301
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Wurzbacher C, Fuchs A, Attermeyer K, Frindte K, Grossart HP, Hupfer M, Casper P, Monaghan MT. Shifts among Eukaryota, Bacteria, and Archaea define the vertical organization of a lake sediment. MICROBIOME 2017; 5:41. [PMID: 28388930 PMCID: PMC5385010 DOI: 10.1186/s40168-017-0255-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 03/15/2017] [Indexed: 05/10/2023]
Abstract
BACKGROUND Lake sediments harbor diverse microbial communities that cycle carbon and nutrients while being constantly colonized and potentially buried by organic matter sinking from the water column. The interaction of activity and burial remained largely unexplored in aquatic sediments. We aimed to relate taxonomic composition to sediment biogeochemical parameters, test whether community turnover with depth resulted from taxonomic replacement or from richness effects, and to provide a basic model for the vertical community structure in sediments. METHODS We analyzed four replicate sediment cores taken from 30-m depth in oligo-mesotrophic Lake Stechlin in northern Germany. Each 30-cm core spanned ca. 170 years of sediment accumulation according to 137Cs dating and was sectioned into layers 1-4 cm thick. We examined a full suite of biogeochemical parameters and used DNA metabarcoding to examine community composition of microbial Archaea, Bacteria, and Eukaryota. RESULTS Community β-diversity indicated nearly complete turnover within the uppermost 30 cm. We observed a pronounced shift from Eukaryota- and Bacteria-dominated upper layers (<5 cm) to Bacteria-dominated intermediate layers (5-14 cm) and to deep layers (>14 cm) dominated by enigmatic Archaea that typically occur in deep-sea sediments. Taxonomic replacement was the prevalent mechanism in structuring the community composition and was linked to parameters indicative of microbial activity (e.g., CO2 and CH4 concentration, bacterial protein production). Richness loss played a lesser role but was linked to conservative parameters (e.g., C, N, P) indicative of past conditions. CONCLUSIONS By including all three domains, we were able to directly link the exponential decay of eukaryotes with the active sediment microbial community. The dominance of Archaea in deeper layers confirms earlier findings from marine systems and establishes freshwater sediments as a potential low-energy environment, similar to deep sea sediments. We propose a general model of sediment structure and function based on microbial characteristics and burial processes. An upper "replacement horizon" is dominated by rapid taxonomic turnover with depth, high microbial activity, and biotic interactions. A lower "depauperate horizon" is characterized by low taxonomic richness, more stable "low-energy" conditions, and a dominance of enigmatic Archaea.
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Affiliation(s)
- Christian Wurzbacher
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, Berlin, 12587 Germany
- Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Str. 6-8, Berlin, 14195 Germany
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 100, Göteborg, Sweden
| | - Andrea Fuchs
- Carl-von-Ossietzky University Oldenburg, Ammerländer Heerstraße 114-118, Oldenburg, 26129 Germany
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, Stechlin, 16775 Germany
| | - Katrin Attermeyer
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, Stechlin, 16775 Germany
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18d, Uppsala, 75236 Sweden
| | - Katharina Frindte
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, Stechlin, 16775 Germany
- Institute of Crop Science and Resource Conservation – Molecular Biology of the Rhizosphere, Nussallee 13, Bonn, 53115 Germany
| | - Hans-Peter Grossart
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, Stechlin, 16775 Germany
- Institute for Biochemistry and Biology, Potsdam University, Maulbeerallee 2, Potsdam, 14469 Germany
| | - Michael Hupfer
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, Berlin, 12587 Germany
| | - Peter Casper
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, Stechlin, 16775 Germany
| | - Michael T. Monaghan
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, Berlin, 12587 Germany
- Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Str. 6-8, Berlin, 14195 Germany
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302
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Ferousi C, Lindhoud S, Baymann F, Kartal B, Jetten MSM, Reimann J. Iron assimilation and utilization in anaerobic ammonium oxidizing bacteria. Curr Opin Chem Biol 2017; 37:129-136. [DOI: 10.1016/j.cbpa.2017.03.009] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 03/08/2017] [Accepted: 03/14/2017] [Indexed: 02/07/2023]
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303
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Sun T, Levin BDA, Guzman JJL, Enders A, Muller DA, Angenent LT, Lehmann J. Rapid electron transfer by the carbon matrix in natural pyrogenic carbon. Nat Commun 2017; 8:14873. [PMID: 28361882 PMCID: PMC5380966 DOI: 10.1038/ncomms14873] [Citation(s) in RCA: 240] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 02/09/2017] [Indexed: 12/29/2022] Open
Abstract
Surface functional groups constitute major electroactive components in pyrogenic carbon. However, the electrochemical properties of pyrogenic carbon matrices and the kinetic preference of functional groups or carbon matrices for electron transfer remain unknown. Here we show that environmentally relevant pyrogenic carbon with average H/C and O/C ratios of less than 0.35 and 0.09 can directly transfer electrons more than three times faster than the charging and discharging cycles of surface functional groups and have a 1.5 V potential range for biogeochemical reactions that invoke electron transfer processes. Surface functional groups contribute to the overall electron flux of pyrogenic carbon to a lesser extent with greater pyrolysis temperature due to lower charging and discharging capacities, although the charging and discharging kinetics remain unchanged. This study could spur the development of a new generation of biogeochemical electron flux models that focus on the bacteria–carbon–mineral conductive network. Electron transfer reactions govern most biogeochemical processes, yet we have a limited knowledge of the electrochemistry of pyrogenic carbon, a major component of organic matter. Here, the authors quantify electron transfers between pyrogenic carbon and mineral phases under different pyrolysis temperatures.
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Affiliation(s)
- Tianran Sun
- Department of Soil and Crop Sciences, School of Integrated Plant Sciences, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York 14853, USA
| | - Barnaby D A Levin
- School of Applied and Engineering Physics, College of Engineering, Cornell University, Ithaca, New York 14853, USA
| | - Juan J L Guzman
- Department of Biological and Environmental Engineering, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York 14853, USA
| | - Akio Enders
- Department of Soil and Crop Sciences, School of Integrated Plant Sciences, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York 14853, USA
| | - David A Muller
- School of Applied and Engineering Physics, College of Engineering, Cornell University, Ithaca, New York 14853, USA.,Kavli Institute for Nanoscale Science, Cornell University, Ithaca, New York 14853, USA
| | - Largus T Angenent
- Department of Biological and Environmental Engineering, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York 14853, USA.,Atkinson Center for a Sustainable Future, Cornell University, Ithaca, New York 14583, USA.,Center for Applied Geosciences, University of Tübingen, Tübingen, 72074, Germany
| | - Johannes Lehmann
- Department of Soil and Crop Sciences, School of Integrated Plant Sciences, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York 14853, USA.,Atkinson Center for a Sustainable Future, Cornell University, Ithaca, New York 14583, USA
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304
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Liu G, Qiu S, Liu B, Pu Y, Gao Z, Wang J, Jin R, Zhou J. Microbial reduction of Fe(III)-bearing clay minerals in the presence of humic acids. Sci Rep 2017; 7:45354. [PMID: 28358048 PMCID: PMC5371790 DOI: 10.1038/srep45354] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 02/23/2017] [Indexed: 11/09/2022] Open
Abstract
Both Fe(III)-bearing clay minerals and humic acids (HAs) are abundant in the soils and sediments. Previous studies have shown that bioreduction of structural Fe(III) in clay minerals could be accelerated by adding anthraquinone compound as a redox-active surrogate of HAs. However, a quinoid analogue could not reflect the adsorption and complexation properties of HA, and little is known about the effects of real HAs at environmental concentration on bioreduction of clay minerals. Here, it was shown that 10-200 mg l-1 of natural or artificially synthesized HAs could effectively stimulate the bioreduction rate and extent of Fe(III) in both iron-rich nontronite NAu-2 and iron-deficient montmorillonite SWy-2. After adsorption to NAu-2, electron-transfer activities of different HA fractions were compared. Additionally, Fe(II) complexation by HAs also contributed to improvement of clay-Fe(III) bioreduction. Spectrosopic and morphological analyses suggested that HA addition accelerated the transformation of NAu-2 to illite, silica and siderite after reductive dissolution.
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Affiliation(s)
- Guangfei Liu
- Key Laboratory of Industrial Ecology and Environmental Engineering, Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Shuang Qiu
- Key Laboratory of Industrial Ecology and Environmental Engineering, Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Baiqing Liu
- Key Laboratory of Industrial Ecology and Environmental Engineering, Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Yiying Pu
- Key Laboratory of Industrial Ecology and Environmental Engineering, Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Zhanming Gao
- Chemistry Analysis &Research Center, Faculty of Chemical, Environmental &Biological Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Jing Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering, Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Ruofei Jin
- Key Laboratory of Industrial Ecology and Environmental Engineering, Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Jiti Zhou
- Key Laboratory of Industrial Ecology and Environmental Engineering, Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
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305
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Kappler A, Bryce C. Cryptic biogeochemical cycles: unravelling hidden redox reactions. Environ Microbiol 2017; 19:842-846. [DOI: 10.1111/1462-2920.13687] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Andreas Kappler
- Geomicrobiology; Center for Applied Geosciences, University of Tuebingen; Germany
| | - Casey Bryce
- Geomicrobiology; Center for Applied Geosciences, University of Tuebingen; Germany
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306
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Andjelkovic I, Azari S, Erkelens M, Forward P, Lambert MF, Losic D. Bacterial iron-oxide nanowires from biofilm waste as a new adsorbent for the removal of arsenic from water. RSC Adv 2017. [DOI: 10.1039/c6ra26379h] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Biofilm waste material generated by the bacteria in the groundwater pipelines was found is composed of amorphous twisted iron-oxide nanowires which are shown to have considerable adsorption properties for removal As(iii) and As(v) ions from waters.
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Affiliation(s)
- Ivan Andjelkovic
- School of Chemical Engineering
- University of Adelaide
- Adelaide
- Australia
- Innovation Center of the Faculty of Chemistry
| | - Sara Azari
- School of Chemical Engineering
- University of Adelaide
- Adelaide
- Australia
| | - Mason Erkelens
- School of Chemical Engineering
- University of Adelaide
- Adelaide
- Australia
| | | | - Martin F. Lambert
- School of Civil, Environmental and Mining Engineering
- University of Adelaide
- Adelaide
- Australia
| | - Dusan Losic
- School of Chemical Engineering
- University of Adelaide
- Adelaide
- Australia
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307
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Hu M, Chen P, Sun W, Li F, Cui J. A novel organotrophic nitrate-reducing Fe(ii)-oxidizing bacterium isolated from paddy soil and draft genome sequencing indicate its metabolic versatility. RSC Adv 2017. [DOI: 10.1039/c7ra09328d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Physiological and genomic information of this strain provide preliminary evidence for nitrate-reduction coupled Fe(ii)-oxidation in microorganisms from paddy soil.
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Affiliation(s)
- Min Hu
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management
- Guangdong Institute of Eco-Environmental Science & Technology
- Guangzhou 510650
- P. R. China
| | - Pengcheng Chen
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management
- Guangdong Institute of Eco-Environmental Science & Technology
- Guangzhou 510650
- P. R. China
- Guangzhou Institute of Geochemistry
| | - Weimin Sun
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management
- Guangdong Institute of Eco-Environmental Science & Technology
- Guangzhou 510650
- P. R. China
| | - Fangbai Li
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management
- Guangdong Institute of Eco-Environmental Science & Technology
- Guangzhou 510650
- P. R. China
| | - Jianghu Cui
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management
- Guangdong Institute of Eco-Environmental Science & Technology
- Guangzhou 510650
- P. R. China
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308
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Shirokova VL, Enright AML, Kennedy CB, Ferris FG. Thermal intensification of microbial Fe(II)/Fe(III) redox cycling in a pristine shallow sand aquifer on the Canadian Shield. WATER RESEARCH 2016; 106:604-612. [PMID: 27780075 DOI: 10.1016/j.watres.2016.10.050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 10/18/2016] [Accepted: 10/19/2016] [Indexed: 06/06/2023]
Abstract
This investigation evaluates spatial relationships between summer (July) groundwater temperatures and Fe(II)/Fe(III) biogeochemical cycling over a five year period in a shallow pristine sand aquifer at Meilleurs Bay near Deep River, Ontario, Canada. A warm subsurface thermal island of 12.5-16.1 °C, compared to background conditions of 10-11 °C, was manifest in contour maps of average groundwater temperature over the study period. The warm zone coincided with an area of convergent groundwater flow, implicating horizontal heat transfer by advective convection as the reason for elevated temperatures. Additionally, high concentrations of dissolved Fe(II) and Fe(III) overlapped the warm thermal island, indicative of increased rates of bacterial Fe(II)-oxidation and Fe(III)-reduction. A depletion in the modal abundance of Fe(II)-bearing minerals, notably amphibole and biotite, inside the area of the warm thermal island was also observed, suggesting enhanced mineral dissolution owing to chemoautotrophic Fe(II)-oxidation coupled to the reduction and fixation of dissolved inorganic carbon as biomass. Throughout the aquifer, redox conditions were poised in terms of Eh and pH close to equilibrium with respect to the Fe(II)/Fe(OH)3 couple, feasibly enabling simultaneous bacterial Fe(II)-oxidation and Fe(III)-reduction with an adequate supply of electron acceptors and donors, respectively. The significance of higher groundwater temperature as a determinant of elevated dissolved Fe(II) and Fe(III) concentrations induced by thermal intensification of microbial biogeochemical activities yielded Pearson product-moment correlations in which temperature alone, as a single independent variable, explains almost 30 to nearly 60 percent of the variation in the measured dissolved Fe(II) and Fe(III) concentrations in the groundwater. These results emphasize the important influence of thermal conditions on biogeochemical processes in aquifers coupled to the development of steep gradients in groundwater quality over short distances in shallow unconfined groundwater systems.
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Affiliation(s)
- V L Shirokova
- Department of Earth Sciences, University of Toronto, 22 Russell Street, M5S 3B1, Toronto, Ontario, Canada
| | - A M L Enright
- Department of Earth Sciences, University of Toronto, 22 Russell Street, M5S 3B1, Toronto, Ontario, Canada
| | - C B Kennedy
- Department of Earth Sciences, University of Toronto, 22 Russell Street, M5S 3B1, Toronto, Ontario, Canada
| | - F G Ferris
- Department of Earth Sciences, University of Toronto, 22 Russell Street, M5S 3B1, Toronto, Ontario, Canada.
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309
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Koch C, Harnisch F. What Is the Essence of Microbial Electroactivity? Front Microbiol 2016; 7:1890. [PMID: 27933052 PMCID: PMC5122576 DOI: 10.3389/fmicb.2016.01890] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 11/11/2016] [Indexed: 11/13/2022] Open
Affiliation(s)
- Christin Koch
- Department of Environmental Microbiology, UFZ-Helmholtz Centre for Environmental Research Leipzig, Germany
| | - Falk Harnisch
- Department of Environmental Microbiology, UFZ-Helmholtz Centre for Environmental Research Leipzig, Germany
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310
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Scott JJ, Glazer BT, Emerson D. Bringing microbial diversity into focus: high-resolution analysis of iron mats from the Lō'ihi Seamount. Environ Microbiol 2016; 19:301-316. [PMID: 27871143 DOI: 10.1111/1462-2920.13607] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 10/27/2016] [Accepted: 11/16/2016] [Indexed: 01/22/2023]
Abstract
Thirty kilometers south of the island of Hawai'i lies the Lō'ihi Seamount, an active submarine volcano that hosts a network of low-temperature hydrothermal vents enriched in ferrous iron that supports extensive microbial mats. These mats, which can be a half a meter deep, are composed of ferric iron bound to organic polymers - the metabolic byproduct of iron-oxidizing Zetaproteobacteria. Though the role of Zetaproteobacteria in mat formation is well established, we have a limited understanding of how differences in diversity are related to mat morphology. We used Minimum Entropy Decomposition and ZetaOtu classification to demonstrate cryptic diversity between closely related Zetaproteobacteria while showing habitat and geographic specificity. Veiled mats, common structures at Lō'ihi, exhibit distinct community composition and contain diversity not detected in other mat types, including specific Zetaproteobacteria and an unclassified Gammaproteobacteria. Our analyses also indicate that diversity can change dramatically across small spatial transects from points of active venting, yet we found comparatively few differences between major sampling sites. This study provides a better picture of the microbiome responsible for iron mat production at Lō'ihi and has broad implications for our understanding of these globally distributed communities.
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Affiliation(s)
- Jarrod J Scott
- Ocean Microbiome & Blue Biotechnology Center, Bigelow Laboratory for Ocean Sciences, PO Box 380, East Boothbay, ME, 04544, USA
| | - Brian T Glazer
- Department of Oceanography, University of Hawai'i at Mānoa, 1000 Pope Rd. Honolulu, HI, 96822, USA
| | - David Emerson
- Ocean Microbiome & Blue Biotechnology Center, Bigelow Laboratory for Ocean Sciences, PO Box 380, East Boothbay, ME, 04544, USA
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311
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Yang Z, Kappler A, Jiang J. Reducing Capacities and Distribution of Redox-Active Functional Groups in Low Molecular Weight Fractions of Humic Acids. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:12105-12113. [PMID: 27759370 DOI: 10.1021/acs.est.6b02645] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Humic substances (HS) are redox-active organic compounds with a broad spectrum of molecular sizes and reducing capacities, that is, number of electrons donated or accepted. However, it is unknown which role the distribution of redox-active functional groups in different molecule sizes plays for HS redox reactions in varying pore sizes microenvironments. We used dialysis experiments to separate bulk humic acids (HA) into low molecular weight fractions (LMWF) and retentate, for example, the remaining HA in the dialysis bag. LMWF accounted for only 2% of the total organic carbon content of the HA. However, their reducing capacities per gram of carbon were up to 33 times greater than either those of the bulk HA or the retentate. For a structural/mechanistic understanding of the high reducing capacity of the LMWF, we used fluorescence spectroscopy. We found that the LWMF showed significant fluorescence intensities for quinone-like functional groups, as indicated by the quinoid π-π* transition, that are probably responsible for the high reducing capacities. Therefore, the small-sized HS fraction can play a major role for redox transformation of metals or pollutants trapped in soil micropores (<2.5 nm diameter).
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Affiliation(s)
- Zhen Yang
- College of Environmental Science and Engineering, Beijing Forestry University , Beijing 100083, China
| | - Andreas Kappler
- Geomicrobiology Group, Center for Applied Geosciences, University of Tüebingen , 72074 Tüebingen, Germany
| | - Jie Jiang
- College of Environmental Science and Engineering, Beijing Forestry University , Beijing 100083, China
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312
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Berg JS, Michellod D, Pjevac P, Martinez-Perez C, Buckner CRT, Hach PF, Schubert CJ, Milucka J, Kuypers MMM. Intensive cryptic microbial iron cycling in the low iron water column of the meromictic Lake Cadagno. Environ Microbiol 2016; 18:5288-5302. [DOI: 10.1111/1462-2920.13587] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 10/18/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Jasmine S. Berg
- Max Planck Institute for Marine Microbiology; Bremen 28359 Germany
| | - Dolma Michellod
- Max Planck Institute for Marine Microbiology; Bremen 28359 Germany
| | - Petra Pjevac
- Max Planck Institute for Marine Microbiology; Bremen 28359 Germany
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science; University of Vienna; Vienna Austria
| | | | | | - Philipp F. Hach
- Max Planck Institute for Marine Microbiology; Bremen 28359 Germany
| | - Carsten J. Schubert
- Eawag, Swiss Federal Institute of Aquatic Science and Technology; Kastanienbaum Switzerland
| | - Jana Milucka
- Max Planck Institute for Marine Microbiology; Bremen 28359 Germany
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313
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Oswald K, Jegge C, Tischer J, Berg J, Brand A, Miracle MR, Soria X, Vicente E, Lehmann MF, Zopfi J, Schubert CJ. Methanotrophy under Versatile Conditions in the Water Column of the Ferruginous Meromictic Lake La Cruz (Spain). Front Microbiol 2016; 7:1762. [PMID: 27891115 PMCID: PMC5104750 DOI: 10.3389/fmicb.2016.01762] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 10/20/2016] [Indexed: 11/13/2022] Open
Abstract
Lakes represent a considerable natural source of methane to the atmosphere compared to their small global surface area. Methanotrophs in sediments and in the water column largely control methane fluxes from these systems, yet the diversity, electron accepting capacity, and nutrient requirements of these microorganisms have only been partially identified. Here, we investigated the role of electron acceptors alternative to oxygen and sulfate in microbial methane oxidation at the oxycline and in anoxic waters of the ferruginous meromictic Lake La Cruz, Spain. Active methane turnover in a zone extending well below the oxycline was evidenced by stable carbon isotope-based rate measurements. We observed a strong methane oxidation potential throughout the anoxic water column, which did not vary substantially from that at the oxic/anoxic interface. Both in the redox-transition and anoxic zones, only aerobic methane-oxidizing bacteria (MOB) were detected by fluorescence in situ hybridization and sequencing techniques, suggesting a close coupling of cryptic photosynthetic oxygen production and aerobic methane turnover. Additions of nitrate, nitrite and to a lesser degree iron and manganese oxides also stimulated bacterial methane consumption. We could not confirm a direct link between the reduction of these compounds and methane oxidation and we cannot exclude the contribution of unknown anaerobic methanotrophs. Nevertheless, our findings from Lake La Cruz support recent laboratory evidence that aerobic methanotrophs may be able to utilize alternative terminal electron acceptors under oxygen limitation.
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Affiliation(s)
- Kirsten Oswald
- Department of Surface Waters - Research and Management, Swiss Federal Institute of Aquatic Science and TechnologyKastanienbaum, Switzerland; Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, Swiss Federal Institute of TechnologyZurich, Switzerland
| | - Corinne Jegge
- Department of Surface Waters - Research and Management, Swiss Federal Institute of Aquatic Science and TechnologyKastanienbaum, Switzerland; School of Architecture, Civil and Environmental Engineering, EPFL, Swiss Federal Institute of TechnologyLausanne, Switzerland
| | - Jana Tischer
- Department of Environmental Sciences, University of Basel Basel, Switzerland
| | - Jasmine Berg
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Andreas Brand
- Department of Surface Waters - Research and Management, Swiss Federal Institute of Aquatic Science and TechnologyKastanienbaum, Switzerland; Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, Swiss Federal Institute of TechnologyZurich, Switzerland
| | - María R Miracle
- Department of Microbiology and Ecology, Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia Burjassot, Spain
| | - Xavier Soria
- Department of Microbiology and Ecology, Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia Burjassot, Spain
| | - Eduardo Vicente
- Department of Microbiology and Ecology, Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia Burjassot, Spain
| | - Moritz F Lehmann
- Department of Environmental Sciences, University of Basel Basel, Switzerland
| | - Jakob Zopfi
- Department of Environmental Sciences, University of Basel Basel, Switzerland
| | - Carsten J Schubert
- Department of Surface Waters - Research and Management, Swiss Federal Institute of Aquatic Science and Technology Kastanienbaum, Switzerland
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314
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Enright AML, Ferris FG. Fluctuation Analysis of Redox Potential to Distinguish Microbial Fe(II) Oxidation. ASTROBIOLOGY 2016; 16:846-852. [PMID: 27827533 DOI: 10.1089/ast.2016.1509] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We developed a novel method for distinguishing abiotic and biological iron oxidation in liquid media using oxidation-reduction (redox) potential time series data. The instrument and processing algorithm were tested by immersing the tip of a Pt electrode with an Ag-AgCl reference electrode into an active iron-oxidizing biofilm in a groundwater discharge zone, as well as in two abiotic systems: a killed sample and a chemical control from the same site. We used detrended fluctuation analysis to characterize average root mean square fluctuation behavior, which was distinct in the live system. The calculated α value scaling exponents determined by detrended fluctuation analysis were significantly different at p < 0.001. This indicates that time series of electrode response data may be used to distinguish live and abiotic chemical reaction pathways. Due to the simplicity, portability, and small size, it may be suitable for characterization of extraterrestrial environments where water has been observed, such as Mars and Europa. Key Words: Oxidation-reduction potential-Detrended fluctuation analysis-Iron-oxidizing bacteria. Astrobiology 16, 846-852.
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Affiliation(s)
- A M L Enright
- Department of Earth Sciences, University of Toronto , Toronto, Canada
| | - F G Ferris
- Department of Earth Sciences, University of Toronto , Toronto, Canada
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315
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Shopska M, Paneva D, Kadinov G, Cherkezova-Zheleva Z, Mitov I, Iliev M. Study on the Composition of Biogenic Iron-Containing Materials Obtained Under Cultivation of the Leptothrix sp. on Different Media. Appl Biochem Biotechnol 2016; 181:867-883. [PMID: 27696336 DOI: 10.1007/s12010-016-2255-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 09/19/2016] [Indexed: 10/20/2022]
Abstract
The biogenic iron oxide/hydroxide materials possess useful combination of physicochemical properties and are considered for application in various areas. Their production does not require special investments because these compounds are formed during cultivation of neurophilic iron bacteria. Bacteria from genus Leptothrix develop intensively in the Sphaerotilus-Leptothrix group of bacteria isolation medium and feeding media of Fedorov and Lieske. These media are different in their composition which determined the present study as an attempt to clear up the reasons that define the differences in the composition of the laboratory-obtained biomasses and the natural biomass finds. FTIRS, Mössbauer spectroscopy, and XRD were used in the research. Comparative analysis showed that the biomass and control samples contain iron compounds (α-FeOOH, γ-FeOOH, β-FeOOH, γ-Fe2O3) in different ratios. The biomass samples were enriched in oxyhydroxides of higher dispersion. Organic residuals of bacterial origin, SO4, CO3, and PO4 groups were registered in the biogenic materials.
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Affiliation(s)
- M Shopska
- Institute of Catalysis, Bulgarian Academy of Sciences, Acad. G. Bonchev St., Bldg. 11, 1113, Sofia, Bulgaria.
| | - D Paneva
- Institute of Catalysis, Bulgarian Academy of Sciences, Acad. G. Bonchev St., Bldg. 11, 1113, Sofia, Bulgaria
| | - G Kadinov
- Institute of Catalysis, Bulgarian Academy of Sciences, Acad. G. Bonchev St., Bldg. 11, 1113, Sofia, Bulgaria
| | - Z Cherkezova-Zheleva
- Institute of Catalysis, Bulgarian Academy of Sciences, Acad. G. Bonchev St., Bldg. 11, 1113, Sofia, Bulgaria
| | - I Mitov
- Institute of Catalysis, Bulgarian Academy of Sciences, Acad. G. Bonchev St., Bldg. 11, 1113, Sofia, Bulgaria
| | - M Iliev
- Faculty of Biology, St. Kliment Ohridski University of Sofia, 8 Dragan Tsankov Blvd, 1164, Sofia, Bulgaria
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316
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Dong Y, Sanford RA, Boyanov MI, Kemner KM, Flynn TM, O’Loughlin EJ, Locke RA, Weber JR, Egan SM, Fouke BW. Tepidibacillus decaturensis sp. nov., a microaerophilic, moderately thermophilic iron-reducing bacterium isolated from 1.7 km depth groundwater. Int J Syst Evol Microbiol 2016; 66:3964-3971. [DOI: 10.1099/ijsem.0.001295] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yiran Dong
- Department of Geology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Robert A. Sanford
- Department of Geology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Maxim I. Boyanov
- Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
- Institute of Chemical Engineering, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | | | | | | | - Randall A. Locke
- Illinois State Geology Survey, University of Illinois Urbana-Champaign, Champaign, IL, USA
| | - Joseph R. Weber
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Sheila M. Egan
- Department of Biochemistry, University of Illinois Urbana-Champaign, Champaign, IL, USA
| | - Bruce W. Fouke
- Department of Geology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Illinois State Geology Survey, University of Illinois Urbana-Champaign, Champaign, IL, USA
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317
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Evidence for the Existence of Autotrophic Nitrate-Reducing Fe(II)-Oxidizing Bacteria in Marine Coastal Sediment. Appl Environ Microbiol 2016; 82:6120-6131. [PMID: 27496777 PMCID: PMC5068159 DOI: 10.1128/aem.01570-16] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 08/02/2016] [Indexed: 11/23/2022] Open
Abstract
Nitrate-reducing Fe(II)-oxidizing microorganisms were described for the first time ca. 20 years ago. Most pure cultures of nitrate-reducing Fe(II) oxidizers can oxidize Fe(II) only under mixotrophic conditions, i.e., when an organic cosubstrate is provided. A small number of nitrate-reducing Fe(II)-oxidizing cultures have been proposed to grow autotrophically, but unambiguous evidence for autotrophy has not always been provided. Thus, it is still unclear whether or to what extent Fe(II) oxidation coupled to nitrate reduction is an enzymatically catalyzed and energy-yielding autotrophic process or whether Fe(II) is abiotically oxidized by nitrite from heterotrophic nitrate reduction. The aim of the present study was to find evidence for the existence of autotrophic nitrate-reducing Fe(II) oxidizers in coastal marine sediments. Microcosm incubations showed that with increasing incubation times, the stoichiometric ratio of reduced nitrate/oxidized Fe(II) [NO3−reduced/Fe(II)oxidized] decreased, indicating a decreasing contribution of heterotrophic denitrification and/or an increasing contribution of autotrophic nitrate-reducing Fe(II) oxidation over time. After incubations of sediment slurries for >10 weeks, nitrate-reducing activity ceased, although nitrate was still present. This suggests that heterotrophic nitrate reduction had ceased due to the depletion of readily available organic carbon. However, after the addition of Fe(II) to these batch incubation mixtures, the nitrate-reducing activity resumed, and Fe(II) was oxidized, indicating the activity of autotrophic nitrate-reducing Fe(II) oxidizers. The concurrent reduction of 14C-labeled bicarbonate concentrations unambiguously proved that autotrophic C fixation occurred during Fe(II) oxidation and nitrate reduction. Our results clearly demonstrated that autotrophic nitrate-reducing Fe(II)-oxidizing bacteria were present in the investigated coastal marine sediments.
IMPORTANCE Twenty years after the discovery of nitrate-reducing Fe(II) oxidizers, it is still controversially discussed whether autotrophic nitrate-reducing Fe(II)-oxidizing microorganisms exist and to what extent Fe(II) oxidation in this reduction/oxidation process is enzymatically catalyzed or which role abiotic side reactions of Fe(II) with reactive N species play. Most pure cultures of nitrate-reducing Fe(II) oxidizers are mixotrophic; i.e., they need an organic cosubstrate to maintain their activity over several cultural transfers. For the few existing autotrophic isolates and enrichment cultures, either the mechanism of nitrate-reducing Fe(II) oxidation is not known or evidence for their autotrophic lifestyle is controversial. In the present study, we provide evidence for the existence of autotrophic nitrate-reducing Fe(II) oxidizers in coastal marine sediments. The evidence is based on stoichiometries of nitrate reduction and Fe(II) oxidation determined in microcosm incubations and the incorporation of carbon from CO2 under conditions that favor the activity of nitrate-reducing Fe(II) oxidizers.
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318
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Sun J, Chillrud SN, Mailloux BJ, Bostick BC. In Situ Magnetite Formation and Long-Term Arsenic Immobilization under Advective Flow Conditions. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:10162-71. [PMID: 27533278 PMCID: PMC5725337 DOI: 10.1021/acs.est.6b02362] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
In situ precipitation of magnetite and other minerals potentially sequesters dissolved arsenic (As) in contaminated aquifers. This study examines As retention and transport in aquifer sediments using a multistage column experiment in which magnetite and other minerals formed from added nitrate and ferrous iron (Fe). Sediments were collected from the Dover Municipal Landfill Superfund site. Prior to nitrate-Fe(II) addition, As was not effectively retained within the sediments in the column. The combination of nitrate (10 mM) and Fe(II) (4 mM), resulted in mineral precipitation and rapidly decreased effluent As concentrations to <10 μg L(-1). Mineralogical analyses of sectioned replicate columns using sequential extractions, magnetic susceptibility and X-ray absorption spectroscopy indicate that magnetite and ferrihydrite formed in the column following nitrate-Fe(II) addition. This magnetite persisted in the column even as conditions became reducing, whereas ferrihydrite was transformed to more stable Fe oxides. This magnetite incorporated As into its structure during precipitation and subsequently adsorbed As. Adsorption to the minerals kept effluent As concentrations <10 μg L(-1) for more than 100 pore volumes despite considerable Fe reduction. The results indicate that it should be feasible to produce an in situ reactive filter by nitrate-Fe(II) injection.
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Affiliation(s)
- Jing Sun
- Department of Earth and Environmental Sciences, Columbia University, Mail Code 5505, New York, New York 10027, United States
- Lamont-Doherty Earth Observatory, PO Box 1000, 61 Route 9W, Palisades, New York 10964, United States
| | - Steven N. Chillrud
- Lamont-Doherty Earth Observatory, PO Box 1000, 61 Route 9W, Palisades, New York 10964, United States
| | - Brian J. Mailloux
- Department of Environmental Sciences, Barnard College, 3009 Broadway, New York, New York 10027, United States
| | - Benjamin C. Bostick
- Lamont-Doherty Earth Observatory, PO Box 1000, 61 Route 9W, Palisades, New York 10964, United States
- Corresponding Author: Phone: (+1) 845-365-8659; fax: (+1) 845-365-8155;
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319
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Chan CS, Emerson D, Luther GW. The role of microaerophilic Fe-oxidizing micro-organisms in producing banded iron formations. GEOBIOLOGY 2016; 14:509-528. [PMID: 27392195 DOI: 10.1111/gbi.12192] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 04/25/2016] [Indexed: 06/06/2023]
Abstract
Despite the historical and economic significance of banded iron formations (BIFs), we have yet to resolve the formation mechanisms. On modern Earth, neutrophilic microaerophilic Fe-oxidizing micro-organisms (FeOM) produce copious amounts of Fe oxyhydroxides, leading us to wonder whether similar organisms played a role in producing BIFs. To evaluate this, we review the current knowledge of modern microaerophilic FeOM in the context of BIF paleoenvironmental studies. In modern environments wherever Fe(II) and O2 co-exist, microaerophilic FeOM proliferate. These organisms grow in a variety of environments, including the marine water column redoxcline, which is where BIF precursor minerals likely formed. FeOM can grow across a range of O2 concentrations, measured as low as 2 μm to date, although lower concentrations have not been tested. While some extant FeOM can tolerate high O2 concentrations, many FeOM appear to prefer and thrive at low O2 concentrations (~3-25 μm). These are similar to the estimated dissolved O2 concentrations in the few hundred million years prior to the 'Great Oxidation Event' (GOE). We compare biotic and abiotic Fe oxidation kinetics in the presence of varying levels of O2 and show that microaerophilic FeOM contribute substantially to Fe oxidation, at rates fast enough to account for BIF deposition. Based on this synthesis, we propose that microaerophilic FeOM were capable of playing a significant role in depositing the largest, most well-known BIFs associated with the GOE, as well as afterward when global O2 levels increased.
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Affiliation(s)
- C S Chan
- Department of Geological Sciences, University of Delaware, and the Delaware Biotechnology Institute, Newark, DE, USA
- School of Marine Science and Policy, University of Delaware, Newark & Lewes, DE, USA
| | - D Emerson
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - G W Luther
- School of Marine Science and Policy, University of Delaware, Newark & Lewes, DE, USA
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320
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Extracellular electron transfer mechanisms between microorganisms and minerals. Nat Rev Microbiol 2016; 14:651-62. [DOI: 10.1038/nrmicro.2016.93] [Citation(s) in RCA: 850] [Impact Index Per Article: 106.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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321
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Gorski CA, Edwards R, Sander M, Hofstetter TB, Stewart SM. Thermodynamic Characterization of Iron Oxide-Aqueous Fe(2+) Redox Couples. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:8538-47. [PMID: 27427506 DOI: 10.1021/acs.est.6b02661] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Iron is present in virtually all terrestrial and aquatic environments, where it participates in redox reactions with surrounding metals, organic compounds, contaminants, and microorganisms. The rates and extent of these redox reactions strongly depend on the speciation of the Fe2+ and Fe3+ phases, although the underlying reasons remain unclear. In particular, numerous studies have observed that Fe2+ associated with iron oxide surfaces (i.e., oxide-associated Fe2+) often reduces oxidized contaminants much faster than aqueous Fe2+ alone. Here, we tested two hypotheses related to this observation by determining if solutions containing two commonly studied iron oxides—hematite and goethite—and aqueous Fe2+ reached thermodynamic equilibrium over the course of a day. We measured reduction potential (EH) values in solutions containing these oxides at different pH values and aqueous Fe2+ concentrations using mediated potentiometry. This analysis yielded standard reduction potential (EH0) values of 768 ± 1 mV for the aqueous Fe2+–goethite redox couple and 769 ± 2 mV for the aqueous Fe2+–hematite redox couple. These values were in excellent agreement with those calculated from existing thermodynamic data, and the data could be explained by the presence of an iron oxide lowering EH values of aqueous Fe3+/Fe2+ redox couples.
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Affiliation(s)
- Christopher A Gorski
- Department of Civil & Environmental Engineering, Pennsylvania State University , 212 Sackett Building, University Park, Pennsylvania 16802, United States
| | - Rebecca Edwards
- Department of Civil & Environmental Engineering, Pennsylvania State University , 212 Sackett Building, University Park, Pennsylvania 16802, United States
| | - Michael Sander
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), Swiss Federal Institute of Technology, ETH Zürich , 8092 Zürich, Switzerland
| | - Thomas B Hofstetter
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), Swiss Federal Institute of Technology, ETH Zürich , 8092 Zürich, Switzerland
- Eawag, Swiss Federal Institute of Aquatic Science and Technology , CH-8600 Dübendorf, Switzerland
| | - Sydney M Stewart
- Department of Civil & Environmental Engineering, Pennsylvania State University , 212 Sackett Building, University Park, Pennsylvania 16802, United States
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322
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Size dependent microbial oxidation and reduction of magnetite nano- and micro-particles. Sci Rep 2016; 6:30969. [PMID: 27492680 PMCID: PMC4974511 DOI: 10.1038/srep30969] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 07/12/2016] [Indexed: 01/30/2023] Open
Abstract
The ability for magnetite to act as a recyclable electron donor and acceptor for Fe-metabolizing bacteria has recently been shown. However, it remains poorly understood whether microbe-mineral interfacial electron transfer processes are limited by the redox capacity of the magnetite surface or that of whole particles. Here we examine this issue for the phototrophic Fe(II)-oxidizing bacteria Rhodopseudomonas palustris TIE-1 and the Fe(III)-reducing bacteria Geobacter sulfurreducens, comparing magnetite nanoparticles (d ≈ 12 nm) against microparticles (d ≈ 100–200 nm). By integrating surface-sensitive and bulk-sensitive measurement techniques we observed a particle surface that was enriched in Fe(II) with respect to a more oxidized core. This enables microbial Fe(II) oxidation to occur relatively easily at the surface of the mineral suggesting that the electron transfer is dependent upon particle size. However, microbial Fe(III) reduction proceeds via conduction of electrons into the particle interior, i.e. it can be considered as more of a bulk electron transfer process that is independent of particle size. The finding has potential implications on the ability of magnetite to be used for long range electron transport in soils and sediments.
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323
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Kumeria T, Maher S, Wang Y, Kaur G, Wang L, Erkelens M, Forward P, Lambert MF, Evdokiou A, Losic D. Naturally Derived Iron Oxide Nanowires from Bacteria for Magnetically Triggered Drug Release and Cancer Hyperthermia in 2D and 3D Culture Environments: Bacteria Biofilm to Potent Cancer Therapeutic. Biomacromolecules 2016; 17:2726-36. [DOI: 10.1021/acs.biomac.6b00786] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Shaheer Maher
- Faculty
of Pharmacy, Assiut University, Assiut, 71526, Egypt
| | | | | | | | | | - Peter Forward
- South Australian (SA)
Water, Adelaide, SA-5005, Australia
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324
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Laufer K, Byrne JM, Glombitza C, Schmidt C, Jørgensen BB, Kappler A. Anaerobic microbial Fe(II) oxidation and Fe(III) reduction in coastal marine sediments controlled by organic carbon content. Environ Microbiol 2016; 18:3159-74. [DOI: 10.1111/1462-2920.13387] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Revised: 05/18/2016] [Accepted: 05/20/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Katja Laufer
- Geomicrobiology, Center for Applied Geosciences; University of Tuebingen; Tuebingen Germany
| | - James M. Byrne
- Geomicrobiology, Center for Applied Geosciences; University of Tuebingen; Tuebingen Germany
| | - Clemens Glombitza
- Department of Bioscience; Center for Geomicrobiology, Aarhus University; Aarhus Denmark
| | - Caroline Schmidt
- Geomicrobiology, Center for Applied Geosciences; University of Tuebingen; Tuebingen Germany
| | - Bo Barker Jørgensen
- Department of Bioscience; Center for Geomicrobiology, Aarhus University; Aarhus Denmark
| | - Andreas Kappler
- Geomicrobiology, Center for Applied Geosciences; University of Tuebingen; Tuebingen Germany
- Department of Bioscience; Center for Geomicrobiology, Aarhus University; Aarhus Denmark
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325
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Perez-Garcia O, Lear G, Singhal N. Metabolic Network Modeling of Microbial Interactions in Natural and Engineered Environmental Systems. Front Microbiol 2016; 7:673. [PMID: 27242701 PMCID: PMC4870247 DOI: 10.3389/fmicb.2016.00673] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 04/25/2016] [Indexed: 12/14/2022] Open
Abstract
We review approaches to characterize metabolic interactions within microbial communities using Stoichiometric Metabolic Network (SMN) models for applications in environmental and industrial biotechnology. SMN models are computational tools used to evaluate the metabolic engineering potential of various organisms. They have successfully been applied to design and optimize the microbial production of antibiotics, alcohols and amino acids by single strains. To date however, such models have been rarely applied to analyze and control the metabolism of more complex microbial communities. This is largely attributed to the diversity of microbial community functions, metabolisms, and interactions. Here, we firstly review different types of microbial interaction and describe their relevance for natural and engineered environmental processes. Next, we provide a general description of the essential methods of the SMN modeling workflow including the steps of network reconstruction, simulation through Flux Balance Analysis (FBA), experimental data gathering, and model calibration. Then we broadly describe and compare four approaches to model microbial interactions using metabolic networks, i.e., (i) lumped networks, (ii) compartment per guild networks, (iii) bi-level optimization simulations, and (iv) dynamic-SMN methods. These approaches can be used to integrate and analyze diverse microbial physiology, ecology and molecular community data. All of them (except the lumped approach) are suitable for incorporating species abundance data but so far they have been used only to model simple communities of two to eight different species. Interactions based on substrate exchange and competition can be directly modeled using the above approaches. However, interactions based on metabolic feedbacks, such as product inhibition and synthropy require extensions to current models, incorporating gene regulation and compounding accumulation mechanisms. SMN models of microbial interactions can be used to analyze complex “omics” data and to infer and optimize metabolic processes. Thereby, SMN models are suitable to capitalize on advances in high-throughput molecular and metabolic data generation. SMN models are starting to be applied to describe microbial interactions during wastewater treatment, in-situ bioremediation, microalgae blooms methanogenic fermentation, and bioplastic production. Despite their current challenges, we envisage that SMN models have future potential for the design and development of novel growth media, biochemical pathways and synthetic microbial associations.
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Affiliation(s)
- Octavio Perez-Garcia
- Department of Civil and Environmental Engineering, University of Auckland Auckland, New Zealand
| | - Gavin Lear
- School of Biological Sciences, The University of Auckland Auckland, New Zealand
| | - Naresh Singhal
- Department of Civil and Environmental Engineering, University of Auckland Auckland, New Zealand
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326
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Picard A, Obst M, Schmid G, Zeitvogel F, Kappler A. Limited influence of Si on the preservation of Fe mineral-encrusted microbial cells during experimental diagenesis. GEOBIOLOGY 2016; 14:276-292. [PMID: 26695194 DOI: 10.1111/gbi.12171] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 11/10/2015] [Indexed: 06/05/2023]
Abstract
The reconstruction of the history of microbial life since its emergence on early Earth is impaired by the difficulty to prove the biogenicity of putative microfossils in the rock record. While most of the oldest rocks on Earth have been exposed to different grades of diagenetic alterations, little is known about how the remains of micro-organisms evolve when exposed to pressure (P) and temperature (T) conditions typical of diagenesis. Using spectroscopy and microscopy, we compared morphological, mineralogical, and chemical biosignatures exhibited by Fe mineral-encrusted cells of the bacterium Acidovorax sp. BoFeN1 after long-term incubation under ambient conditions and after experimental diagenesis. We also evaluated the effects of Si on the preservation of microbial cells during the whole process. At ambient conditions, Si affected the morphology but not the identity (goethite) of Fe minerals that formed around cells. Fe-encrusted cells were morphologically well preserved after 1 week at 250 °C-140 MPa and after 16 weeks at 170 °C-120 MPa in the presence or in the absence of Si. Some goethite transformed to hematite and magnetite at 250 °C-140 MPa, but in the presence of Si more goethite was preserved. Proteins-the most abundant cellular components-were preserved over several months at ambient conditions but disappeared after incubations at high temperature and pressure conditions, both in the presence and in the absence of Si. Other organic compounds, such as lipids and extracellular polysaccharides seemed well preserved after exposure to diagenetic conditions. This study provides insights about the composition and potential preservation of microfossils that could have formed in Fe- and Si-rich Precambrian oceans.
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Affiliation(s)
- A Picard
- Center for Applied Geoscience, Eberhard Karls University Tübingen, Tübingen, Germany
| | - M Obst
- Center for Applied Geoscience, Eberhard Karls University Tübingen, Tübingen, Germany
| | - G Schmid
- Center for Applied Geoscience, Eberhard Karls University Tübingen, Tübingen, Germany
| | - F Zeitvogel
- Center for Applied Geoscience, Eberhard Karls University Tübingen, Tübingen, Germany
| | - A Kappler
- Center for Applied Geoscience, Eberhard Karls University Tübingen, Tübingen, Germany
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327
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Yan W, Wang H, Jing C. Adhesion of Shewanella oneidensis MR-1 to Goethite: A Two-Dimensional Correlation Spectroscopic Study. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:4343-4349. [PMID: 27029565 DOI: 10.1021/acs.est.6b00066] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Bacterial adhesion to mineral surfaces is an important but underappreciated process. To decipher the molecular level process and mechanism, the adhesion of Shewanella oneidensis MR-1 cells to goethite was investigated using flow-cell attenuated total reflectance (ATR) Fourier transform infrared (FTIR) spectroscopy coupled with two-dimensional correlation spectroscopy (2D-COS) analysis. The FTIR results indicate that bacterial phosphate-moieties play an important role in the formation of mono- and bidentate inner-sphere complexes, whereas carboxylic groups on cell surface only have a minor contribution to its adhesion. The 2D-COS analysis in short-term (0-120 min) and long-term (2-18 h) stages reveal that the adhesion process was in the following sequence: change in H-bonds of proteins on cell surfaces > formation of monodentate inner-sphere surface complexes > formation of outer-sphere surface complexes > transformation of protein secondary structure on cell surfaces > formation of additional bridging bidentate surface complexes. In addition, the adhesion of MR-1 cells on goethite was pH dependent due to pH impacts on the cell structure and the interface charge. The in situ ATR-FTIR integrated with 2D-COS analysis highlights its great potential in exploring complex surface reactions with microbes involved. These results improve our understanding of microbe-mineral interactions at the molecular level and have significant implications for a series of biogeochemical processes.
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Affiliation(s)
- Wei Yan
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, China
| | - Hongbo Wang
- School of Municipal and Environmental Engineering, Shandong Jianzhu University , Jinan 250101, China
| | - Chuanyong Jing
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, China
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328
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Mejia J, Roden EE, Ginder-Vogel M. Influence of Oxygen and Nitrate on Fe (Hydr)oxide Mineral Transformation and Soil Microbial Communities during Redox Cycling. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:3580-8. [PMID: 26949922 PMCID: PMC5066396 DOI: 10.1021/acs.est.5b05519] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Oscillations between reducing and oxidizing conditions are observed at the interface of anaerobic/oxic and anaerobic/anoxic environments, and are often stimulated by an alternating flux of electron donors (e.g., organic carbon) and electron acceptors (e.g., O2 and NO3(-)). In iron (Fe) rich soils and sediments, these oscillations may stimulate the growth of both Fe-reducing bacteria (FeRB) and Fe-oxidizing bacteria (FeOB), and their metabolism may induce cycling between Fe(II) and Fe(III), promoting the transformation of Fe (hydr)oxide minerals. Here, we examine the mineralogical evolution of lepidocrocite and ferrihydrite, and the adaptation of a natural microbial community to alternating Fe-reducing (anaerobic with addition of glucose) and Fe-oxidizing (with addition of nitrate or air) conditions. The growth of FeRB (e.g., Geobacter) is stimulated under anaerobic conditions in the presence of glucose. However, the abundance of these organisms depends on the availability of Fe(III) (hydr)oxides. Redox cycling with nitrate results in decreased Fe(II) oxidation thereby decreasing the availability of Fe(III) for FeRB. Additionally, magnetite is detected as the main product of both lepidocrocite and ferrihydrite reduction. In contrast, introduction of air results in increased Fe(II) oxidation, increasing the availability of Fe(III) and the abundance of Geobacter. In the lepidocrocite reactors, Fe(II) oxidation by dissolved O2 promotes the formation of ferrihydrite and lepidocrocite, whereas in the ferrihydrite reactors we observe a decrease in magnetite stoichiometry (e.g., oxidation). Understanding Fe (hydr)oxide transformation under environmentally relevant redox cycling conditions provides insight into nutrient availability and transport, contaminant mobility, and microbial metabolism in soils and sediments.
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Affiliation(s)
- Jacqueline Mejia
- Environmental Chemistry and Technology Program, Department of Civil and Environmental Engineering, The University of Wisconsin–Madison, 660 North Park Street, Madison, Wisconsin 53706, United States
| | - Eric E. Roden
- Department of Geoscience, The University of Wisconsin–Madison, 1215 West Dayton Street, Madison, Wisconsin 53706, United States
| | - Matthew Ginder-Vogel
- Environmental Chemistry and Technology Program, Department of Civil and Environmental Engineering, The University of Wisconsin–Madison, 660 North Park Street, Madison, Wisconsin 53706, United States
- Corresponding Author, Matthew Ginder-Vogel. . Phone: 608-262-0768. Fax: 608-262-0454
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Ribolzi O, Rochelle-Newall E, Dittrich S, Auda Y, Newton PN, Rattanavong S, Knappik M, Soulileuth B, Sengtaheuanghoung O, Dance DAB, Pierret A. Land use and soil type determine the presence of the pathogen Burkholderia pseudomallei in tropical rivers. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:7828-7839. [PMID: 26758304 PMCID: PMC4846699 DOI: 10.1007/s11356-015-5943-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 12/07/2015] [Indexed: 06/05/2023]
Abstract
Burkholderia pseudomallei is the bacterium that causes melioidosis in humans. While B. pseudomallei is known to be endemic in South East Asia (SEA), the occurrence of the disease in other parts of the tropics points towards a potentially large global distribution. We investigated the environmental factors that influence the presence (and absence) of B. pseudomallei in a tropical watershed in SEA. Our main objective was to determine whether there is a link between the presence of the organism in the hydrographic network and the upstream soil and land-use type. The presence of B. pseudomallei was determined using a specific quantitative real-time PCR assay following enrichment culture. Land use, soil, geomorphology, and environmental data were then analyzed using partial least squares discriminant analysis (PLSDA) to compare the B. pseudomallei positive and negative sites. Soil type in the surrounding catchment and turbidity had a strong positive influence on the presence (acrisols and luvisols) or absence (ferralsols) of B. pseudomallei. Given the strong apparent links between soil characteristics, water turbidity, and the presence/absence of B. pseudomallei, actions to raise public awareness about factors increasing the risk of exposure should be undertaken in order to reduce the incidence of melioidosis in regions of endemicity.
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Affiliation(s)
- Olivier Ribolzi
- Géosciences Environnement Toulouse (GET), UMR 5563, (IRD, CNRS, UPS), Université de Toulouse, UPS (OMP), CNRS, Toulouse, France.
| | - Emma Rochelle-Newall
- iEES-Paris (IRD-UPMC-CNRS-INRA-UDD-UPEC), Sorbonne Universités, UPMC Univ Paris 06, Institut de Recherche pour le Développement (IRD), case 23, 4 place Jussieu, Paris cedex, 75252, France
| | - Sabine Dittrich
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Yves Auda
- Géosciences Environnement Toulouse (GET), UMR 5563, (IRD, CNRS, UPS), Université de Toulouse, UPS (OMP), CNRS, Toulouse, France
| | - Paul N Newton
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sayaphet Rattanavong
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Michael Knappik
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Bounsamai Soulileuth
- Institute of Ecology and Environmental Science-Paris, Institut de Recherche pour le Développement (IRD), Vientiane, Lao People's Democratic Republic
| | - Oloth Sengtaheuanghoung
- Department of Agricultural Land Management (DALaM), P.O. Box 4199, Ban Nogviengkham, Xaythany District, Vientiane, Lao People's Democratic Republic
| | - David A B Dance
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Alain Pierret
- Institute of Ecology and Environmental Science-Paris, Institut de Recherche pour le Développement (IRD), Vientiane, Lao People's Democratic Republic
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330
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Gauger T, Konhauser K, Kappler A. Protection of Nitrate-Reducing Fe(II)-Oxidizing Bacteria from UV Radiation by Biogenic Fe(III) Minerals. ASTROBIOLOGY 2016; 16:301-310. [PMID: 27027418 DOI: 10.1089/ast.2015.1365] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Due to the lack of an ozone layer in the Archean, ultraviolet radiation (UVR) reached early Earth's surface almost unattenuated; as a consequence, a terrestrial biosphere in the form of biological soil crusts would have been highly susceptible to lethal doses of irradiation. However, a self-produced external screen in the form of nanoparticular Fe(III) minerals could have effectively protected those early microorganisms. In this study, we use viability studies by quantifying colony-forming units (CFUs), as well as Fe(II) oxidation and nitrate reduction rates, to show that encrustation in biogenic and abiogenic Fe(III) minerals can protect a common soil bacteria such as the nitrate-reducing Fe(II)-oxidizing microorganisms Acidovorax sp. strain BoFeN1 and strain 2AN from harmful UVC radiation. Analysis of DNA damage by quantifying cyclobutane pyrimidine dimers (CPD) confirmed the protecting effect by Fe(III) minerals. This study suggests that Fe(II)-oxidizing microorganisms, as would have grown in association with mafic and ultramafic soils/outcrops, would have been able to produce their own UV screen, enabling them to live in terrestrial habitats on early Earth.
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Affiliation(s)
- Tina Gauger
- 1 Geomicrobiology, Center for Applied Geosciences, University of Tübingen , Tübingen, Germany
| | - Kurt Konhauser
- 2 Department of Earth and Atmospheric Sciences, University of Alberta , Edmonton, Canada
| | - Andreas Kappler
- 1 Geomicrobiology, Center for Applied Geosciences, University of Tübingen , Tübingen, Germany
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331
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Characteristics and Kinetic Analysis of AQS Transformation and Microbial Goethite Reduction:Insight into "Redox mediator-Microbe-Iron oxide" Interaction Process. Sci Rep 2016; 6:23718. [PMID: 27020166 PMCID: PMC4810424 DOI: 10.1038/srep23718] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 03/14/2016] [Indexed: 11/22/2022] Open
Abstract
The characteristics and kinetics of redox transformation of a redox mediator, anthraquinone-2-sulfonate (AQS), during microbial goethite reduction by Shewanella decolorationis S12, a dissimilatory iron reduction bacterium (DIRB), were investigated to provide insights into “redox mediator-iron oxide” interaction in the presence of DIRB. Two pre-incubation reaction systems of the “strain S12- goethite” and the “strain S12-AQS” were used to investigate the dynamics of goethite reduction and AQS redox transformation. Results show that the concentrations of goethite and redox mediator, and the inoculation cell density all affect the characteristics of microbial goethite reduction, kinetic transformation between oxidized and reduced species of the redox mediator. Both abiotic and biotic reactions and their coupling regulate the kinetic process for “Quinone-Iron” interaction in the presence of DIRB. Our results provide some new insights into the characteristics and mechanisms of interaction among “quinone-DIRB- goethite” under biotic/abiotic driven.
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332
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Lv J, Zhang S, Wang S, Luo L, Cao D, Christie P. Molecular-Scale Investigation with ESI-FT-ICR-MS on Fractionation of Dissolved Organic Matter Induced by Adsorption on Iron Oxyhydroxides. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:2328-36. [PMID: 26815589 DOI: 10.1021/acs.est.5b04996] [Citation(s) in RCA: 224] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Adsorption by minerals is a common geochemical process of dissolved organic matter (DOM) which may induce fractionation of DOM at the mineral-water interface. Here, we examine the molecular fractionation of DOM induced by adsorption onto three common iron oxyhydroxides using electrospray ionization coupled with Fourier-transform ion cyclotron resonance mass spectrometry (ESI-FT-ICR-MS). Ferrihydrite exhibited higher affinity to DOM and induced more pronounced molecular fractionation of DOM than did goethite or lepidocrocite. High molecular weight (>500 Da) compounds and compounds high in unsaturation or rich in oxygen including polycyclic aromatics, polyphenols and carboxylic compounds had higher affinity to iron oxyhydroxides and especially to ferrihydrite. Low molecular weight compounds and compounds low in unsaturation or containing few oxygenated groups (mainly alcohols and ethers) were preferentially maintained in solution. This study confirms that the double bond equivalence and the number of oxygen atoms are valuable parameters indicating the selective fractionation of DOM at mineral and water interfaces. The results of this study provide important information for further understanding the behavior of DOM in the natural environment.
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Affiliation(s)
- Jitao Lv
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, China
| | - Shuzhen Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, China
| | - Songshan Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, China
| | - Lei Luo
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, China
| | - Dong Cao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, China
| | - Peter Christie
- Agri-Environment Branch, Agri-Food and Biosciences Institute , Newforge Lane, Belfast BT9 5PX, United Kingdom
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333
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Sun J, Chillrud SN, Mailloux BJ, Stute M, Singh R, Dong H, Lepre CJ, Bostick BC. Enhanced and stabilized arsenic retention in microcosms through the microbial oxidation of ferrous iron by nitrate. CHEMOSPHERE 2016; 144:1106-15. [PMID: 26454120 PMCID: PMC4779597 DOI: 10.1016/j.chemosphere.2015.09.045] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 08/28/2015] [Accepted: 09/10/2015] [Indexed: 05/23/2023]
Abstract
Magnetite strongly retains As, and is relatively stable under Fe(III)-reducing conditions common in aquifers that release As. Here, laboratory microcosm experiments were conducted to investigate a potential As remediation method involving magnetite formation, using groundwater and sediments from the Vineland Superfund site. The microcosms were amended with various combinations of nitrate, Fe(II) (aq) (as ferrous sulfate) and lactate, and were incubated for more than 5 weeks. In the microcosms enriched with 10 mM nitrate and 5 mM Fe(II) (aq), black magnetic particles were produced, and As removal from solution was observed even under sustained Fe(III) reduction stimulated by the addition of 10 mM lactate. The enhanced As retention was mainly attributed to co-precipitation within magnetite and adsorption on a mixture of magnetite and ferrihydrite. Sequential chemical extraction, X-ray absorption spectroscopy and magnetic susceptibility measurements showed that these minerals formed at pH 6-7 following nitrate-Fe(II) addition, and As-bearing magnetite was stable under reducing conditions. Scanning electron microscopy and X-ray diffraction indicated that nano-particulate magnetite was produced as coatings on fine sediments, and no aging effect was detected on morphology over the course of incubation. These results suggest that a magnetite based strategy may be a long-term remedial option for As-contaminated aquifers.
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Affiliation(s)
- Jing Sun
- Department of Earth and Environmental Sciences, Columbia University, Mail Code 5505, New York, NY, 10027, USA; Lamont-Doherty Earth Observatory, PO Box 1000, 61 Route 9W, Palisades, NY, 10964, USA
| | - Steven N Chillrud
- Lamont-Doherty Earth Observatory, PO Box 1000, 61 Route 9W, Palisades, NY, 10964, USA
| | - Brian J Mailloux
- Department of Environmental Sciences, Barnard College, 3009 Broadway, New York, NY, 10027, USA
| | - Martin Stute
- Lamont-Doherty Earth Observatory, PO Box 1000, 61 Route 9W, Palisades, NY, 10964, USA; Department of Environmental Sciences, Barnard College, 3009 Broadway, New York, NY, 10027, USA
| | - Rajesh Singh
- Department of Geology and Environmental Earth Science, Miami University, Oxford, OH, 45056, USA
| | - Hailiang Dong
- Department of Geology and Environmental Earth Science, Miami University, Oxford, OH, 45056, USA
| | - Christopher J Lepre
- Lamont-Doherty Earth Observatory, PO Box 1000, 61 Route 9W, Palisades, NY, 10964, USA
| | - Benjamin C Bostick
- Lamont-Doherty Earth Observatory, PO Box 1000, 61 Route 9W, Palisades, NY, 10964, USA.
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334
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Yang Z, Du M, Jiang J. Reducing capacities and redox potentials of humic substances extracted from sewage sludge. CHEMOSPHERE 2016; 144:902-908. [PMID: 26432531 DOI: 10.1016/j.chemosphere.2015.09.037] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 08/17/2015] [Accepted: 09/08/2015] [Indexed: 06/05/2023]
Abstract
Humic substances (HS) are redox active organic materials that can be extracted from sewage sludge generated in wastewater treatment processes. Due to the poor understanding of reducing capacity, redox potentials and redox active functional groups of HS in sewage sludge, the potential contribution of sludge HS in transformation of wastewater contaminants is unclear. In the present study, the number of electrons donated or accepted by sewage sludge HS were quantified before and after reduction by iron compounds that possess different redox potentials and defined as the reducing capacity of the sewage sludge. In contrast to previous studies of soil and commercial humic acids (HA), reduced sludge HA showed a lower reducing capacity than that of native HA, which implies formation of semiquinone radicals since the semiquinone radical/hydroquinone pair has a much higher redox potential than the quinone/hydroquinone pair. It is novel that reducing capacities of sludge HA were determined in the redox potential range from -314 to 430 mV. The formation of semiquinone radicals formed during the reduction of quinone moieties in sludge HA is shown by three-dimensional excitation/emission matrix fluorescence spectroscopies information, increasing fluorescence intensities and blue-shifting of the excitation/emission peak of reduced sludge HA. Knowledge of sludge HS redox potentials and corresponding reducing capacities makes it possible to predict the transformation of redox active pollutants and facilitate manipulation and optimization of sludge loading wastewater treatment processes.
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Affiliation(s)
- Zhen Yang
- College of Environmental Science & Engineering, Beijing Forestry University, China
| | - Mengchan Du
- College of Environmental Science & Engineering, Beijing Forestry University, China
| | - Jie Jiang
- College of Environmental Science & Engineering, Beijing Forestry University, China.
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335
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Schmid G, Zeitvogel F, Hao L, Ingino P, Adaktylou I, Eickhoff M, Obst M. Submicron-Scale Heterogeneities in Nickel Sorption of Various Cell-Mineral Aggregates Formed by Fe(II)-Oxidizing Bacteria. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:114-125. [PMID: 26588096 DOI: 10.1021/acs.est.5b02955] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Fe(II)-oxidizing bacteria form biogenic cell-mineral aggregates (CMAs) composed of microbial cells, extracellular organic compounds, and ferric iron minerals. CMAs are capable of immobilizing large quantities of heavy metals, such as nickel, via sorption processes. CMAs play an important role for the fate of heavy metals in the environment, particularly in systems characterized by elevated concentrations of dissolved metals, such as mine drainage or contaminated sediments. We applied scanning transmission (soft) X-ray microscopy (STXM) spectrotomography for detailed 3D chemical mapping of nickel sorbed to CMAs on the submicron scale. We analyzed different CMAs produced by phototrophic or nitrate-reducing microbial Fe(II) oxidation and, in addition, a twisted stalk structure obtained from an environmental biofilm. Nickel showed a heterogeneous distribution and was found to be preferentially sorbed to biogenically precipitated iron minerals such as Fe(III)-(oxyhydr)oxides and, to a minor extent, associated with organic compounds. Some distinct nickel accumulations were identified on the surfaces of CMAs. Additional information obtained from scatter plots and angular distance maps, showing variations in the nickel-iron and nickel-organic carbon ratios, also revealed a general correlation between nickel and iron. Although a high correlation between nickel and iron was observed in 2D maps, 3D maps revealed this to be partly due to projection artifacts. In summary, by combining different approaches for data analysis, we unambiguously showed the heterogeneous sorption behavior of nickel to CMAs.
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Affiliation(s)
- Gregor Schmid
- Environmental Analytical Microscopy, Center for Applied Geoscience, University of Tübingen , Hölderlinstrasse 12, 72074 Tübingen, Germany
| | - Fabian Zeitvogel
- Environmental Analytical Microscopy, Center for Applied Geoscience, University of Tübingen , Hölderlinstrasse 12, 72074 Tübingen, Germany
| | - Likai Hao
- Environmental Analytical Microscopy, Center for Applied Geoscience, University of Tübingen , Hölderlinstrasse 12, 72074 Tübingen, Germany
| | - Pablo Ingino
- Environmental Analytical Microscopy, Center for Applied Geoscience, University of Tübingen , Hölderlinstrasse 12, 72074 Tübingen, Germany
| | - Irini Adaktylou
- Environmental Analytical Microscopy, Center for Applied Geoscience, University of Tübingen , Hölderlinstrasse 12, 72074 Tübingen, Germany
| | - Merle Eickhoff
- Environmental Analytical Microscopy, Center for Applied Geoscience, University of Tübingen , Hölderlinstrasse 12, 72074 Tübingen, Germany
| | - Martin Obst
- Environmental Analytical Microscopy, Center for Applied Geoscience, University of Tübingen , Hölderlinstrasse 12, 72074 Tübingen, Germany
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336
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Cismasu AC, Williams KH, Nico PS. Iron and Carbon Dynamics during Aging and Reductive Transformation of Biogenic Ferrihydrite. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:25-35. [PMID: 26605981 DOI: 10.1021/acs.est.5b03021] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Natural organic matter is often associated with Fe(III) oxyhydroxides, and may be stabilized as a result of coprecipitation or sorption to their surfaces. However, the significance of this association in relation to Fe and C dynamics and biogeochemical cycling, and the mechanisms responsible for organic matter stabilization as a result of interaction with minerals under various environmental conditions (e.g., pH, Eh, etc.) are not entirely understood. The preservation of mineral-bound OM may be affected by OM structure and mineral identity, and bond types between OM and minerals may be central to influencing the stability, transformation and composition of both organic and mineral components under changing environmental conditions. Here we use bulk and submicron-scale spectroscopic synchrotron methods to examine the in situ transformation of OM-bearing, biogenic ferrihydrite stalks (Gallionella ferruginea-like), which formed following injection of oxygenated groundwater into a saturated alluvial aquifer at the Rifle, CO field site. A progression from oxidizing to reducing conditions during an eight-month period triggered the aging and reductive transformation of Gallionella-like ferrihydrite stalks to Fe (hydroxy)carbonates and Fe sulfides, as well as alteration of the composition and amount of OM. Spectromicroscopic measurements showed a gradual decrease in reduced carbon forms (aromatic/alkene, aliphatic C), a relative increase in amide/carboxyl functional groups and a significant increase in carbonate in the stalk structures, and the appearance of organic globules not associated with stalk structures. Biogenic stalks lost ∼30% of their initial organic carbon content. Conversely, a significant increase in bulk organic matter accompanied these transformations. The character of bulk OM changed in parallel with mineralogical transformations, showing an increase in aliphatic, aromatic and amide functional groups. These changes likely occurred as a result of an increase in microbial activity, or biomass production under anoxic conditions. By the end of this experiment, a substantial fraction of organic matter remained in identifiable Fe containing stalks, but carbon was also present in additional pools, for example, organic matter globules and iron carbonate minerals.
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Affiliation(s)
- A Cristina Cismasu
- Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, California, United States
| | - Kenneth H Williams
- Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, California, United States
| | - Peter S Nico
- Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, California, United States
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337
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Fabisch M, Freyer G, Johnson CA, Büchel G, Akob DM, Neu TR, Küsel K. Dominance of 'Gallionella capsiferriformans' and heavy metal association with Gallionella-like stalks in metal-rich pH 6 mine water discharge. GEOBIOLOGY 2016; 14:68-90. [PMID: 26407813 DOI: 10.1111/gbi.12162] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 08/28/2015] [Indexed: 06/05/2023]
Abstract
Heavy metal-contaminated, pH 6 mine water discharge created new streams and iron-rich terraces at a creek bank in a former uranium-mining area near Ronneburg, Germany. The transition from microoxic groundwater with ~5 mm Fe(II) to oxic surface water may provide a suitable habitat for microaerobic iron-oxidizing bacteria (FeOB). In this study, we investigated the potential contribution of these FeOB to iron oxidation and metal retention in this high-metal environment. We (i) identified and quantified FeOB in water and sediment at the outflow, terraces, and creek, (ii) studied the composition of biogenic iron oxides (Gallionella-like twisted stalks) with scanning and transmission electron microscopy (SEM, TEM) as well as confocal laser scanning microscopy (CLSM), and (iii) examined the metal distribution in sediments. Using quantitative PCR, a very high abundance of FeOB was demonstrated at all sites over a 6-month study period. Gallionella spp. clearly dominated the communities, accounting for up to 88% of Bacteria, with a minor contribution of other FeOB such as Sideroxydans spp. and 'Ferrovum myxofaciens'. Classical 16S rRNA gene cloning showed that 96% of the Gallionella-related sequences had ≥ 97% identity to the putatively metal-tolerant 'Gallionella capsiferriformans ES-2', in addition to known stalk formers such as Gallionella ferruginea and Gallionellaceae strain R-1. Twisted stalks from glass slides incubated in water and sediment were composed of the Fe(III) oxyhydroxide ferrihydrite, as well as polysaccharides. SEM and scanning TEM-energy-dispersive X-ray spectroscopy revealed that stalk material contained Cu and Sn, demonstrating the association of heavy metals with biogenic iron oxides and the potential for metal retention by these stalks. Sequential extraction of sediments suggested that Cu (52-61% of total sediment Cu) and other heavy metals were primarily bound to the iron oxide fractions. These results show the importance of 'G. capsiferriformans' and biogenic iron oxides in slightly acidic but highly metal-contaminated freshwater environments.
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MESH Headings
- Aerobiosis
- Biota
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Ferric Compounds/analysis
- Gallionellaceae/chemistry
- Gallionellaceae/classification
- Gallionellaceae/genetics
- Gallionellaceae/isolation & purification
- Germany
- Hydrogen-Ion Concentration
- Iron/metabolism
- Metals, Heavy/analysis
- Microscopy, Confocal
- Microscopy, Electrochemical, Scanning
- Microscopy, Electron, Transmission
- Molecular Sequence Data
- Oxidation-Reduction
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Water/chemistry
- Water Microbiology
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Affiliation(s)
- M Fabisch
- Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany
| | - G Freyer
- Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany
| | - C A Johnson
- Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany
- Department of Geosciences, Virginia Tech, Blacksburg, VA, USA
| | - G Büchel
- Institute of Geosciences, Friedrich Schiller University Jena, Jena, Germany
| | - D M Akob
- Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany
- U.S. Geological Survey, Reston, VA, USA
| | - T R Neu
- Department of River Ecology, Helmholtz Centre for Environmental Research Leipzig-Halle - UFZ, Magdeburg, Germany
| | - K Küsel
- Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
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338
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In Situ Analysis of a Silver Nanoparticle-Precipitating Shewanella Biofilm by Surface Enhanced Confocal Raman Microscopy. PLoS One 2015; 10:e0145871. [PMID: 26709923 PMCID: PMC4692441 DOI: 10.1371/journal.pone.0145871] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 12/09/2015] [Indexed: 11/19/2022] Open
Abstract
Shewanella oneidensis MR-1 is an electroactive bacterium, capable of reducing extracellular insoluble electron acceptors, making it important for both nutrient cycling in nature and microbial electrochemical technologies, such as microbial fuel cells and microbial electrosynthesis. When allowed to anaerobically colonize an Ag/AgCl solid interface, S. oneidensis has precipitated silver nanoparticles (AgNp), thus providing the means for a surface enhanced confocal Raman microscopy (SECRaM) investigation of its biofilm. The result is the in-situ chemical mapping of the biofilm as it developed over time, where the distribution of cytochromes, reduced and oxidized flavins, polysaccharides and phosphate in the undisturbed biofilm is monitored. Utilizing AgNp bio-produced by the bacteria colonizing the Ag/AgCl interface, we could perform SECRaM while avoiding the use of a patterned or roughened support or the introduction of noble metal salts and reducing agents. This new method will allow a spatially and temporally resolved chemical investigation not only of Shewanella biofilms at an insoluble electron acceptor, but also of other noble metal nanoparticle-precipitating bacteria in laboratory cultures or in complex microbial communities in their natural habitats.
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339
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Microbial Surface Colonization and Biofilm Development in Marine Environments. Microbiol Mol Biol Rev 2015; 80:91-138. [PMID: 26700108 DOI: 10.1128/mmbr.00037-15] [Citation(s) in RCA: 462] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Biotic and abiotic surfaces in marine waters are rapidly colonized by microorganisms. Surface colonization and subsequent biofilm formation and development provide numerous advantages to these organisms and support critical ecological and biogeochemical functions in the changing marine environment. Microbial surface association also contributes to deleterious effects such as biofouling, biocorrosion, and the persistence and transmission of harmful or pathogenic microorganisms and their genetic determinants. The processes and mechanisms of colonization as well as key players among the surface-associated microbiota have been studied for several decades. Accumulating evidence indicates that specific cell-surface, cell-cell, and interpopulation interactions shape the composition, structure, spatiotemporal dynamics, and functions of surface-associated microbial communities. Several key microbial processes and mechanisms, including (i) surface, population, and community sensing and signaling, (ii) intraspecies and interspecies communication and interaction, and (iii) the regulatory balance between cooperation and competition, have been identified as critical for the microbial surface association lifestyle. In this review, recent progress in the study of marine microbial surface colonization and biofilm development is synthesized and discussed. Major gaps in our knowledge remain. We pose questions for targeted investigation of surface-specific community-level microbial features, answers to which would advance our understanding of surface-associated microbial community ecology and the biogeochemical functions of these communities at levels from molecular mechanistic details through systems biological integration.
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340
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Ben Maamar S, Aquilina L, Quaiser A, Pauwels H, Michon-Coudouel S, Vergnaud-Ayraud V, Labasque T, Roques C, Abbott BW, Dufresne A. Groundwater Isolation Governs Chemistry and Microbial Community Structure along Hydrologic Flowpaths. Front Microbiol 2015; 6:1457. [PMID: 26733990 PMCID: PMC4686674 DOI: 10.3389/fmicb.2015.01457] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 12/04/2015] [Indexed: 11/19/2022] Open
Abstract
This study deals with the effects of hydrodynamic functioning of hard-rock aquifers on microbial communities. In hard-rock aquifers, the heterogeneous hydrologic circulation strongly constrains groundwater residence time, hydrochemistry, and nutrient supply. Here, residence time and a wide range of environmental factors were used to test the influence of groundwater circulation on active microbial community composition, assessed by high throughput sequencing of 16S rRNA. Groundwater of different ages was sampled along hydrogeologic paths or loops, in three contrasting hard-rock aquifers in Brittany (France). Microbial community composition was driven by groundwater residence time and hydrogeologic loop position. In recent groundwater, in the upper section of the aquifers or in their recharge zone, surface water inputs caused high nitrate concentration and the predominance of putative denitrifiers. Although denitrification does not seem to fully decrease nitrate concentrations due to low dissolved organic carbon concentrations, nitrate input has a major effect on microbial communities. The occurrence of taxa possibly associated with the application of organic fertilizers was also noticed. In ancient isolated groundwater, an ecosystem based on Fe(II)/Fe(III) and S/SO4 redox cycling was observed down to several 100 of meters below the surface. In this depth section, microbial communities were dominated by iron oxidizing bacteria belonging to Gallionellaceae. The latter were associated to old groundwater with high Fe concentrations mixed to a small but not null percentage of recent groundwater inducing oxygen concentrations below 2.5 mg/L. These two types of microbial community were observed in the three sites, independently of site geology and aquifer geometry, indicating hydrogeologic circulation exercises a major control on microbial communities.
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Affiliation(s)
- Sarah Ben Maamar
- OSUR-UMR 6553 ECOBIO, Université de Rennes 1 and Centre National de la Recherche ScientifiqueRennes, France; OSUR-UMR 6118 Géosciences, Université de Rennes 1 and Centre National de la Recherche ScientifiqueRennes, France; BRGM, Laboratory DepartmentOrléans, France
| | - Luc Aquilina
- OSUR-UMR 6118 Géosciences, Université de Rennes 1 and Centre National de la Recherche Scientifique Rennes, France
| | - Achim Quaiser
- OSUR-UMR 6553 ECOBIO, Université de Rennes 1 and Centre National de la Recherche Scientifique Rennes, France
| | | | - Sophie Michon-Coudouel
- OSUR-UMS 3343, Université de Rennes 1 and Centre National de la Recherche Scientifique Rennes, France
| | - Virginie Vergnaud-Ayraud
- OSUR-UMR 6118 Géosciences, Université de Rennes 1 and Centre National de la Recherche Scientifique Rennes, France
| | - Thierry Labasque
- OSUR-UMR 6118 Géosciences, Université de Rennes 1 and Centre National de la Recherche Scientifique Rennes, France
| | - Clément Roques
- OSUR-UMR 6118 Géosciences, Université de Rennes 1 and Centre National de la Recherche Scientifique Rennes, France
| | - Benjamin W Abbott
- OSUR-UMS 3343, Université de Rennes 1 and Centre National de la Recherche Scientifique Rennes, France
| | - Alexis Dufresne
- OSUR-UMR 6553 ECOBIO, Université de Rennes 1 and Centre National de la Recherche Scientifique Rennes, France
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341
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Abstract
Oxidations of phenylacetic acid to benzaldehyde, benzyl alcohol to benzaldehyde, and benzaldehyde to benzoic acid have been observed, in water as the solvent and using only copper(II) chloride as the oxidant. The reactions are performed at 250 °C and 40 bar, conditions that mimic hydrothermal reactions that are geochemically relevant. Speciation calculations show that the oxidizing agent is not freely solvated copper(II) ions, but complexes of copper(II) with chloride and carboxylate anions. Measurements of the reaction stoichiometries and also of substituent effects on reactivity allow plausible mechanisms to be proposed. These oxidation reactions are relevant to green chemistry in that they proceed in high chemical yield in water as the solvent and avoid the use of toxic heavy metal oxidizing reagents.
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Affiliation(s)
- Ziming Yang
- The School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Hilairy E Hartnett
- The School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States.,School of Earth and Space Exploration, Arizona State University , Tempe, Arizona 85287, United States
| | - Everett L Shock
- The School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States.,School of Earth and Space Exploration, Arizona State University , Tempe, Arizona 85287, United States
| | - Ian R Gould
- The School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
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342
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Laufer K, Nordhoff M, Røy H, Schmidt C, Behrens S, Jørgensen BB, Kappler A. Coexistence of Microaerophilic, Nitrate-Reducing, and Phototrophic Fe(II) Oxidizers and Fe(III) Reducers in Coastal Marine Sediment. Appl Environ Microbiol 2015; 82:1433-1447. [PMID: 26682861 PMCID: PMC4771319 DOI: 10.1128/aem.03527-15] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 12/14/2015] [Indexed: 02/04/2023] Open
Abstract
Iron is abundant in sediments, where it can be biogeochemically cycled between its divalent and trivalent redox states. The neutrophilic microbiological Fe cycle involves Fe(III)-reducing and three different physiological groups of Fe(II)-oxidizing microorganisms, i.e., microaerophilic, anoxygenic phototrophic, and nitrate-reducing Fe(II) oxidizers. However, it is unknown whether all three groups coexist in one habitat and how they are spatially distributed in relation to gradients of O2, light, nitrate, and Fe(II). We examined two coastal marine sediments in Aarhus Bay, Denmark, by cultivation and most probable number (MPN) studies for Fe(II) oxidizers and Fe(III) reducers and by quantitative-PCR (qPCR) assays for microaerophilic Fe(II) oxidizers. Our results demonstrate the coexistence of all three metabolic types of Fe(II) oxidizers and Fe(III) reducers. In qPCR, microaerophilic Fe(II) oxidizers (Zetaproteobacteria) were present with up to 3.2 × 10(6) cells g dry sediment(-1). In MPNs, nitrate-reducing Fe(II) oxidizers, anoxygenic phototrophic Fe(II) oxidizers, and Fe(III) reducers reached cell numbers of up to 3.5 × 10(4), 3.1 × 10(2), and 4.4 × 10(4) g dry sediment(-1), respectively. O2 and light penetrated only a few millimeters, but the depth distribution of the different iron metabolizers did not correlate with the profile of O2, Fe(II), or light. Instead, abundances were homogeneous within the upper 3 cm of the sediment, probably due to wave-induced sediment reworking and bioturbation. In microaerophilic Fe(II)-oxidizing enrichment cultures, strains belonging to the Zetaproteobacteria were identified. Photoferrotrophic enrichments contained strains related to Chlorobium and Rhodobacter; the nitrate-reducing Fe(II) enrichments contained strains related to Hoeflea and Denitromonas. This study shows the coexistence of all three types of Fe(II) oxidizers in two near-shore marine environments and the potential for competition and interrelationships between them.
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Affiliation(s)
- Katja Laufer
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Tübingen, Germany
| | - Mark Nordhoff
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Tübingen, Germany
| | - Hans Røy
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Caroline Schmidt
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Tübingen, Germany
| | - Sebastian Behrens
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Tübingen, Germany
- Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, Minneapolis, Minnesota, USA
| | - Bo Barker Jørgensen
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Andreas Kappler
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Tübingen, Germany
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
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343
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Lowering N2O emissions from soils using eucalypt biochar: the importance of redox reactions. Sci Rep 2015; 5:16773. [PMID: 26615820 PMCID: PMC4663753 DOI: 10.1038/srep16773] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 10/20/2015] [Indexed: 12/02/2022] Open
Abstract
Agricultural soils are the primary anthropogenic source of atmospheric nitrous oxide (N2O), contributing to global warming and depletion of stratospheric ozone. Biochar addition has shown potential to lower soil N2O emission, with the mechanisms remaining unclear. We incubated eucalypt biochar (550 °C) – 0, 1 and 5% (w/w) in Ferralsol at 3 water regimes (12, 39 and 54% WFPS) – in a soil column, following gamma irradiation. After N2O was injected at the base of the soil column, in the 0% biochar control 100% of expected injected N2O was released into headspace, declining to 67% in the 5% amendment. In a 100% biochar column at 6% WFPS, only 16% of the expected N2O was observed. X-ray photoelectron spectroscopy identified changes in surface functional groups suggesting interactions between N2O and the biochar surfaces. We have shown increases in -O-C = N /pyridine pyrrole/NH3, suggesting reactions between N2O and the carbon (C) matrix upon exposure to N2O. With increasing rates of biochar application, higher pH adjusted redox potentials were observed at the lower water contents. Evidence suggests that biochar has taken part in redox reactions reducing N2O to dinitrogen (N2), in addition to adsorption of N2O.
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344
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Affiliation(s)
| | - Bim Graham
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, VIC, Australia
| | | | - Kellie L. Tuck
- School of Chemistry, Monash University, Clayton, VIC, Australia
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345
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The contentious nature of soil organic matter. Nature 2015; 528:60-8. [DOI: 10.1038/nature16069] [Citation(s) in RCA: 1630] [Impact Index Per Article: 181.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 10/08/2015] [Indexed: 01/24/2023]
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346
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Nitzsche KS, Weigold P, Lösekann-Behrens T, Kappler A, Behrens S. Microbial community composition of a household sand filter used for arsenic, iron, and manganese removal from groundwater in Vietnam. CHEMOSPHERE 2015; 138:47-59. [PMID: 26037816 DOI: 10.1016/j.chemosphere.2015.05.032] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Revised: 04/24/2015] [Accepted: 05/08/2015] [Indexed: 05/04/2023]
Abstract
Household sand filters are used in rural areas of Vietnam to remove As, Fe, and Mn from groundwater for drinking water purposes. Currently, it is unknown what role microbial processes play in mineral oxide formation and As removal during water filtration. We performed most probable number counts to quantify the abundance of physiological groups of microorganisms capable of catalyzing Fe- and Mn-redox transformation processes in a household sand filter. We found up to 10(4) cells g(-1) dry sand of nitrate-reducing Fe(II)-oxidizing bacteria and Fe(III)-reducing bacteria, and no microaerophilic Fe(II)-oxidizing bacteria, but up to 10(6) cells g(-1) dry sand Mn-oxidizing bacteria. 16S rRNA gene amplicon sequencing confirmed MPN counts insofar as only low abundances of known taxa capable of performing Fe- and Mn-redox transformations were detected. Instead the microbial community on the sand filter was dominated by nitrifying microorganisms, e.g. Nitrospira, Nitrosomonadales, and an archaeal OTU affiliated to Candidatus Nitrososphaera. Quantitative PCR for Nitrospira and ammonia monooxygenase genes agreed with DNA sequencing results underlining the numerical importance of nitrifiers in the sand filter. Based on our analysis of the microbial community composition and previous studies on the solid phase chemistry of sand filters we conclude that abiotic Fe(II) oxidation processes prevail over biotic Fe(II) oxidation on the filter. Yet, Mn-oxidizing bacteria play an important role for Mn(II) oxidation and Mn(III/IV) oxide precipitation in a distinct layer of the sand filter. The formation of Mn(III/IV) oxides contributes to abiotic As(III) oxidation and immobilization of As(V) by sorption to Fe(III) (oxyhydr)oxides.
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Affiliation(s)
- Katja Sonja Nitzsche
- Geomicrobiology/Microbial Ecology, Center for Applied Geoscience, Eberhard Karls University Tübingen, Germany
| | - Pascal Weigold
- Geomicrobiology/Microbial Ecology, Center for Applied Geoscience, Eberhard Karls University Tübingen, Germany
| | - Tina Lösekann-Behrens
- Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, USA
| | - Andreas Kappler
- Geomicrobiology/Microbial Ecology, Center for Applied Geoscience, Eberhard Karls University Tübingen, Germany
| | - Sebastian Behrens
- Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, USA.
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347
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Yan R, Kappler A, Peiffer S. Interference of Nitrite with Pyrite under Acidic Conditions: Implications for Studies of Chemolithotrophic Denitrification. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:11403-11410. [PMID: 26335043 DOI: 10.1021/acs.est.5b02981] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Chemolithotrophic denitrification coupled to pyrite oxidation is regarded a key process in the removal of nitrate in aquifers. A common product is nitrite, which is a strong oxidant under acidic conditions. Nitrite may thus interfere with Fe(II) during acidic extraction, a procedure typically used to quantify microbial pyrite oxidation, in overestimating Fe(III) production. We studied the reaction between pyrite (5-125 mM) and nitrite (40-2000 μM) at pH 0, 5.5, and 6.8 in the absence and presence of oxygen. Significant oxidation of pyrite was measured at pH 0 with a yield of 100 μM Fe(III) after 5 mM pyrite was incubated with 2000 μM nitrite for 24 h. Dissolved oxygen increased the rate at pH 0. No oxidation of pyrite was observed at pH 5.5 and 6.8. Our data imply a cyclic model for pyrite oxidation by Fe(III) on the basis of the oxidation of residual Fe(II) by NO and NO2. Interference by nitrite could be avoided if nitrite was removed from the pyrite suspensions through a washing procedure prior to acidic extraction. We conclude that such interferences should be considered in studies on microbially mediated pyrite oxidation with nitrate.
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Affiliation(s)
- Ruiwen Yan
- Department of Hydrology, University of Bayreuth , 95440 Bayreuth, Germany
| | - Andreas Kappler
- Geomicrobiology Group, Eberhard-Karls-University Tuebingen , 72076 Tuebingen, Germany
| | - Stefan Peiffer
- Department of Hydrology, University of Bayreuth , 95440 Bayreuth, Germany
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348
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Kirkland CM, Herrling MP, Hiebert R, Bender AT, Grunewald E, Walsh DO, Codd SL. In Situ Detection of Subsurface Biofilm Using Low-Field NMR: A Field Study. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:11045-11052. [PMID: 26308099 DOI: 10.1021/acs.est.5b02690] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Subsurface biofilms are central to bioremediation of chemical contaminants in soil and groundwater whereby micro-organisms degrade or sequester environmental pollutants like nitrate, hydrocarbons, chlorinated solvents and heavy metals. Current methods to monitor subsurface biofilm growth in situ are indirect. Previous laboratory research conducted at MSU has indicated that low-field nuclear magnetic resonance (NMR) is sensitive to biofilm growth in porous media, where biofilm contributes a polymer gel-like phase and enhances T2 relaxation. Here we show that a small diameter NMR well logging tool can detect biofilm accumulation in the subsurface using the change in T2 relaxation behavior over time. T2 relaxation distributions were measured over an 18 day experimental period by two NMR probes, operating at approximately 275 kHz and 400 kHz, installed in 10.2 cm wells in an engineered field testing site. The mean log T2 relaxation times were reduced by 62% and 43%, respectively, while biofilm was cultivated in the soil surrounding each well. Biofilm growth was confirmed by bleaching and flushing the wells and observing the NMR signal's return to baseline. This result provides a direct and noninvasive method to spatiotemporally monitor biofilm accumulation in the subsurface.
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Affiliation(s)
- Catherine M Kirkland
- Center for Biofilm Engineering, Montana State University , Bozeman, Montana 59717, United States
- Department of Chemical and Biological Engineering, Montana State University , Bozeman, Montana 59717, United States
| | - Maria P Herrling
- Chair of Water Chemistry and Water Technology, Karlsruhe Institute of Technology , Karlsruhe 76131, Germany
| | - Randy Hiebert
- Center for Biofilm Engineering, Montana State University , Bozeman, Montana 59717, United States
| | - Andrew T Bender
- Center for Biofilm Engineering, Montana State University , Bozeman, Montana 59717, United States
- Department of Mechanical and Industrial Engineering, Montana State University , Bozeman, Montana 59717, United States
| | - Elliot Grunewald
- Vista Clara Inc. , 12201 Cyrus Way Ste. 104, Mukilteo, Washington 98275, United States
| | - David O Walsh
- Vista Clara Inc. , 12201 Cyrus Way Ste. 104, Mukilteo, Washington 98275, United States
| | - Sarah L Codd
- Center for Biofilm Engineering, Montana State University , Bozeman, Montana 59717, United States
- Department of Mechanical and Industrial Engineering, Montana State University , Bozeman, Montana 59717, United States
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349
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The Electrochemical Properties of Biochars and How They Affect Soil Redox Properties and Processes. AGRONOMY-BASEL 2015. [DOI: 10.3390/agronomy5030322] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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350
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Silva LCR, Doane TA, Corrêa RS, Valverde V, Pereira EIP, Horwath WR. Iron-mediated stabilization of soil carbon amplifies the benefits of ecological restoration in degraded lands. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2015; 25:1226-1234. [PMID: 26485951 DOI: 10.1890/14-2151.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Recent observations across a 14-year restoration chronosequence have shown an unexpected accumulation of soil organic carbon in strip-mined areas of central Brazil. This was attributed to the rapid plant colonization that followed the incorporation of biosolids into exposed regoliths, but the specific mechanisms involved in the stabilization of carbon inputs from the vegetation remained unclear. Using isotopic and elemental analyses, we tested the hypothesis that plant-derived carbon accumulation was triggered by the formation of iron-coordinated complexes, stabilized into physically protected (occluded) soil fractions. Confirming this hypothesis, we identified a fast formation of microaggregates shortly after the application of iron-rich biosolids, which was characterized by a strong association between pyrophosphate-extractable iron and plant-derived organic matter. The formation of microaggregates preceded the development of macroaggregates, which drastically increased soil carbon content (-140 Mg C/ha) a few years after restoration. Consistent with previous theoretical work, iron-coordinated organic complexes served as nuclei for aggregate formation, reflecting the synergistic effect of biological, chemical, and physical mechanisms of carbon stabilization in developing soils. Nevertheless, iron was not the only factor affecting soil carbon content. The highest carbon accumulation was observed during the period of highest plant diversity (> 30 species; years 3-6), declining significantly with the exclusion of native species by invasive grasses (years 9-14). Furthermore, the increasing dominance of invasive grasses was associated with a steady decline in the concentration of soil nitrogen and phosphorus per unit of accumulated carbon. These results demonstrate the importance of interdependent ecological and biogeochemical processes, and the role of soil-plant interactions in determining the success of restoration efforts. In contrast with previous but unsuccessful attempts to restore mined areas through nutrient application alone, iron-mediated stabilization of vegetation inputs favored the regeneration of a barren stable state that had persisted for over five decades since disturbance. The effectiveness of coupled organic matter and iron "fertilization," combined with management of invasive species, has the possibility to enhance terrestrial carbon sequestration and accelerate the restoration of degraded lands, while addressing important challenges associated with urban waste disposal.
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