,Earth and Environmental Systems Institute, The Pennsylvania State University, University Park, PA 16802, USA
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Hot in Cold: Microbial Life in the Hottest Springs in Permafrost. Microorganisms 2020; 8:microorganisms8091308. [PMID: 32867302 PMCID: PMC7565842 DOI: 10.3390/microorganisms8091308] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 08/22/2020] [Accepted: 08/25/2020] [Indexed: 12/26/2022] Open
Abstract
Chukotka is an arctic region located in the continuous permafrost zone, but thermal springs are abundant there. In this study, for the first time, the microbial communities of the Chukotka hot springs (CHS) biofilms and sediments with temperatures 54–94 °C were investigated and analyzed by NGS sequencing of 16S rRNA gene amplicons. In microbial mats (54–75 °C), phototrophic bacteria of genus Chloroflexus dominated (up to 89% of all prokaryotes), while Aquificae were the most numerous at higher temperatures in Fe-rich sediments and filamentous “streamers” (up to 92%). The electron donors typical for Aquificae, such as H2S and H2, are absent or present only in trace amounts, and the prevalence of Aquificae might be connected with their ability to oxidize the ferrous iron present in CHS sediments. Armatimonadetes, Proteobacteria, Deinococcus-Thermus, Dictyoglomi, and Thermotogae, as well as uncultured bacteria (candidate divisions Oct-Spa1-106, GAL15, and OPB56), were numerous, and Cyanobacteria were present in low numbers. Archaea (less than 8% of the total community of each tested spring) belonged to Bathyarchaeota, Aigarchaeota, and Thaumarchaeota. The geographical location and the predominantly autotrophic microbial community, built on mechanisms other than the sulfur cycle-based ones, make CHS a special and unique terrestrial geothermal ecosystem.
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Giddings LA, Chlipala G, Kunstman K, Green S, Morillo K, Bhave K, Peterson H, Driscoll H, Maienschein-Cline M. Characterization of an acid rock drainage microbiome and transcriptome at the Ely Copper Mine Superfund site. PLoS One 2020; 15:e0237599. [PMID: 32785287 PMCID: PMC7423320 DOI: 10.1371/journal.pone.0237599] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/29/2020] [Indexed: 01/20/2023] Open
Abstract
The microbial oxidation of metal sulfides plays a major role in the formation of acid rock drainage (ARD). We aimed to broadly characterize the ARD at Ely Brook, which drains the Ely Copper Mine Superfund site in Vermont, USA, using metagenomics and metatranscriptomics to assess the metabolic potential and seasonal ecological roles of microorganisms in water and sediment. Using Centrifuge against the NCBI "nt" database, ~25% of reads in sediment and water samples were classified as acid-tolerant Proteobacteria (61 ± 4%) belonging to the genera Pseudomonas (2.6-3.3%), Bradyrhizobium (1.7-4.1%), and Streptomyces (2.9-5.0%). Numerous genes (12%) were differentially expressed between seasons and played significant roles in iron, sulfur, carbon, and nitrogen cycling. The most abundant RNA transcript encoded the multidrug resistance protein Stp, and most expressed KEGG-annotated transcripts were involved in amino acid metabolism. Biosynthetic gene clusters involved in secondary metabolism (BGCs, 449) as well as metal- (133) and antibiotic-resistance (8501) genes were identified across the entire dataset. Several antibiotic and metal resistance genes were colocalized and coexpressed with putative BGCs, providing insight into the protective roles of the molecules BGCs produce. Our study shows that ecological stimuli, such as metal concentrations and seasonal variations, can drive ARD taxa to produce novel bioactive metabolites.
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Affiliation(s)
- Lesley-Ann Giddings
- Department of Chemistry & Biochemistry, Middlebury College, Middlebury, Vermont, United States of America
- Department of Chemistry, Smith College, Northampton, Massachusetts, United States of America
| | - George Chlipala
- Research Resources Center, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Kevin Kunstman
- Research Resources Center, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Stefan Green
- Research Resources Center, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Katherine Morillo
- Department of Chemistry & Biochemistry, Middlebury College, Middlebury, Vermont, United States of America
| | - Kieran Bhave
- Department of Chemistry & Biochemistry, Middlebury College, Middlebury, Vermont, United States of America
| | - Holly Peterson
- Department of Geology, Guilford College, Greensboro, North Carolina, United States of America
| | - Heather Driscoll
- Vermont Genetics Network, Department of Biology, Norwich University, Northfield, Vermont, United States of America
| | - Mark Maienschein-Cline
- Research Resources Center, University of Illinois at Chicago, Chicago, Illinois, United States of America
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25
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Mansor M, Xu J. Benefits at the nanoscale: a review of nanoparticle-enabled processes favouring microbial growth and functionality. Environ Microbiol 2020; 22:3633-3649. [PMID: 32705763 DOI: 10.1111/1462-2920.15174] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/17/2020] [Accepted: 07/21/2020] [Indexed: 11/29/2022]
Abstract
Nanoparticles are ubiquitous and co-occur with microbial life in every environment on Earth. Interactions between microbes and nanoparticles impact the biogeochemical cycles via accelerating various reaction rates and enabling biological processes at the smallest scales. Distinct from microbe-mineral interactions at large, microbe-nanoparticle interactions may involve higher levels of active recognition and utilization of the reactive, changeable, and thereby 'moldable' nano-sized inorganic phases by microbes, which has been given minimal attention in previous reviews. Here we have compiled the various cases of microbe-nanoparticle interactions with clear and potential benefits to the microbial cells and communities. Specifically, we discussed (i) the high bioavailabilities of nanoparticles due to increased specific surface areas and size-dependent solubility, with a focus on environmentally-relevant iron(III) (oxyhydr)oxides and pyrite, (ii) microbial utilization of nanoparticles as 'nano-tools' for electron transfer, chemotaxis, and storage units, and (iii) speculated benefits of precipitating 'moldable' nanoparticles in extracellular biomineralization. We further discussed emergent questions concerning cellular level responses to nanoparticle-associated cues, and the factors that affect nanoparticles' bioavailabilities beyond size-dependent effects. We end the review by proposing a framework towards more quantitative approaches and by highlighting promising techniques to guide future research in this exciting field.
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Affiliation(s)
- Muammar Mansor
- Geomicrobiology, Center for Applied Geoscience, University of Tuebingen, Tuebingen, 72076, Germany
| | - Jie Xu
- Department of Geological Sciences, the University of Texas at El Paso, El Paso, Texas, 79968, USA
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26
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Hu Y, Wu G, Li R, Xiao L, Zhan X. Iron sulphides mediated autotrophic denitrification: An emerging bioprocess for nitrate pollution mitigation and sustainable wastewater treatment. WATER RESEARCH 2020; 179:115914. [PMID: 32413614 DOI: 10.1016/j.watres.2020.115914] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 03/16/2020] [Accepted: 05/02/2020] [Indexed: 05/09/2023]
Abstract
Iron sulphides, mainly in the form of mackinawite (FeS), pyrrhotite (Fe1-xS, x = 0-0.125) and pyrite (FeS2), are the most abundant sulphide minerals and can be oxidized under anoxic and circumneutral pH conditions by chemoautotrophic denitrifying bacteria to reduce nitrate to N2. Iron sulphides mediated autotrophic denitrification (ISAD) represents an important natural attenuation process of nitrate pollution and plays a pivotal role in linking nitrogen, sulphur and iron cycles in a variety of anoxic environments. Recently, it has emerged as a promising bioprocess for nutrient removal from various organic-deficient water and wastewater, due to its specific advantages including high denitrification capacity, simultaneous nitrogen and phosphorus removal, self-buffering properties, and fewer by-products generation (sulphate, waste sludge, N2O, NH4+, etc.). This paper provides a critical overview of fundamental and engineering aspects of ISAD, including the theoretical knowledge (biochemistry, and microbial diversity), its natural occurrence and engineering applications. Its potential and limitations are elucidated by summarizing the key influencing factors including availability of iron sulphides, low denitrification rates, sulphate emission and leaching heavy metals. This review also put forward two key questions in the mechanism of anoxic iron sulphides oxidation, i.e. dissolution of iron sulphides and direct substrates for denitrifiers. Finally, its prospects for future sustainable wastewater treatment are highlighted. An iron sulphides-based biotechnology towards next-generation wastewater treatment (NEO-GREEN) is proposed, which can potentially harness bioenergy in wastewater, incorporate resources (P and Fe) recovery, achieve simultaneous nutrient and emerging contaminants removal, and minimize waste sludge production.
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Affiliation(s)
- Yuansheng Hu
- Civil Engineering, College of Engineering and Informatics, National University of Ireland, Galway, Ireland; Ryan Institute, National University of Ireland, Galway, Ireland
| | - Guangxue Wu
- Institute of Environmental Engineering and Management, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, China
| | - Ruihua Li
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163# Xianlin Avenue, Nanjing, 210023, China
| | - Liwen Xiao
- Department of Civil, Structural and Environmental Engineering, Trinity College Dublin, Dublin 2, Ireland
| | - Xinmin Zhan
- Civil Engineering, College of Engineering and Informatics, National University of Ireland, Galway, Ireland; Ryan Institute, National University of Ireland, Galway, Ireland; MaREI Centre for Marine and Renewable Energy, Ireland.
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27
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Hou J, Sievert SM, Wang Y, Seewald JS, Natarajan VP, Wang F, Xiao X. Microbial succession during the transition from active to inactive stages of deep-sea hydrothermal vent sulfide chimneys. MICROBIOME 2020; 8:102. [PMID: 32605604 PMCID: PMC7329443 DOI: 10.1186/s40168-020-00851-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 04/28/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Deep-sea hydrothermal vents are highly productive biodiversity hotspots in the deep ocean supported by chemosynthetic microorganisms. Prominent features of these systems are sulfide chimneys emanating high-temperature hydrothermal fluids. While several studies have investigated the microbial diversity in both active and inactive sulfide chimneys that have been extinct for up to thousands of years, little is known about chimneys that have ceased activity more recently, as well as the microbial succession occurring during the transition from active to inactive chimneys. RESULTS Genome-resolved metagenomics was applied to an active and a recently extinct (~ 7 years) sulfide chimney from the 9-10° N hydrothermal vent field on the East Pacific Rise. Full-length 16S rRNA gene and a total of 173 high-quality metagenome assembled genomes (MAGs) were retrieved for comparative analysis. In the active chimney (L-vent), sulfide- and/or hydrogen-oxidizing Campylobacteria and Aquificae with the potential for denitrification were identified as the dominant community members and primary producers, fixing carbon through the reductive tricarboxylic acid (rTCA) cycle. In contrast, the microbiome of the recently extinct chimney (M-vent) was largely composed of heterotrophs from various bacterial phyla, including Delta-/Beta-/Alphaproteobacteria and Bacteroidetes. Gammaproteobacteria were identified as the main primary producers, using the oxidation of metal sulfides and/or iron oxidation coupled to nitrate reduction to fix carbon through the Calvin-Benson-Bassham (CBB) cycle. Further analysis revealed a phylogenetically distinct Nitrospirae cluster that has the potential to oxidize sulfide minerals coupled to oxygen and/or nitrite reduction, as well as for sulfate reduction, and that might serve as an indicator for the early stages of chimneys after venting has ceased. CONCLUSIONS This study sheds light on the composition, metabolic functions, and succession of microbial communities inhabiting deep-sea hydrothermal vent sulfide chimneys. Collectively, microbial succession during the life span of a chimney could be described to proceed from a "fluid-shaped" microbial community in newly formed and actively venting chimneys supported by the oxidation of reductants in the hydrothermal fluid to a "mineral-shaped" community supported by the oxidation of minerals after hydrothermal activity has ceased. Remarkably, the transition appears to occur within the first few years, after which the communities stay stable for thousands of years. Video Abstract.
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Affiliation(s)
- Jialin Hou
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Stefan M Sievert
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Yinzhao Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jeffrey S Seewald
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Vengadesh Perumal Natarajan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China.
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China.
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28
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Thomas F, Morris JT, Wigand C, Sievert SM. Short-term effect of simulated salt marsh restoration by sand-amendment on sediment bacterial communities. PLoS One 2019; 14:e0215767. [PMID: 31034478 PMCID: PMC6488055 DOI: 10.1371/journal.pone.0215767] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 04/08/2019] [Indexed: 01/23/2023] Open
Abstract
Coastal climate adaptation strategies are needed to build salt marsh resiliency and maintain critical ecosystem services in response to impacts caused by climate change. Although resident microbial communities perform crucial biogeochemical cycles for salt marsh functioning, their response to restoration practices is still understudied. One promising restoration strategy is the placement of sand or sediment onto the marsh platform to increase marsh resiliency. A previous study examined the above- and below-ground structure, soil carbon dioxide emissions, and pore water constituents in Spartina alterniflora-vegetated natural marsh sediments and sand-amended sediments at varying inundation regimes. Here, we analyzed samples from the same experiment to test the effect of sand-amendments on the microbial communities after 5 months. Along with the previously observed changes in biogeochemistry, sand amendments drastically modified the bacterial communities, decreasing richness and diversity. The dominant sulfur-cycling bacterial community found in natural sediments was replaced by one dominated by iron oxidizers and aerobic heterotrophs, the abundance of which correlated with higher CO2-flux. In particular, the relative abundance of iron-oxidizing Zetaproteobacteria increased in the sand-amended sediments, possibly contributing to acidification by the formation of iron oxyhydroxides. Our data suggest that the bacterial community structure can equilibrate if the inundation regime is maintained within the optimal range for S. alterniflora. While long-term effects of changes in bacterial community on the growth of S. alterniflora are not clear, our results suggest that analyzing the microbial community composition could be a useful tool to monitor climate adaptation and restoration efforts.
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Affiliation(s)
- François Thomas
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States of America
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - James T. Morris
- Belle Baruch Institute for Marine & Coastal Sciences, University of South Carolina, Columbia, SC, United States of America
| | - Cathleen Wigand
- U.S. EPA, Office of Research and Development, National Health and Environmental Effects Research Laboratory, Atlantic Ecology Division, Narragansett, RI, United States of America
| | - Stefan M. Sievert
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States of America
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Meier DV, Pjevac P, Bach W, Markert S, Schweder T, Jamieson J, Petersen S, Amann R, Meyerdierks A. Microbial metal-sulfide oxidation in inactive hydrothermal vent chimneys suggested by metagenomic and metaproteomic analyses. Environ Microbiol 2019; 21:682-701. [PMID: 30585382 PMCID: PMC6850669 DOI: 10.1111/1462-2920.14514] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 12/17/2018] [Accepted: 12/19/2018] [Indexed: 01/02/2023]
Abstract
Metal-sulfides are wide-spread in marine benthic habitats. At deep-sea hydrothermal vents, they occur as massive sulfide chimneys formed by mineral precipitation upon mixing of reduced vent fluids with cold oxygenated sea water. Although microorganisms inhabiting actively venting chimneys and utilizing compounds supplied by the venting fluids are well studied, only little is known about microorganisms inhabiting inactive chimneys. In this study, we combined 16S rRNA gene-based community profiling of sulfide chimneys from the Manus Basin (SW Pacific) with radiometric dating, metagenome (n = 4) and metaproteome (n = 1) analyses. Our results shed light on potential lifestyles of yet poorly characterized bacterial clades colonizing inactive chimneys. These include sulfate-reducing Nitrospirae and sulfide-oxidizing Gammaproteobacteria dominating most of the inactive chimney communities. Our phylogenetic analysis attributed the gammaproteobacterial clades to the recently described Woeseiaceae family and the SSr-clade found in marine sediments around the world. Metaproteomic data identified these Gammaproteobacteria as autotrophic sulfide-oxidizers potentially facilitating metal-sulfide dissolution via extracellular electron transfer. Considering the wide distribution of these gammaproteobacterial clades in marine environments such as hydrothermal vents and sediments, microbially accelerated neutrophilic mineral oxidation might be a globally relevant process in benthic element cycling and a considerable energy source for carbon fixation in marine benthic habitats.
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Affiliation(s)
- Dimitri V. Meier
- Max Planck Institute for Marine MicrobiologyCelsiusstrasse 1, 28359, BremenGermany
| | - Petra Pjevac
- Max Planck Institute for Marine MicrobiologyCelsiusstrasse 1, 28359, BremenGermany
| | - Wolfgang Bach
- MARUM – Center for Marine Environmental Sciences, Petrology of the Ocean Crust groupUniversity of BremenLeobener Str., 28359, BremenGermany
| | - Stephanie Markert
- Institute of PharmacyErnst‐Moritz‐Arndt‐UniversityFriedrich‐Ludwig‐Jahn‐Straße 17, 17489, GreifswaldGermany
| | - Thomas Schweder
- Institute of PharmacyErnst‐Moritz‐Arndt‐UniversityFriedrich‐Ludwig‐Jahn‐Straße 17, 17489, GreifswaldGermany
| | - John Jamieson
- Department of Earth SciencesMemorial University of Newfoundland40 Arctic Ave, Saint John'sNL, A1B 3X7Canada
| | - Sven Petersen
- GEOMAR Helmholtz Centre for Ocean ResearchWischhofstraße 1‐3, 24148, KielGermany
| | - Rudolf Amann
- Max Planck Institute for Marine MicrobiologyCelsiusstrasse 1, 28359, BremenGermany
| | - Anke Meyerdierks
- Max Planck Institute for Marine MicrobiologyCelsiusstrasse 1, 28359, BremenGermany
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New understanding of the reduction mechanism of pyrolusite in the Acidithiobacillus ferrooxidans bio-leaching system. Electrochim Acta 2019. [DOI: 10.1016/j.electacta.2018.12.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Chen H, Liu Y, Xu X, Sun M, Jiang M, Xue G, Li X, Liu Z. How does iron facilitate the aerated biofilter for tertiary simultaneous nutrient and refractory organics removal from real dyeing wastewater? WATER RESEARCH 2019; 148:344-358. [PMID: 30391863 DOI: 10.1016/j.watres.2018.10.059] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 09/30/2018] [Accepted: 10/21/2018] [Indexed: 06/08/2023]
Abstract
Textile dyeing wastewater is characterized by low biodegradability and high nitrogen strength, which is difficult to meet the increasingly stringent discharge requirements. Therefore, the tertiary nutrient and refractory organics removal is considered and aerated biofilter is often adopted. However, the aerobic condition and carbon source shortage restrict tertiary biological nitrogen removal. In this study, iron scrap was introduced as the filter medium to enhance the pollutant removal capacity, and three aerobic biofilters were constructed. Biofilter Fe-CE was filled with iron scrap and ceramisite; biofilter Fe-AC was added with iron scrap and granular activated carbon, and biofilter CE only had ceramisite to pad as control system. After the biofilters were acclimatized by synthetic wastewater and actual dyeing wastewater, the optimal operation parameters based on nitrogen removal were determined as pH 7, gas-water ratio 5:1, hydraulic retention time 8 h and C/N ratio 8.5:1. The iron scraps improved total nitrogen (TN) removal significantly, with TN removal efficiency of 68.7% and 57.3% in biofilter Fe-AC and biofilter Fe-CE, comparing with biofilter CE of 29.9%. Additionally, phosphorus and COD had better removal performance as well when iron scrap existed. Further investigation interpreted the reason for iron's facilitating effect on tertiary nutrient and refractory organics removal. The introduction of iron scrap made the habitat conditions such as pH values, DO concentrations and biomass contents inside the biofilters change towards the direction beneficial for pollutant elimination especially for nitrogen removal. In iron containing biofilters, the majority of nitrogen, phosphorus and organic pollutants were removed in the iron scrap layers, and more pollutants types appeared, implying that iron triggered pollutants to go through more diverse degradation or transformation pathways. Moreover, the phylum Proteoabcteria dominated in samples of ceramisite-containing biofilters, with abundances more than 40%. The iron scrap existence increased the abundances of phyla Bacteroidetes and Firmicutes, and triggered higher abundance of denitrification bacteria.
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Affiliation(s)
- Hong Chen
- School of Environmental Science and Engineering, Donghua University, 2999 North Renmin Road, Songjiang District, Shanghai, 201620, China; Jiangsu Tongyan Environm Prod Sci & Technol Co Lt, Yancheng, 224000, China
| | - Yunfan Liu
- School of Environmental Science and Engineering, Donghua University, 2999 North Renmin Road, Songjiang District, Shanghai, 201620, China
| | - Xiaoqiang Xu
- School of Environmental Science and Engineering, Donghua University, 2999 North Renmin Road, Songjiang District, Shanghai, 201620, China
| | - Min Sun
- School of Environmental Science and Engineering, Donghua University, 2999 North Renmin Road, Songjiang District, Shanghai, 201620, China
| | - Mingji Jiang
- School of Environmental Science and Engineering, Donghua University, 2999 North Renmin Road, Songjiang District, Shanghai, 201620, China
| | - Gang Xue
- School of Environmental Science and Engineering, Donghua University, 2999 North Renmin Road, Songjiang District, Shanghai, 201620, China; Shanghai Institute of Pollution Control and Ecological Security, 200000, China.
| | - Xiang Li
- School of Environmental Science and Engineering, Donghua University, 2999 North Renmin Road, Songjiang District, Shanghai, 201620, China; Jiangsu Tongyan Environm Prod Sci & Technol Co Lt, Yancheng, 224000, China
| | - Zhenhong Liu
- School of Environmental Science and Engineering, Donghua University, 2999 North Renmin Road, Songjiang District, Shanghai, 201620, China
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Fan L, Zhao F, Liu J, Hudson-Edwards KA. Dissolution of realgar by Acidithiobacillus ferrooxidans in the presence and absence of zerovalent iron: Implications for remediation of iron-deficient realgar tailings. CHEMOSPHERE 2018; 209:381-391. [PMID: 29935467 DOI: 10.1016/j.chemosphere.2018.05.192] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 05/25/2018] [Accepted: 05/31/2018] [Indexed: 05/27/2023]
Abstract
Realgar (As4S4)-rich tailings are iron-deficient arsenical mine wastes. The mechanisms and products of the dissolution of realgar by Acidithiobacillus ferrooxidans (A. ferrooxidans) in the presence (0.2 g and 2 g) and absence of zerovalent iron (ZVI) are investigated for three stages (each of 7 d with fresh A. ferrooxidans medium addition between the stages). SEM-EDX, FTIR, XPS and selective extraction analysis are used to characterize the solid-phase during the experiments. ZVI addition causes the systems to become more acid-generating, although pH increases are observed in the first day due to ZVI dissolution. Arsenic is released to solution due to realgar oxidation (∼30 mg L-1 in the 0 g ZVI system in Stage I), but low concentrations are observed in the ZVI-added systems (<5 mg L-1) and in Stages II and III of the 0 g ZVI system. As(III) dominates the released As(T) at day 1 (83-89% of As(T)), but is largely oxidized to As(V) at day 7 of each stage (53-98% of As(T)). Arsenic attenuation is attributed to the formation of mixed As-Fe oxyhydroxides and oxyhydroxy sulfates that take up released arsenic and are abundant in the 2.0 g ZVI system, and to passivation of the realgar surface. Consequently, a new strategy that combines A. ferrooxidans and exogenous ZVI addition for treating in-situ iron-deficient realgar-rich tailings is proposed, although its long-term effects need to be monitored.
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Affiliation(s)
- Lijun Fan
- College of Geoscience and Surveying Engineering, China University of Mining & Technology, Beijing, 100083, China
| | - Fenghua Zhao
- College of Geoscience and Surveying Engineering, China University of Mining & Technology, Beijing, 100083, China
| | - Jing Liu
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Agricultural Resources and Environment, College of Resources and Environment, Department of Environment Science and Engineering, Southwest University, Chongqing 400716, China.
| | - Karen A Hudson-Edwards
- Environment & Sustainability Institute and Camborne School of Mines, University of Exeter, Penryn, Cornwall, TR10 9DF, UK.
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Fu H, Zhang H, Sui Y, Hu N, Ding D, Ye Y, Li G, Wang Y, Dai Z. Transformation of uranium species in soil during redox oscillations. CHEMOSPHERE 2018; 208:846-853. [PMID: 30068027 DOI: 10.1016/j.chemosphere.2018.06.059] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 05/19/2018] [Accepted: 06/07/2018] [Indexed: 06/08/2023]
Abstract
Redox oscillation is commonly found in near-surface environment, where soils are often polluted with many redox active contaminants, including uranium (U). In order to investigate the transformation of U species in near-surface soil under redox oscillations conditions, redox oscillations and reduction experiments were performed, biogeochemical parameters and native microbial community composition were monitored, main elements on the surface of solid-phase were analyzed by XPS, and labile U(IV) species and stable U(IV) species in solid-phase were provisionally defined using an anoxic 1 M sodium bicarbonate extraction. It was found that redox oscillations slightly increased the water-soluble U but significantly increased the stable U(IV) species (P < 0.05) in soil. In reduction experiment, there was upper limit value for percentage of stable U(IV) species, and the labile U(IV) species could not transform to stable U(IV) species in a short period of time under reduction conditions. The redox transition of Fe enriched on the surface of soil and the conversion of microbial community composition played a major role in speciation transformation of U under redox oscillations conditions. In addition, sequential extraction revealed that the increase of stable U(IV) species content reflected the U speciation transition from acetate extract to more recalcitrant hydroxylamine extract. The finding provides a potential method for improving the stability of U when bio-reduction is used to remediate the U-contaminated soils.
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Affiliation(s)
- Haiying Fu
- Key Discipline Laboratory for National Defense for Biotechnology in Uranium Mining and Hydrometallurgy, University of South China, Hengyang, 421001, China; School of Environment and Safety Engineering, University of South China, Hengyang, Hunan, 421001, China
| | - Hui Zhang
- Key Discipline Laboratory for National Defense for Biotechnology in Uranium Mining and Hydrometallurgy, University of South China, Hengyang, 421001, China
| | - Yang Sui
- School of Environment and Safety Engineering, University of South China, Hengyang, Hunan, 421001, China; Hunan Taohuajiang Nuclear Power Co., Ltd, Yiyang, 413000, China
| | - Nan Hu
- Key Discipline Laboratory for National Defense for Biotechnology in Uranium Mining and Hydrometallurgy, University of South China, Hengyang, 421001, China
| | - Dexin Ding
- Key Discipline Laboratory for National Defense for Biotechnology in Uranium Mining and Hydrometallurgy, University of South China, Hengyang, 421001, China; School of Environment and Safety Engineering, University of South China, Hengyang, Hunan, 421001, China.
| | - Yongjun Ye
- Key Discipline Laboratory for National Defense for Biotechnology in Uranium Mining and Hydrometallurgy, University of South China, Hengyang, 421001, China; School of Environment and Safety Engineering, University of South China, Hengyang, Hunan, 421001, China
| | - Guangyue Li
- Key Discipline Laboratory for National Defense for Biotechnology in Uranium Mining and Hydrometallurgy, University of South China, Hengyang, 421001, China
| | - Yongdong Wang
- Key Discipline Laboratory for National Defense for Biotechnology in Uranium Mining and Hydrometallurgy, University of South China, Hengyang, 421001, China
| | - Zhongran Dai
- Key Discipline Laboratory for National Defense for Biotechnology in Uranium Mining and Hydrometallurgy, University of South China, Hengyang, 421001, China
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Triple oxygen isotope evidence for limited mid-Proterozoic primary productivity. Nature 2018; 559:613-616. [PMID: 30022163 DOI: 10.1038/s41586-018-0349-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 06/01/2018] [Indexed: 11/08/2022]
Abstract
The global biosphere is commonly assumed to have been less productive before the rise of complex eukaryotic ecosystems than it is today1. However, direct evidence for this assertion is lacking. Here we present triple oxygen isotope measurements (∆17O) from sedimentary sulfates from the Sibley basin (Ontario, Canada) dated to about 1.4 billion years ago, which provide evidence for a less productive biosphere in the middle of the Proterozoic eon. We report what are, to our knowledge, the most-negative ∆17O values (down to -0.88‰) observed in sulfates, except for those from the terminal Cryogenian period2. This observation demonstrates that the mid-Proterozoic atmosphere was distinct from what persisted over approximately the past 0.5 billion years, directly reflecting a unique interplay among the atmospheric partial pressures of CO2 and O2 and the photosynthetic O2 flux at this time3. Oxygenic gross primary productivity is stoichiometrically related to the photosynthetic O2 flux to the atmosphere. Under current estimates of mid-Proterozoic atmospheric partial pressure of CO2 (2-30 times that of pre-anthropogenic levels), our modelling indicates that gross primary productivity was between about 6% and 41% of pre-anthropogenic levels if atmospheric O2 was between 0.1-1% or 1-10% of pre-anthropogenic levels, respectively. When compared to estimates of Archaean4-6 and Phanerozoic primary production7, these model solutions show that an increasingly more productive biosphere accompanied the broad secular pattern of increasing atmospheric O2 over geologic time8.
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He S, Barco RA, Emerson D, Roden EE. Comparative Genomic Analysis of Neutrophilic Iron(II) Oxidizer Genomes for Candidate Genes in Extracellular Electron Transfer. Front Microbiol 2017; 8:1584. [PMID: 28871245 PMCID: PMC5566968 DOI: 10.3389/fmicb.2017.01584] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 08/04/2017] [Indexed: 11/13/2022] Open
Abstract
Extracellular electron transfer (EET) is recognized as a key biochemical process in circumneutral pH Fe(II)-oxidizing bacteria (FeOB). In this study, we searched for candidate EET genes in 73 neutrophilic FeOB genomes, among which 43 genomes are complete or close-to-complete and the rest have estimated genome completeness ranging from 5 to 91%. These neutrophilic FeOB span members of the microaerophilic, anaerobic phototrophic, and anaerobic nitrate-reducing FeOB groups. We found that many microaerophilic and several anaerobic FeOB possess homologs of Cyc2, an outer membrane cytochrome c originally identified in Acidithiobacillus ferrooxidans. The "porin-cytochrome c complex" (PCC) gene clusters homologous to MtoAB/PioAB are present in eight FeOB, accounting for 19% of complete and close-to-complete genomes examined, whereas PCC genes homologous to OmbB-OmaB-OmcB in Geobacter sulfurreducens are absent. Further, we discovered gene clusters that may potentially encode two novel PCC types. First, a cluster (tentatively named "PCC3") encodes a porin, an extracellular and a periplasmic cytochrome c with remarkably large numbers of heme-binding motifs. Second, a cluster (tentatively named "PCC4") encodes a porin and three periplasmic multiheme cytochromes c. A conserved inner membrane protein (IMP) encoded in PCC3 and PCC4 gene clusters might be responsible for translocating electrons across the inner membrane. Other bacteria possessing PCC3 and PCC4 are mostly Proteobacteria isolated from environments with a potential niche for Fe(II) oxidation. In addition to cytochrome c, multicopper oxidase (MCO) genes potentially involved in Fe(II) oxidation were also identified. Notably, candidate EET genes were not found in some FeOB, especially the anaerobic ones, probably suggesting EET genes or Fe(II) oxidation mechanisms are different from the searched models. Overall, based on current EET models, the search extends our understanding of bacterial EET and provides candidate genes for future research.
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Affiliation(s)
- Shaomei He
- Department of Geoscience, University of Wisconsin-MadisonMadison, WI, United States.,NASA Astrobiology Institute, University of WisconsinMadison, WI, United States.,Department of Bacteriology, University of Wisconsin-MadisonMadison, WI, United States
| | - Roman A Barco
- Bigelow Laboratory for Ocean SciencesEast Boothbay Harbor, ME, United States.,Department of Earth Sciences, University of Southern CaliforniaLos Angeles, CA, United States
| | - David Emerson
- Bigelow Laboratory for Ocean SciencesEast Boothbay Harbor, ME, United States
| | - Eric E Roden
- Department of Geoscience, University of Wisconsin-MadisonMadison, WI, United States.,NASA Astrobiology Institute, University of WisconsinMadison, WI, United States
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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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