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Zhang N, Liu Y, Wan Z, Zhang Y, Xie W, Zhang P, Tong M, Yuan S. Dependence of Biotic and Abiotic H 2O 2 and •OH Production on the Redox Conditions and Compositions of Sediment during Oxygenation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:3849-3857. [PMID: 38349952 DOI: 10.1021/acs.est.3c10424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
Reactive oxygen species (ROS) production in O2-perturbed subsurface environments has been increasingly documented in recent years. However, the constraining conditions under which abiotic and/or biotic mechanisms predominate for ROS production remain ambiguous. Here, we demonstrate that the ROS production mechanism, biotic and abiotic, is determined by sediment redox properties and sediment compositions. Upon the oxygenation of 10 field sediments, the cumulative H2O2 concentrations reached up to 554 μmol/kg within 2 h. The autoclaving sterilization experiments showed that H2O2 could be produced by both biotic and abiotic processes depending on the redox conditions. However, only the abiotic process could produce significant levels of •OH, and the production yield was closely related to the sediment components, particularly sediment Fe(II) and organic matter. Fe(II) bound with organic matter led to high yields of H2O2 and •OH production. Sediment oxygenation contributed to the appearance of H2O2 in groundwater, with the abiotic mechanism producing higher instantaneous H2O2 concentrations than the biotic mechanism. These findings reveal that the redox conditions, compositions, and texture of sediments collectively control abiotic and biotic mechanisms for ROS production, which assists the identification of ROS production hotspots and the understanding of ROS distribution and utilization in the subsurface.
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Affiliation(s)
- Na Zhang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, No. 68 Jincheng Street, East Lake High-Tech Development Zone, Wuhan 430078, P. R. China
- Hebei Key Laboratory of Wetland Ecology and Conservation, Hengshui University, 1088 Heping West Road, Hengshui 053000, P. R. China
| | - Ying Liu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, No. 68 Jincheng Street, East Lake High-Tech Development Zone, Wuhan 430078, P. R. China
| | - Zhenchen Wan
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, No. 68 Jincheng Street, East Lake High-Tech Development Zone, Wuhan 430078, P. R. China
| | - Yanting Zhang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, No. 68 Jincheng Street, East Lake High-Tech Development Zone, Wuhan 430078, P. R. China
| | - Wenjing Xie
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, No. 68 Jincheng Street, East Lake High-Tech Development Zone, Wuhan 430078, P. R. China
| | - Peng Zhang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, No. 68 Jincheng Street, East Lake High-Tech Development Zone, Wuhan 430078, P. R. China
| | - Man Tong
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, No. 68 Jincheng Street, East Lake High-Tech Development Zone, Wuhan 430078, P. R. China
| | - Songhu Yuan
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, No. 68 Jincheng Street, East Lake High-Tech Development Zone, Wuhan 430078, P. R. China
- Hubei Key Laboratory of Yangze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, No. 68 Jincheng Street, East Lake High-Tech Development Zone, Wuhan 430078, P. R. China
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2
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Michaud AB, Massé RO, Emerson D. Microbial iron cycling is prevalent in water-logged Alaskan Arctic tundra habitats, but sensitive to disturbance. FEMS Microbiol Ecol 2023; 99:7022315. [PMID: 36725207 DOI: 10.1093/femsec/fiad013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/23/2023] [Accepted: 01/31/2023] [Indexed: 02/03/2023] Open
Abstract
Water logged habitats in continuous permafrost regions provide extensive oxic-anoxic interface habitats for iron cycling. The iron cycle interacts with the methane and phosphorus cycles, and is an important part of tundra biogeochemistry. Our objective was to characterize microbial communities associated with the iron cycle within natural and disturbed habitats of the Alaskan Arctic tundra. We sampled aquatic habitats within natural, undisturbed and anthropogenically disturbed areas and sequenced the 16S rRNA gene to describe the microbial communities, then supported these results with process rate and geochemical measurements. Undisturbed habitats have microbial communities that are significantly different than disturbed habitats. Microbial taxa known to participate in the iron and methane cycles are significantly associated with natural habitats, whereas they are not significantly associated with disturbed sites. Undisturbed habitats have significantly higher extractable iron and are more acidic than disturbed habitats sampled. Iron reduction is not measurable in disturbed aquatic habitats and is not stimulated by the addition of biogenic iron mats. Our study highlights the prevalence of Fe-cycling in undisturbed water-logged habitats, and demonstrates that anthropogenic disturbance of the tundra, due to legacy gravel mining, alters the microbiology of aquatic habitats and disrupts important biogeochemical cycles in the Arctic tundra.
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Affiliation(s)
- Alexander B Michaud
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME 04544, United States
| | - Rémi O Massé
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME 04544, United States
| | - David Emerson
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME 04544, United States
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3
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Zhou N, Kupper RJ, Catalano JG, Thompson A, Chan CS. Biological Oxidation of Fe(II)-Bearing Smectite by Microaerophilic Iron Oxidizer Sideroxydans lithotrophicus Using Dual Mto and Cyc2 Iron Oxidation Pathways. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:17443-17453. [PMID: 36417801 PMCID: PMC9731265 DOI: 10.1021/acs.est.2c05142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/03/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
Fe(II) clays are common across many environments, making them a potentially significant microbial substrate, yet clays are not well established as an electron donor. Therefore, we explored whether Fe(II)-smectite supports the growth of Sideroxydans lithotrophicus ES-1, a microaerophilic Fe(II)-oxidizing bacterium (FeOB), using synthesized trioctahedral Fe(II)-smectite and 2% oxygen. S. lithotrophicus grew substantially and can oxidize Fe(II)-smectite to a higher extent than abiotic oxidation, based on X-ray near-edge spectroscopy (XANES). Sequential extraction showed that edge-Fe(II) is oxidized before interior-Fe(II) in both biotic and abiotic experiments. The resulting Fe(III) remains in smectite, as secondary minerals were not detected in biotic and abiotic oxidation products by XANES and Mössbauer spectroscopy. To determine the genes involved, we compared S. lithotrophicus grown on smectite versus Fe(II)-citrate using reverse-transcription quantitative PCR and found that cyc2 genes were highly expressed on both substrates, while mtoA was upregulated on smectite. Proteomics confirmed that Mto proteins were only expressed on smectite, indicating that ES-1 uses the Mto pathway to access solid Fe(II). We integrate our results into a biochemical and mineralogical model of microbial smectite oxidation. This work increases the known substrates for FeOB growth and expands the mechanisms of Fe(II)-smectite alteration in the environment.
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Affiliation(s)
- Nanqing Zhou
- School
of Marine Science and Policy, University
of Delaware, Newark, Delaware 19716, United
States
| | - Robert J. Kupper
- Department
of Earth and Planetary Sciences, Washington
University in St. Louis, Saint
Louis, Missouri 63130, United States
| | - Jeffrey G. Catalano
- Department
of Earth and Planetary Sciences, Washington
University in St. Louis, Saint
Louis, Missouri 63130, United States
| | - Aaron Thompson
- Department
of Crop and Soil Sciences, University of
Georgia, Athens, Georgia 30602, United States
| | - Clara S. Chan
- School
of Marine Science and Policy, University
of Delaware, Newark, Delaware 19716, United
States
- Department
of Earth Sciences, University of Delaware, Newark, Delaware 19716, United States
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4
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Chakraborty A, Suchy M, Hubert CRJ, Ryan MC. Vertical stratification of microbial communities and isotope geochemistry tie groundwater denitrification to sampling location within a nitrate-contaminated aquifer. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 820:153092. [PMID: 35038526 DOI: 10.1016/j.scitotenv.2022.153092] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 12/29/2021] [Accepted: 01/09/2022] [Indexed: 06/14/2023]
Abstract
Nitrate pollution is a major threat to groundwater quality in agricultural areas. Natural attenuation of nitrate in contaminated aquifers is mediated by denitrifying microbial populations in anoxic environments. Vertical distribution of denitrifying microbial communities in aquifers is greatly influenced by groundwater redox conditions, local hydrogeological parameters, and seasonal variability in groundwater flow and recharge. In this study, we investigated groundwater geochemistry and the composition of bacterial and archaeal communities with increasing depth in a shallow nitrate-contaminated aquifer in British Columbia, Canada. High-resolution passive diffusion sampling was conducted to collect groundwater at 10-cm intervals from 4 to 20 m below ground surface (mbgs) in the aquifer. Geochemical analyses of major ions indicated a general shift in the groundwater chemistry below 16 mbgs including decreasing chloride concentrations that suggest two-end member mixing of shallow and deep groundwater with different chemistries. A redoxcline was further observed within a 2 m transition zone at 18-20 mbgs characterized by sharp declines in nitrate concentrations and increases in sulfate and total inorganic carbon. Excursions in δ15N-NO3- and δ18O-NO3- in the same depth interval are consistent with denitrification, and a concomitant decrease in δ34S-SO42- suggested that denitrification was coupled to sulfide or sulfur oxidation. Microbial communities within this depth interval were significantly dissimilar to those above and below, featuring putative lithotrophic denitrifying bacteria belonging to the genera Sulfurifustis, Sulfuritalea and Sulfuricella. These lineages were detected in greatest abundance at 19 mbgs while the abundances of putative heterotrophic sulfate-reducing bacteria belonging to the genus Desulfosporosinus were greatest at 20 mbgs. In addition to help distinguish denitrification from mixing-induced changes in groundwater chemistry, the above observed vertical stratification of the microbial key players connects nitrate removal to the locations of the aquifer sampled.
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Affiliation(s)
- Anirban Chakraborty
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.
| | - Martin Suchy
- Environment and Climate Change Canada, Vancouver, British Columbia, Canada
| | - Casey R J Hubert
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - M Cathryn Ryan
- Department of Geoscience, University of Calgary, Calgary, Alberta, Canada
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5
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Hudson JM, Michaud AB, Emerson D, Chin YP. Spatial distribution and biogeochemistry of redox active species in arctic sedimentary porewaters and seeps. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2022; 24:426-438. [PMID: 35170586 DOI: 10.1039/d1em00505g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Redox active species in Arctic lacustrine sediments play an important, regulatory role in the carbon cycle, yet there is little information on their spatial distribution, abundance, and oxidation states. Here, we use voltammetric microelectrodes to quantify the in situ concentrations of redox-active species at high vertical resolution (mm to cm) in the benthic porewaters of an oligotrophic Arctic lake (Toolik Lake, AK, USA). Mn(II), Fe(II), O2, and Fe(III)-organic complexes were detected as the major redox-active species in these porewaters, indicating both Fe(II) oxidation and reductive dissolution of Fe(III) and Mn(IV) minerals. We observed significant spatial heterogeneity in their abundance and distribution as a function of both location within the lake and depth. Microbiological analyses and solid phase Fe(III) measurements were performed in one of the Toolik Lake cores to determine the relationship between biogeochemical redox gradients and microbial communities. Our data reveal iron cycling involving both oxidizing (FeOB) and reducing (FeRB) bacteria. Additionally, we profiled a large microbial iron mat in a tundra seep adjacent to an Arctic stream (Oksrukuyik Creek) where we observed Fe(II) and soluble Fe(III) in a highly reducing environment. The variable distribution of redox-active substances at all the sites yields insights into the nature and distribution of the important terminal electron acceptors in both lacustrine and tundra environments capable of exerting significant influences on the carbon cycle.
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Affiliation(s)
- Jeffrey M Hudson
- Department of Civil and Environmental Engineering, University of Delaware, Newark, Delaware 19716, USA.
| | | | - David Emerson
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, 04544, USA
| | - Yu-Ping Chin
- Department of Civil and Environmental Engineering, University of Delaware, Newark, Delaware 19716, USA.
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6
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Pang Y, Wang J. Inhibition of ferrous iron (Fe 2+) to sulfur-driven autotrophic denitrification: Insight into microbial community and functional genes. BIORESOURCE TECHNOLOGY 2021; 342:125960. [PMID: 34560437 DOI: 10.1016/j.biortech.2021.125960] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/09/2021] [Accepted: 09/13/2021] [Indexed: 06/13/2023]
Abstract
The effect of Fe2+ on the performance of sulfur-driven autotrophic denitrification (SDAD) using S0 as electron donor was evaluated. The experimental results showed that as initial Fe2+ concentration increased, nitrate (NO3-) removal rate significantly decreased. Fe2+ ion (0.1 mM and 1 Mm) inhibited SDAD rate (approximately 10% and 50%) and resulted in an accumulation of nitrite (NO2-) and nitrous oxide (N2O). The relative abundance of Thiobacillus was positively correlated with NO3- removal rate, whereas negatively correlated with Fe2+ concentration, suggesting that Fe2+ inhibited the sulfur-oxidizing denitrifying bacteria. Moreover, the abundance of bacterial 16S rRNA, denitrifying genes (narG, nirS, nirK and nosZ) and sulfur-oxidizing genes (soxB and dsrA) decreased with the increase of Fe2+ concentration, among them nosZ and soxB were the most sensitive genes to Fe2+, and nosZ/narG, soxB/(bacterial 16S rRNA) and soxB/nirK had influence on NO3- removal rate, while nosZ/(bacterial 16S rRNA) affected N2O accumulation rate.
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Affiliation(s)
- Yunmeng Pang
- Laboratory of Environmental Technology, INET, Tsinghua University, Beijing 100084, PR China
| | - Jianlong Wang
- Laboratory of Environmental Technology, INET, Tsinghua University, Beijing 100084, PR China; Beijing Key Laboratory of Radioactive Waste Treatment, INET, Tsinghua University, Beijing 100084, PR China.
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7
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Garber AI, Cohen AB, Nealson KH, Ramírez GA, Barco RA, Enzingmüller-Bleyl TC, Gehringer MM, Merino N. Metagenomic Insights Into the Microbial Iron Cycle of Subseafloor Habitats. Front Microbiol 2021; 12:667944. [PMID: 34539592 PMCID: PMC8446621 DOI: 10.3389/fmicb.2021.667944] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 07/30/2021] [Indexed: 11/13/2022] Open
Abstract
Microbial iron cycling influences the flux of major nutrients in the environment (e.g., through the adsorptive capacity of iron oxides) and includes biotically induced iron oxidation and reduction processes. The ecological extent of microbial iron cycling is not well understood, even with increased sequencing efforts, in part due to limitations in gene annotation pipelines and limitations in experimental studies linking phenotype to genotype. This is particularly true for the marine subseafloor, which remains undersampled, but represents the largest contiguous habitat on Earth. To address this limitation, we used FeGenie, a database and bioinformatics tool that identifies microbial iron cycling genes and enables the development of testable hypotheses on the biogeochemical cycling of iron. Herein, we survey the microbial iron cycle in diverse subseafloor habitats, including sediment-buried crustal aquifers, as well as surficial and deep sediments. We inferred the genetic potential for iron redox cycling in 32 of the 46 metagenomes included in our analysis, demonstrating the prevalence of these activities across underexplored subseafloor ecosystems. We show that while some processes (e.g., iron uptake and storage, siderophore transport potential, and iron gene regulation) are near-universal, others (e.g., iron reduction/oxidation, siderophore synthesis, and magnetosome formation) are dependent on local redox and nutrient status. Additionally, we detected niche-specific differences in strategies used for dissimilatory iron reduction, suggesting that geochemical constraints likely play an important role in dictating the dominant mechanisms for iron cycling. Overall, our survey advances the known distribution, magnitude, and potential ecological impact of microbe-mediated iron cycling and utilization in sub-benthic ecosystems.
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Affiliation(s)
- Arkadiy I Garber
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Ashley B Cohen
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, United States
| | - Kenneth H Nealson
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Gustavo A Ramírez
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel.,College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA, United States
| | - Roman A Barco
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | | | - Michelle M Gehringer
- Department of Microbiology, Technical University of Kaiserslautern, Kaiserslautern, Germany
| | - Nancy Merino
- Biosciences & Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, United States
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8
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Spieck E, Wegen S, Keuter S. Relevance of Candidatus Nitrotoga for nitrite oxidation in technical nitrogen removal systems. Appl Microbiol Biotechnol 2021; 105:7123-7139. [PMID: 34508283 PMCID: PMC8494671 DOI: 10.1007/s00253-021-11487-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 07/29/2021] [Accepted: 07/31/2021] [Indexed: 01/10/2023]
Abstract
Abstract Many biotechnological applications deal with nitrification, one of the main steps of the global nitrogen cycle. The biological oxidation of ammonia to nitrite and further to nitrate is critical to avoid environmental damage and its functioning has to be retained even under adverse conditions. Bacteria performing the second reaction, oxidation of nitrite to nitrate, are fastidious microorganisms that are highly sensitive against disturbances. One important finding with relevance for nitrogen removal systems was the discovery of the mainly cold-adapted Cand. Nitrotoga, whose activity seems to be essential for the recovery of nitrite oxidation in wastewater treatment plants at low temperatures, e.g., during cold seasons. Several new strains of this genus have been recently described and ecophysiologically characterized including genome analyses. With increasing diversity, also mesophilic Cand. Nitrotoga representatives have been detected in activated sludge. This review summarizes the natural distribution and driving forces defining niche separation in artificial nitrification systems. Further critical aspects for the competition with Nitrospira and Nitrobacter are discussed. Knowledge about the physiological capacities and limits of Cand. Nitrotoga can help to define physico-chemical parameters for example in reactor systems that need to be run at low temperatures. Key points • Characterization of the psychrotolerant nitrite oxidizer Cand. Nitrotoga • Comparison of the physiological features of Cand. Nitrotoga with those of other NOB • Identification of beneficial environmental/operational parameters for proliferation Supplementary Information The online version contains supplementary material available at 10.1007/s00253-021-11487-5.
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Affiliation(s)
- Eva Spieck
- Department of Microbiology and Biotechnology, Universität Hamburg, Hamburg, Germany.
| | - Simone Wegen
- Department of Microbiology and Biotechnology, Universität Hamburg, Hamburg, Germany
| | - Sabine Keuter
- Department of Microbiology and Biotechnology, Universität Hamburg, Hamburg, Germany
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9
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Whitaker AH, Austin RE, Holden KL, Jones JL, Michel FM, Peak D, Thompson A, Duckworth OW. The Structure of Natural Biogenic Iron (Oxyhydr)oxides Formed in Circumneutral pH Environments. GEOCHIMICA ET COSMOCHIMICA ACTA 2021; 308:237-255. [PMID: 34305159 PMCID: PMC8294128 DOI: 10.1016/j.gca.2021.05.059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Biogenic iron (Fe) (oxyhydr)oxides (BIOS) partially control the cycling of organic matter, nutrients, and pollutants in soils and water via sorption and redox reactions. Although recent studies have shown that the structure of BIOS resembles that of two-line ferrihydrite (2LFh), we lack detailed knowledge of the BIOS local coordination environment and structure required to understand the drivers of BIOS reactivity in redox active environments. Therefore, we used a combination of microscopy, scattering, and spectroscopic methods to elucidate the structure of BIOS sampled from a groundwater seep in North Carolina and compare them to 2LFh. We also simulated the effects of wet-dry cycles by varying sample preparation (e.g., freezing, flash freezing with freeze drying, freezing with freeze drying and oven drying). In general, the results show that both the long- and short-range ordering in BIOS are structurally distinct and notably more disordered than 2LFh. Our structure analysis, which utilized Fe K-edge X-ray absorption spectroscopy, Mössbauer spectroscopy, X-ray diffraction, and pair distribution function analyses, showed that the BIOS samples were more poorly ordered than 2LFh and intimately mixed with organic matter. Furthermore, pair distribution function analyses resulted in coherent scattering domains for the BIOS samples ranging from 12-18 Å, smaller than those of 2LFh (21-27 Å), consistent with reduced ordering. Additionally, Fe L-edge XAS indicated that the local coordination environment of 2LFh samples consisted of minor amounts of tetrahedral Fe(III), whereas BIOS were dominated by octahedral Fe(III), consistent with depletion of the sites due to small domain size and incorporation of impurities (e.g., organic C, Al, Si, P). Within sample sets, the frozen freeze dried and oven dried sample preparation increased the crystallinity of the 2LFh samples when compared to the frozen treatment, whereas the BIOS samples remained more poorly crystalline under all sample preparations. This research shows that BIOS formed in circumneutral pH waters are poorly ordered and more environmentally stable than 2LFh.
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Affiliation(s)
- Andrew H. Whitaker
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Robert E. Austin
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Kathryn L. Holden
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Jacob L. Jones
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - F. Marc Michel
- Department of Geosciences, Virginia Tech, Blacksburg, Virginia 24060, USA
| | - Derek Peak
- Department of Soil Science, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A8, Canada
| | - Aaron Thompson
- Department of Crop and Soil Sciences, University of Georgia, Athens, Georgia 30602, USA
| | - Owen W. Duckworth
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA
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10
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Patil PK, Baskaran V, Vinay TN, Avunje S, Leo-Antony M, Shekhar MS, Alavandi SV, Vijayan KK. Abundance, community structure and diversity of nitrifying bacterial enrichments from low and high saline brackishwater environments. Lett Appl Microbiol 2021; 73:96-106. [PMID: 33780023 DOI: 10.1111/lam.13480] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/09/2021] [Accepted: 03/09/2021] [Indexed: 11/29/2022]
Abstract
The study reports diversity in nitrifying microbial enrichments from low (0·5-5‰) and high (18-35‰) saline ecosystems. Microbial community profiling of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) enrichments was analysed by sequencing 16S rRNA and was processed using Mothur pipeline. The α-diversity indices showed the richness of nitrifying bacterial consortia from the high saline environment and were clustering based on the source of the sample. AOB and NOB enrichments from both the environments showed diverse lineages of phyla distributed in both groups with 38 and 34 phyla from low saline and 53 and 40 phyla in high saline sources, respectively. At class level, α- and γ-proteobacteria were found to be more dominant in both the enrichments. AOBs and NOBs in enrichments from low saline environments were dominated by Nitrosomonadaceae, Gallionellaceae (Nitrotoga sp.) and Ectothiorhodospiraceae and Nitrospira, respectively. Though Chromatiaceae were present in both AOB and NOB enrichments, Nitrosoglobus and Nitrosococcus dominated the AOBs while NOBs were dominated by uncultured genera, whereas Rhizobiales were found in both the enrichments. AOBs and NOBs in enrichments from high saline environments were dominated by Nitrospira-like AOBs, Nitrosomonas and Nitrosococcus genera, whereas ammonia-oxidizing archaea (AOA) group included Nitrosopumilus and Nitrososphaera genera comprising and Nitrospirae, respectively. The majority of the genera obtained in both the salinities were found to be either uncultured or unclassified groups. Results of the study suggest that the AOB and NOB consortia have unique and diverse microbes in each of the enrichments, capable of functioning in aquaculture systems practised at different salinities (0-60 ppt).
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Affiliation(s)
- P K Patil
- Central Institute of Brackishwater Aquaculture, ICAR, Chennai, India
| | - V Baskaran
- Central Institute of Brackishwater Aquaculture, ICAR, Chennai, India
| | - T-N Vinay
- Central Institute of Brackishwater Aquaculture, ICAR, Chennai, India
| | - S Avunje
- Central Institute of Brackishwater Aquaculture, ICAR, Chennai, India
| | - M Leo-Antony
- Central Institute of Brackishwater Aquaculture, ICAR, Chennai, India
| | - M S Shekhar
- Central Institute of Brackishwater Aquaculture, ICAR, Chennai, India
| | - S V Alavandi
- Central Institute of Brackishwater Aquaculture, ICAR, Chennai, India
| | - K K Vijayan
- Central Institute of Brackishwater Aquaculture, ICAR, Chennai, India
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11
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Fortney NW, Beard BL, Hutchings JA, Shields MR, Bianchi TS, Boyd ES, Johnson CM, Roden EE. Geochemical and Stable Fe Isotopic Analysis of Dissimilatory Microbial Iron Reduction in Chocolate Pots Hot Spring, Yellowstone National Park. ASTROBIOLOGY 2021; 21:83-102. [PMID: 32580560 DOI: 10.1089/ast.2019.2058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Chocolate Pots hot spring (CP) is an Fe-rich, circumneutral-pH geothermal spring in Yellowstone National Park. Relic hydrothermal systems have been identified on Mars, and modern hydrothermal environments such as CP are useful for gaining insight into potential pathways for generation of biosignatures of ancient microbial life on Earth and Mars. Fe isotope fractionation is recognized as a signature of dissimilatory microbial iron oxide reduction (DIR) in both the rock record and modern sedimentary environments. Previous studies in CP have demonstrated the presence of DIR in vent pool deposits and show aqueous-/solid-phase Fe isotope variations along the hot spring flow path that may be linked to this process. In this study, we examined the geochemistry and stable Fe isotopic composition of spring water and sediment core samples collected from the vent pool and along the flow path, with the goal of evaluating whether Fe isotopes can serve as a signature of past or present DIR activity. Bulk sediment Fe redox speciation confirmed that DIR is active within the hot spring vent pool sediments (but not in more distal deposits), and the observed Fe isotope fractionation between Fe(II) and Fe(III) is consistent with previous studies of DIR-driven Fe isotope fractionation. However, modeling of sediment Fe isotope distributions indicates that DIR does not produce a unique Fe isotopic signature of DIR in the vent pool environment. Because of rapid chemical and isotopic communication between the vent pool fluid and sediment, sorption of Fe(II) to Fe(III) oxides would produce an isotopic signature similar to DIR despite DIR-driven generation of large quantities of isotopically light solid-associated Fe(II). The possibility exists, however, for preservation of specific DIR-derived Fe(II) minerals such as siderite (which is present in the vent pool deposits), whose isotopic composition could serve as a long-term signature of DIR in relic hot spring environments.
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Affiliation(s)
- Nathaniel W Fortney
- Department of Geoscience, NASA Astrobiology Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Brian L Beard
- Department of Geoscience, NASA Astrobiology Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jack A Hutchings
- Department of Geological Sciences, University of Florida, Gainesville, Florida, USA
| | - Michael R Shields
- Department of Geological Sciences, University of Florida, Gainesville, Florida, USA
| | - Thomas S Bianchi
- Department of Geological Sciences, University of Florida, Gainesville, Florida, USA
| | - Eric S Boyd
- Department of Microbiology and Immunology, NASA Astrobiology Institute, Montana State University, Bozeman, Montana, USA
| | - Clark M Johnson
- Department of Geoscience, NASA Astrobiology Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Eric E Roden
- Department of Geoscience, NASA Astrobiology Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
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12
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Cooper RE, Wegner CE, Kügler S, Poulin RX, Ueberschaar N, Wurlitzer JD, Stettin D, Wichard T, Pohnert G, Küsel K. Iron is not everything: unexpected complex metabolic responses between iron-cycling microorganisms. THE ISME JOURNAL 2020; 14:2675-2690. [PMID: 32690937 PMCID: PMC7784907 DOI: 10.1038/s41396-020-0718-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 06/30/2020] [Accepted: 07/08/2020] [Indexed: 02/02/2023]
Abstract
Coexistence of microaerophilic Fe(II)-oxidizers and anaerobic Fe(III)-reducers in environments with fluctuating redox conditions is a prime example of mutualism, in which both partners benefit from the sustained Fe-pool. Consequently, the Fe-cycling machineries (i.e., metal-reducing or -oxidizing pathways) should be most affected during co-cultivation. However, contrasting growth requirements impeded systematic elucidation of their interactions. To disentangle underlying interaction mechanisms, we established a suboxic co-culture system of Sideroxydans sp. CL21 and Shewanella oneidensis. We showed that addition of the partner's cell-free supernatant enhanced both growth and Fe(II)-oxidizing or Fe(III)-reducing activity of each partner. Metabolites of the exometabolome of Sideroxydans sp. CL21 are generally upregulated if stimulated with the partner´s spent medium, while S. oneidensis exhibits a mixed metabolic response in accordance with a balanced response to the partner. Surprisingly, RNA-seq analysis revealed genes involved in Fe-cycling were not differentially expressed during co-cultivation. Instead, the most differentially upregulated genes included those encoding for biopolymer production, lipoprotein transport, putrescine biosynthesis, and amino acid degradation suggesting a regulated inter-species biofilm formation. Furthermore, the upregulation of hydrogenases in Sideroxydans sp. CL21 points to competition for H2 as electron donor. Our findings reveal that a complex metabolic and transcriptomic response, but not accelerated formation of Fe-end products, drive interactions of Fe-cycling microorganisms.
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Affiliation(s)
- Rebecca E Cooper
- Institute of Biodiversity, Aquatic Geomicrobiology, Friedrich Schiller University Jena, Dornburger Strasse 159, 07743, Jena, Germany
| | - Carl-Eric Wegner
- Institute of Biodiversity, Aquatic Geomicrobiology, Friedrich Schiller University Jena, Dornburger Strasse 159, 07743, Jena, Germany
| | - Stefan Kügler
- Institute of Biodiversity, Aquatic Geomicrobiology, Friedrich Schiller University Jena, Dornburger Strasse 159, 07743, Jena, Germany
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743, Jena, Germany
| | - Remington X Poulin
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743, Jena, Germany
| | - Nico Ueberschaar
- Mass Spectrometry Platform, Faculty of Chemistry and Earth Sciences, Friedrich Schiller University Jena, Humboldstr. 8, 07743, Jena, Germany
| | - Jens D Wurlitzer
- Institute of Biodiversity, Aquatic Geomicrobiology, Friedrich Schiller University Jena, Dornburger Strasse 159, 07743, Jena, Germany
| | - Daniel Stettin
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743, Jena, Germany
| | - Thomas Wichard
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743, Jena, Germany
| | - Georg Pohnert
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743, Jena, Germany
| | - Kirsten Küsel
- Institute of Biodiversity, Aquatic Geomicrobiology, Friedrich Schiller University Jena, Dornburger Strasse 159, 07743, Jena, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany.
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13
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Woda J, Wen T, Lemon J, Marcon V, Keeports CM, Zelt F, Steffy LY, Brantley SL. Methane concentrations in streams reveal gas leak discharges in regions of oil, gas, and coal development. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 737:140105. [PMID: 32783833 DOI: 10.1016/j.scitotenv.2020.140105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 06/07/2020] [Accepted: 06/08/2020] [Indexed: 05/12/2023]
Abstract
As natural gas has grown in importance as a global energy source, leakage of methane (CH4) from wells has sometimes been noted. Leakage of this greenhouse gas is important because it affects groundwater quality and, when emitted to the atmosphere, climate. We hypothesized that streams might be most contaminated by CH4 in the northern Appalachian Basin in regions with the longest history of hydrocarbon extraction activities. To test this, we searched for CH4-contaminated streams in the basin. Methane concentrations ([CH4]) for 529 stream sites are reported in New York, West Virginia and (mostly) Pennsylvania. Despite targeting contaminated areas, the median [CH4], 1.1 μg/L, was lower than a recently identified threshold indicating potential contamination, 4.0 μg/L. [CH4] values were higher in a few streams because they receive high-[CH4] groundwaters, often from upwelling seeps. By analogy to the more commonly observed type of groundwater seep known as abandoned mine drainage (AMD), we introduce the term, "gas leak discharge" (GLD) for these waters where they are not associated with coal mines. GLD and AMD, observed in all parts of the study area, are both CH4-rich. Surprisingly, the region of oldest and most productive oil/gas development did not show the highest median for stream [CH4]. Instead, the median was statistically highest where dense coal mining was accompanied by conventional and unconventional oil and gas development, emphasizing the importance of CH4 contamination from coal mines into streams.
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Affiliation(s)
- Josh Woda
- Department of Geosciences, Pennsylvania State University, University Park, PA 16802, USA.
| | - Tao Wen
- Earth and Environmental Systems Institute, Pennsylvania State University, University Park, PA 16802, USA
| | | | - Virginia Marcon
- Department of Geosciences, Pennsylvania State University, University Park, PA 16802, USA
| | | | - Fred Zelt
- Independent Geoscientist, Pittsburgh, PA 15106, USA
| | - Luanne Y Steffy
- Susquehanna River Basin Commission, Harrisburg, PA 17110, USA
| | - Susan L Brantley
- Department of Geosciences, Pennsylvania State University, University Park, PA 16802, USA; Earth and Environmental Systems Institute, Pennsylvania State University, University Park, PA 16802, USA
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14
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Zhang N, Bu X, Li Y, Zhang Y, Yuan S, Wen Z, Tong M, Lin L. Water Table Fluctuations Regulate Hydrogen Peroxide Production and Distribution in Unconfined Aquifers. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:4942-4951. [PMID: 32202769 DOI: 10.1021/acs.est.0c00487] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Significance of reactive oxygen species (ROS) in subsurface has been increasingly documented in recent years, whereas the mechanisms controlling ROS production and distribution in subsurface remain poorly understood. Here we show that water table fluctuations regulate the dynamics of hydrogen peroxide (H2O2) production and distribution in unconfined aquifers. In one hydrological year, we measured the dynamics of H2O2 distribution in an unconfined aquifer impacted by a 14 m water level fluctuation in the adjacent Yangtze River. H2O2 concentrations in groundwater attained up to 123 nM at rising water table stage in summer, but were low or even below the detection limit at the other stages of stable and falling water table. Lab experiments and kinetic models revealed that abiotic reactions between dissolved O2 and reduced species (i.e., Fe(II) and organic matter) were responsible for H2O2 production in the aquifers. Both field observations and reactive transport models unveiled that a rising water table developed a thermodynamically unstable banded zone in the unconfined aquifer in which elevated coexisting dissolved O2 and reduced species favored abiotic H2O2 production. Our findings provide fundamentals for understanding and predicting ROS distribution in unconfined aquifers, and constrain the significance of ROS in aquifers to specific temporal and spatial domains.
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Affiliation(s)
- Na Zhang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, NO. 68 Jincheng Street, East Lake High-Tech Development Zone, Wuhan 430078, P. R. China
| | - Xiaochuang Bu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, NO. 68 Jincheng Street, East Lake High-Tech Development Zone, Wuhan 430078, P. R. China
| | - Yiming Li
- School of Environmental Studies, China University of Geosciences, NO. 68 Jincheng Street, East Lake High-Tech Development Zone, Wuhan, 430078, P. R. China
| | - Yanting Zhang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, NO. 68 Jincheng Street, East Lake High-Tech Development Zone, Wuhan 430078, P. R. China
| | - Songhu Yuan
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, NO. 68 Jincheng Street, East Lake High-Tech Development Zone, Wuhan 430078, P. R. China
| | - Zhang Wen
- School of Environmental Studies, China University of Geosciences, NO. 68 Jincheng Street, East Lake High-Tech Development Zone, Wuhan, 430078, P. R. China
| | - Man Tong
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, NO. 68 Jincheng Street, East Lake High-Tech Development Zone, Wuhan 430078, P. R. China
| | - Li Lin
- Department of Water Environment Research, Changjiang River Scientific Research Institute, Wuhan, Hubei 430010, China
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15
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Kaestli M, O’Donnell M, Rose A, Webb JR, Mayo M, Currie BJ, Gibb K. Opportunistic pathogens and large microbial diversity detected in source-to-distribution drinking water of three remote communities in Northern Australia. PLoS Negl Trop Dis 2019; 13:e0007672. [PMID: 31487283 PMCID: PMC6728021 DOI: 10.1371/journal.pntd.0007672] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 07/29/2019] [Indexed: 12/11/2022] Open
Abstract
In the wet-dry tropics of Northern Australia, drinking water in remote communities is mostly sourced from bores accessing groundwater. Many aquifers contain naturally high levels of iron and some are shallow with surface water intrusion in the wet season. Therefore, environmental bacteria such as iron-cycling bacteria promoting biofilm formation in pipes or opportunistic pathogens can occur in these waters. An opportunistic pathogen endemic to northern Australia and Southeast Asia and emerging worldwide is Burkholderia pseudomallei. It causes the frequently fatal disease melioidosis in humans and animals. As we know very little about the microbial composition of drinking water in remote communities, this study aimed to provide a first snapshot of the microbiota and occurrence of opportunistic pathogens in bulk water and biofilms from the source and through the distribution system of three remote water supplies with varying iron levels. Using 16s-rRNA gene sequencing, we found that the geochemistry of the groundwater had a substantial impact on the untreated microbiota. Different iron-cycling bacteria reflected differences in redox status and nutrients. We cultured and sequenced B. pseudomallei from bores with elevated iron and from a multi-species biofilm which also contained iron-oxidizing Gallionella, nitrifying Nitrospira and amoebae. Gallionella are increasingly used in iron-removal filters in water supplies and more research is needed to examine these interactions. Similar to other opportunistic pathogens, B. pseudomallei occurred in water with low organic carbon levels and with low heterotrophic microbial growth. No B. pseudomallei were detected in treated water; however, abundant DNA of another opportunistic pathogen group, non-tuberculous mycobacteria was recovered from treated parts of one supply. Results from this study will inform future studies to ultimately improve management guidelines for water supplies in the wet-dry tropics.
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Affiliation(s)
- Mirjam Kaestli
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, Australia
- Global and Tropical Health, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | | | - Alea Rose
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Jessica R. Webb
- Global and Tropical Health, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Mark Mayo
- Global and Tropical Health, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Bart J. Currie
- Global and Tropical Health, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Karen Gibb
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, Australia
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16
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Ward LM, Idei A, Nakagawa M, Ueno Y, Fischer WW, McGlynn SE. Geochemical and Metagenomic Characterization of Jinata Onsen, a Proterozoic-Analog Hot Spring, Reveals Novel Microbial Diversity including Iron-Tolerant Phototrophs and Thermophilic Lithotrophs. Microbes Environ 2019; 34:278-292. [PMID: 31413226 PMCID: PMC6759342 DOI: 10.1264/jsme2.me19017] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Hydrothermal systems, including terrestrial hot springs, contain diverse geochemical conditions that vary over short spatial scales due to progressive interactions between reducing hydrothermal fluids, the oxygenated atmosphere, and, in some cases, seawater. At Jinata Onsen on Shikinejima Island, Japan, an intertidal, anoxic, iron-rich hot spring mixes with the oxygenated atmosphere and seawater over short spatial scales, creating diverse chemical potentials and redox pairs over a distance of ~10 m. We characterized geochemical conditions along the outflow of Jinata Onsen as well as the microbial communities present in biofilms, mats, and mineral crusts along its traverse using 16S rRNA gene amplicon and genome-resolved shotgun metagenomic sequencing. Microbial communities significantly changed downstream as temperatures and dissolved iron concentrations decreased and dissolved oxygen increased. Biomass was more limited near the spring source than downstream, and primary productivity appeared to be fueled by the oxidation of ferrous iron and molecular hydrogen by members of Zetaproteobacteria and Aquificae. The microbial community downstream was dominated by oxygenic Cyanobacteria. Cyanobacteria are abundant and active even at ferrous iron concentrations of ~150 μM, which challenges the idea that iron toxicity limited cyanobacterial expansion in Precambrian oceans. Several novel lineages of Bacteria are also present at Jinata Onsen, including previously uncharacterized members of the phyla Chloroflexi and Calditrichaeota, positioning Jinata Onsen as a valuable site for the future characterization of these clades.
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Affiliation(s)
- Lewis M Ward
- Department of Earth and Planetary Sciences, Harvard University.,Earth-Life Science Institute, Tokyo Institute of Technology.,Division of Geological and Planetary Sciences, California Institute of Technology
| | - Airi Idei
- Department of Biological Sciences, Tokyo Metropolitan University
| | | | - Yuichiro Ueno
- Earth-Life Science Institute, Tokyo Institute of Technology.,Department of Earth and Planetary Sciences, Tokyo Institute of Technology.,Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology
| | - Woodward W Fischer
- Division of Geological and Planetary Sciences, California Institute of Technology
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17
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Molecular underpinnings for microbial extracellular electron transfer during biogeochemical cycling of earth elements. SCIENCE CHINA-LIFE SCIENCES 2019; 62:1275-1286. [DOI: 10.1007/s11427-018-9464-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 12/09/2018] [Indexed: 02/07/2023]
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18
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Floyd MAM, Williams AJ, Grubisic A, Emerson D. Metabolic Processes Preserved as Biosignatures in Iron-Oxidizing Microorganisms: Implications for Biosignature Detection on Mars. ASTROBIOLOGY 2019; 19:40-52. [PMID: 30044121 PMCID: PMC6338579 DOI: 10.1089/ast.2017.1745] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Iron-oxidizing bacteria occupy a distinct environmental niche. These chemolithoautotrophic organisms require very little oxygen (when neutrophilic) or outcompete oxygen for access to Fe(II) (when acidophilic). The utilization of Fe(II) as an electron donor makes them strong analog organisms for any potential life that could be found on Mars. Despite their importance to the elucidation of early life on, and potentially beyond, Earth, many details of their metabolism remain unknown. By using on-line thermochemolysis and gas chromatography-mass spectrometry (GC-MS), a distinct signal for a low-molecular-weight molecule was discovered in multiple iron-oxidizing isolates as well as several iron-dominated environmental samples, from freshwater and marine environments and in both modern and older iron rock samples. This GC-MS signal was neither detected in organisms that did not use Fe(II) as an electron donor nor present in iron mats in which organic carbon was destroyed by heating. Mass spectral analysis indicates that the molecule bears the hallmarks of a pterin-bearing molecule. Genomic analysis has previously identified a molybdopterin that could be part of the electron transport chain in a number of lithotrophic iron-oxidizing bacteria, suggesting one possible source for this signal is the pterin component of this protein. The rock samples indicate the possibility that the molecule can be preserved within lithified sedimentary rocks. The specificity of the signal to organisms requiring iron in their metabolism makes this a novel biosignature with which to investigate both the evolution of life on ancient Earth and potential life on Mars.
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Affiliation(s)
| | - Amy J Williams
- 1 NASA Goddard Space Flight Center , Greenbelt, Maryland
- 2 Department of Physics, Astronomy, and Geosciences, Towson University , Towson, Maryland
| | | | - David Emerson
- 3 Bigelow Laboratory for Ocean Sciences , East Boothbay, Maine
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19
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Boddicker AM, Mosier AC. Genomic profiling of four cultivated Candidatus Nitrotoga spp. predicts broad metabolic potential and environmental distribution. THE ISME JOURNAL 2018; 12:2864-2882. [PMID: 30050164 PMCID: PMC6246548 DOI: 10.1038/s41396-018-0240-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 06/28/2018] [Accepted: 07/03/2018] [Indexed: 12/21/2022]
Abstract
Nitrite-oxidizing bacteria (NOB) play a critical role in the mitigation of nitrogen pollution by metabolizing nitrite to nitrate, which is removed via assimilation, denitrification, or anammox. Recent studies showed that NOB are phylogenetically and metabolically diverse, yet most of our knowledge of NOB comes from only a few cultured representatives. Using cultivation and genomic sequencing, we identified four putative Candidatus Nitrotoga NOB species from freshwater sediments and water column samples in Colorado, USA. Genome analyses indicated highly conserved 16S rRNA gene sequences, but broad metabolic potential including genes for nitrogen, sulfur, hydrogen, and organic carbon metabolism. Genomic predictions suggested that Ca. Nitrotoga can metabolize in low oxygen or anoxic conditions, which may support an expanded environmental niche for Ca. Nitrotoga similar to other NOB. An array of antibiotic and metal resistance genes likely allows Ca. Nitrotoga to withstand environmental pressures in impacted systems. Phylogenetic analyses highlighted a deeply divergent nitrite oxidoreductase alpha subunit (NxrA), suggesting a novel evolutionary trajectory for Ca. Nitrotoga separate from any other NOB and further revealing the complex evolutionary history of nitrite oxidation in the bacterial domain. Ca. Nitrotoga-like 16S rRNA gene sequences were prevalent in globally distributed environments over a range of reported temperatures. This work considerably expands our knowledge of the Ca. Nitrotoga genus and suggests that their contribution to nitrogen cycling should be considered alongside other NOB in wide variety of habitats.
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Affiliation(s)
- Andrew M Boddicker
- Department of Integrative Biology, University of Colorado Denver, Campus Box 171, Denver, CO, USA
| | - Annika C Mosier
- Department of Integrative Biology, University of Colorado Denver, Campus Box 171, Denver, CO, USA.
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20
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Fortney NW, He S, Converse BJ, Boyd ES, Roden EE. Investigating the Composition and Metabolic Potential of Microbial Communities in Chocolate Pots Hot Springs. Front Microbiol 2018; 9:2075. [PMID: 30245673 PMCID: PMC6137239 DOI: 10.3389/fmicb.2018.02075] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 08/14/2018] [Indexed: 01/14/2023] Open
Abstract
Iron (Fe) redox-based metabolisms likely supported life on early Earth and may support life on other Fe-rich rocky planets such as Mars. Modern systems that support active Fe redox cycling such as Chocolate Pots (CP) hot springs provide insight into how life could have functioned in such environments. Previous research demonstrated that Fe- and Si-rich and slightly acidic to circumneutral-pH springs at CP host active dissimilatory Fe(III) reducing microorganisms. However, the abundance and distribution of Fe(III)-reducing communities at CP is not well-understood, especially as they exist in situ. In addition, the potential for direct Fe(II) oxidation by lithotrophs in CP springs is understudied, in particular when compared to indirect oxidation promoted by oxygen producing Cyanobacteria. Here, a culture-independent approach, including 16S rRNA gene amplicon and shotgun metagenomic sequencing, was used to determine the distribution of putative Fe cycling microorganisms in vent fluids and sediment cores collected along the outflow channel of CP. Metagenome-assembled genomes (MAGs) of organisms native to sediment and planktonic microbial communities were screened for extracellular electron transfer (EET) systems putatively involved in Fe redox cycling and for CO2 fixation pathways. Abundant MAGs containing putative EET systems were identified as part of the sediment community at locations where Fe(III) reduction activity has previously been documented. MAGs encoding both putative EET systems and CO2 fixation pathways, inferred to be FeOB, were also present, but were less abundant components of the communities. These results suggest that the majority of the Fe(III) oxides that support in situ Fe(III) reduction are derived from abiotic oxidation. This study provides new insights into the interplay between Fe redox cycling and CO2 fixation in sustaining chemotrophic communities in CP with attendant implications for other neutral-pH hot springs.
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Affiliation(s)
- Nathaniel W. Fortney
- Department of Geoscience, NASA Astrobiology Institute, University of Wisconsin-Madison, Madison, WI, United States
| | - Shaomei He
- Department of Geoscience, NASA Astrobiology Institute, University of Wisconsin-Madison, Madison, WI, United States
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - Brandon J. Converse
- Department of Geoscience, NASA Astrobiology Institute, University of Wisconsin-Madison, Madison, WI, United States
| | - Eric S. Boyd
- Department of Microbiology and Immunology, NASA Astrobiology Institute, Montana State University, Bozeman, MT, United States
| | - Eric E. Roden
- Department of Geoscience, NASA Astrobiology Institute, University of Wisconsin-Madison, Madison, WI, United States
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21
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Sheng Y, Wang G, Zhao D, Hao C, Liu C, Cui L, Zhang G. Groundwater Microbial Communities Along a Generalized Flowpath in Nomhon Area, Qaidam Basin, China. GROUND WATER 2018; 56:719-731. [PMID: 29121391 DOI: 10.1111/gwat.12615] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 10/08/2017] [Accepted: 10/11/2017] [Indexed: 06/07/2023]
Abstract
Spatial distribution (horizonal and vertical) of groundwater microbial communities and the hydrogeochemistry in confined aquifers were studied approximately along the groundwater flow path from coteau to plain in the Nomhon area, Qinghai-Tibet plateau, China. The confined groundwater samples at different depths and locations were collected in three boreholes through a hydrogeological section in this arid and semi-arid area. The phylogenetic analysis of 16S rRNA genes and multivariate statistical analysis were used to elucidate similarities and differences between groundwater microbial communities and hydrogeochemical properties. The integrated isotopic geochemical measurements were applied to estimate the source and recharge characteristics of groundwater. The results showed that groundwater varied from fresh to saline water, and modern water to ancient water following the flowpath. The recharge characteristics of the saline water was distinct with that of fresh water. Cell abundance did not vary greatly along the hydrogeochemical zonality; however, dissimilarities in habitat-based microbial community structures were evident, changing from Betaproteobacteria in the apex of alluvial fan to Gammaproteobacteria and then to Epsilonproteobacteria in the core of the basin (alluvial-lacustrine plain). Rhodoferax, Hydrogenophaga, Pseudomonas, and bacterium isolated from similar habitats unevenly thrived in the spatially distinct fresh water environments, while Sulfurimonas dominanted in the saline water environment. The microbial communities presented likely reflected to the hydrogeochemical similarities and zonalities along groundwater flowpath.
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Affiliation(s)
- Yizhi Sheng
- State Key Laboratory of Biogeology and Environmental Geology & Key Laboratory of Groundwater Circulation and Evolution, China University of Geosciences, Beijing, 100083, China
- School of Water Resources and Environment, China University of Geosciences, Beijing, 100083, China
- School of Environment, Tsinghua University, Beijing, 100084, China
| | - Guangcai Wang
- State Key Laboratory of Biogeology and Environmental Geology & Key Laboratory of Groundwater Circulation and Evolution, China University of Geosciences, Beijing, 100083, China
- School of Water Resources and Environment, China University of Geosciences, Beijing, 100083, China
| | - Dan Zhao
- State Key Laboratory of Biogeology and Environmental Geology & Key Laboratory of Groundwater Circulation and Evolution, China University of Geosciences, Beijing, 100083, China
- School of Water Resources and Environment, China University of Geosciences, Beijing, 100083, China
| | - Chunbo Hao
- State Key Laboratory of Biogeology and Environmental Geology & Key Laboratory of Groundwater Circulation and Evolution, China University of Geosciences, Beijing, 100083, China
- School of Water Resources and Environment, China University of Geosciences, Beijing, 100083, China
| | - Chenglong Liu
- Institute of Geology, China Earthquake Administration, Beijing, 100029, China
| | - Linfeng Cui
- State Key Laboratory of Biogeology and Environmental Geology & Key Laboratory of Groundwater Circulation and Evolution, China University of Geosciences, Beijing, 100083, China
- School of Water Resources and Environment, China University of Geosciences, Beijing, 100083, China
| | - Ge Zhang
- Xi'an Center of Geological Survey, China Geological Survey, Xi'an, 710054, China
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22
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Whitaker AH, Peña J, Amor M, Duckworth OW. Cr(vi) uptake and reduction by biogenic iron (oxyhydr)oxides. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2018; 20:1056-1068. [PMID: 29922797 DOI: 10.1039/c8em00149a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The mobility and toxicity of chromium (Cr) in soil and water systems are largely controlled by its oxidation state and interactions with solid phases. Relative to abiotic minerals, biogenic iron (Fe) (oxyhydr)oxides (BIOS) may enhance Cr(vi) adsorption and reduction due to their poorly ordered structures, large surface areas, and incorporation of cell derived organic matter. To determine the extent and mechanisms of the reaction between Cr(vi) and BIOS, sorption isotherm and kinetic studies were conducted using two-line ferrihydrite, BIOS, and BIOS amended with 0.135 M ferrozine (an Fe(ii) chelator). X-ray absorption near edge structure (XANES) spectroscopy of BIOS reacted with Cr(vi) showed approximately 50% reduction of the total sorbed Cr from Cr(vi) to Cr(iii) after 14 days of exposure. Sorbed Cr(iii) was best fit with an organic carboxylate complex after 1 d of reaction, but after 7 d mineral-associated Cr(iii) was the predominant form. In the presence of ferrozine, Cr(vi) reduction by BIOS was inhibited, confirming a key role for Fe(ii) as the Cr(vi) reductant. However, the lack of a 3 : 1 reaction stoichiometry between Fe(ii) and Cr(iii) produced suggests roles for reaction with organic matter and Cr(v) autoreduction in Cr(iii) production. This study thus elucidates an unrecognized mechanism of Cr sequestration by ubiquitous natural Fe (oxyhydr)oxide deposits. Furthermore, the redox transformation of mobile Cr(vi) to less soluble Cr(iii) species observed in our study implies that biogenic Fe (oxyhydr)oxides in soils and natural waters may naturally attenuate Cr(vi) concentrations through sorption and reduction processes, thus limiting its transport to downstream environments.
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Affiliation(s)
- Andrew H Whitaker
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695-7620, USA.
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Flynn ED, Catalano JG. Influence of Oxalate on Ni Fate during Fe(II)-Catalyzed Recrystallization of Hematite and Goethite. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:6920-6927. [PMID: 29806459 DOI: 10.1021/acs.est.8b00641] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
During biogeochemical iron cycling at redox interfaces, dissolved Fe(II) induces the recrystallization of Fe(III) oxides. Oxalate and other organic acids promote dissolution of these minerals and may also induce recrystallization. These processes may redistribute trace metals among the mineral bulk, mineral surface, and aqueous solution. However, the impact of interactions among organic acids, dissolved Fe(II), and iron oxide minerals on trace metal fate in such systems is unclear. The present study thus explores the effect of oxalate on Ni release from and incorporation into hematite and goethite in the absence and presence of Fe(II). When Ni is initially structurally incorporated into the iron oxides, both oxalate and dissolved Fe(II) promote the release of Ni to aqueous solution. When both species are present, their effects on Ni release are synergistic at pH 7 but inhibitory at pH 4, indicating that cooperative and competitive interactions vary with pH. In contrast, oxalate suppresses Ni incorporation into goethite and hematite during Fe(II)-induced recrystallization, decreasing the proportion of Ni substituting in a mineral structure by up to 36%. These observations suggest that at redox interfaces oxalate largely enhances trace metal mobility. In such settings, oxalate, and likely other organic acids, may thus enhance micronutrient availability and inhibit contaminant sequestration.
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Affiliation(s)
- Elaine D Flynn
- Department of Earth and Planetary Sciences , Washington University , St. Louis , Missouri 63130 , United States
| | - Jeffrey G Catalano
- Department of Earth and Planetary Sciences , Washington University , St. Louis , Missouri 63130 , United States
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Valentín-Vargas A, Neilson JW, Root RA, Chorover J, Maier RM. Treatment impacts on temporal microbial community dynamics during phytostabilization of acid-generating mine tailings in semiarid regions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 618:357-368. [PMID: 29132003 PMCID: PMC5773348 DOI: 10.1016/j.scitotenv.2017.11.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Revised: 09/28/2017] [Accepted: 11/01/2017] [Indexed: 05/27/2023]
Abstract
Direct revegetation, or phytostabilization, is a containment strategy for contaminant metals associated with mine tailings in semiarid regions. The weathering of sulfide ore-derived tailings frequently drives acidification that inhibits plant establishment resulting in materials prone to wind and water dispersal. The specific objective of this study was to associate pyritic mine waste acidification, characterized through pore-water chemistry analysis, with dynamic changes in microbial community diversity and phylogenetic composition, and to evaluate the influence of different treatment strategies on the control of acidification dynamics. Samples were collected from a highly instrumented one-year mesocosm study that included the following treatments: 1) unamended tailings control; 2) tailings amended with 15% compost; and 3) the 15% compost-amended tailings planted with Atriplex lentiformis. Tailings samples were collected at 0, 3, 6 and 12months and pore water chemistry was monitored as an indicator of acidification and weathering processes. Results confirmed that the acidification process for pyritic mine tailings is associated with a temporal progression of bacterial and archaeal phylotypes from pH sensitive Thiobacillus and Thiomonas to communities dominated by Leptospirillum and Ferroplasma. Pore-water chemistry indicated that weathering rates were highest when Leptospirillum was most abundant. The planted treatment was most successful in disrupting the successional evolution of the Fe/S-oxidizing community. Plant establishment stimulated growth of plant-growth-promoting heterotrophic phylotypes and controlled the proliferation of lithoautotrophic Fe/S-oxidizers. The results suggest the potential for eco-engineering a microbial inoculum to stimulate plant establishment and inhibit proliferation of the most efficient Fe/S-oxidizing phylotypes.
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Affiliation(s)
- Alexis Valentín-Vargas
- Department of Soil, Water and Environmental Science, 429 Shantz Bldg. #38, 1177 E. Fourth Street, University of Arizona, Tucson, AZ 85721-0038, USA
| | - Julia W Neilson
- Department of Soil, Water and Environmental Science, 429 Shantz Bldg. #38, 1177 E. Fourth Street, University of Arizona, Tucson, AZ 85721-0038, USA.
| | - Robert A Root
- Department of Soil, Water and Environmental Science, 429 Shantz Bldg. #38, 1177 E. Fourth Street, University of Arizona, Tucson, AZ 85721-0038, USA
| | - Jon Chorover
- Department of Soil, Water and Environmental Science, 429 Shantz Bldg. #38, 1177 E. Fourth Street, University of Arizona, Tucson, AZ 85721-0038, USA
| | - Raina M Maier
- Department of Soil, Water and Environmental Science, 429 Shantz Bldg. #38, 1177 E. Fourth Street, University of Arizona, Tucson, AZ 85721-0038, USA
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Meyer-Dombard DR, Casar CP, Simon AG, Cardace D, Schrenk MO, Arcilla CA. Biofilm formation and potential for iron cycling in serpentinization-influenced groundwater of the Zambales and Coast Range ophiolites. Extremophiles 2018; 22:407-431. [PMID: 29450709 DOI: 10.1007/s00792-018-1005-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Accepted: 02/05/2018] [Indexed: 02/01/2023]
Abstract
Terrestrial serpentinizing systems harbor microbial subsurface life. Passive or active microbially mediated iron transformations at alkaline conditions in deep biosphere serpentinizing ecosystems are understudied. We explore these processes in the Zambales (Philippines) and Coast Range (CA, USA) ophiolites, and associated surface ecosystems by probing the relevance of samples acquired at the surface to in situ, subsurface ecosystems, and the nature of microbe-mineral associations in the subsurface. In this pilot study, we use microcosm experiments and batch culturing directed at iron redox transformations to confirm thermodynamically based predictions that iron transformations may be important in subsurface serpentinizing ecosystems. Biofilms formed on rock cores from the Zambales ophiolite on surface and in-pit associations, confirming that organisms from serpentinizing systems can form biofilms in subsurface environments. Analysis by XPS and FTIR confirmed that enrichment culturing utilizing ferric iron growth substrates produced reduced, magnetic solids containing siderite, spinels, and FeO minerals. Microcosms and enrichment cultures supported organisms whose near relatives participate in iron redox transformations. Further, a potential 'principal' microbial community common to solid samples in serpentinizing systems was identified. These results indicate collectively that iron redox transformations should be more thoroughly and universally considered when assessing the function of terrestrial subsurface ecosystems driven by serpentinization.
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Affiliation(s)
- D'Arcy R Meyer-Dombard
- Department of Earth and Environmental Sciences, University of Illinois at Chicago, m/c 186, 845 W. Taylor St., Chicago, IL, 60515, USA.
| | - Caitlin P Casar
- Department of Earth and Environmental Sciences, University of Illinois at Chicago, m/c 186, 845 W. Taylor St., Chicago, IL, 60515, USA
| | - Alexander G Simon
- Department of Earth and Environmental Sciences, University of Illinois at Chicago, m/c 186, 845 W. Taylor St., Chicago, IL, 60515, USA
| | - Dawn Cardace
- Department of Geosciences, University of Rhode Island, Kingston, IL, USA
| | - Matthew O Schrenk
- Department of Earth and Environmental Sciences, Michigan State University, East Lansing, MI, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Carlo A Arcilla
- National Institute of Geological Sciences, University of the Philippines, Diliman, Quezon City, Philippines
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Denitrification by Anaeromyxobacter dehalogenans, a Common Soil Bacterium Lacking the Nitrite Reductase Genes nirS and nirK. Appl Environ Microbiol 2018; 84:AEM.01985-17. [PMID: 29196287 DOI: 10.1128/aem.01985-17] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 11/27/2017] [Indexed: 11/20/2022] Open
Abstract
The versatile soil bacterium Anaeromyxobacter dehalogenans lacks the hallmark denitrification genes nirS and nirK (encoding NO2 -→NO reductases) and couples growth to NO3 - reduction to NH4 + (respiratory ammonification) and to N2O reduction to N2 A. dehalogenans also grows by reducing Fe(III) to Fe(II), which chemically reacts with NO2 - to form N2O (i.e., chemodenitrification). Following the addition of 100 μmol of NO3 - or NO2 - to Fe(III)-grown axenic cultures of A. dehalogenans, 54 (±7) μmol and 113 (±2) μmol N2O-N, respectively, were produced and subsequently consumed. The conversion of NO3 - to N2 in the presence of Fe(II) through linked biotic-abiotic reactions represents an unrecognized ecophysiology of A. dehalogenans The new findings demonstrate that the assessment of gene content alone is insufficient to predict microbial denitrification potential and N loss (i.e., the formation of gaseous N products). A survey of complete bacterial genomes in the NCBI Reference Sequence database coupled with available physiological information revealed that organisms lacking nirS or nirK but with Fe(III) reduction potential and genes for NO3 - and N2O reduction are not rare, indicating that NO3 - reduction to N2 through linked biotic-abiotic reactions is not limited to A. dehalogenans Considering the ubiquity of iron in soils and sediments and the broad distribution of dissimilatory Fe(III) and NO3 - reducers, denitrification independent of NO-forming NO2 - reductases (through combined biotic-abiotic reactions) may have substantial contributions to N loss and N2O flux.IMPORTANCE Current attempts to gauge N loss from soils rely on the quantitative measurement of nirK and nirS genes and/or transcripts. In the presence of iron, the common soil bacterium Anaeromyxobacter dehalogenans is capable of denitrification and the production of N2 without the key denitrification genes nirK and nirS Such chemodenitrifiers denitrify through combined biotic and abiotic reactions and have potentially large contributions to N loss to the atmosphere and fill a heretofore unrecognized ecological niche in soil ecosystems. The findings emphasize that the comprehensive understanding of N flux and the accurate assessment of denitrification potential can be achieved only when integrated studies of interlinked biogeochemical cycles are performed.
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Ward LM, Idei A, Terajima S, Kakegawa T, Fischer WW, McGlynn SE. Microbial diversity and iron oxidation at Okuoku-hachikurou Onsen, a Japanese hot spring analog of Precambrian iron formations. GEOBIOLOGY 2017; 15:817-835. [PMID: 29035022 DOI: 10.1111/gbi.12266] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 09/21/2017] [Indexed: 06/07/2023]
Abstract
Banded iron formations (BIFs) are rock deposits common in the Archean and Paleoproterozoic (and regionally Neoproterozoic) sedimentary successions. Multiple hypotheses for their deposition exist, principally invoking the precipitation of iron via the metabolic activities of oxygenic, photoferrotrophic, and/or aerobic iron-oxidizing bacteria. Some isolated environments support chemistry and mineralogy analogous to processes involved in BIF deposition, and their study can aid in untangling the factors that lead to iron precipitation. One such process analog system occurs at Okuoku-hachikurou (OHK) Onsen in Akita Prefecture, Japan. OHK is an iron- and CO2 -rich, circumneutral hot spring that produces a range of precipitated mineral textures containing fine laminae of aragonite and iron oxides that resemble BIF fabrics. Here, we have performed 16S rRNA gene amplicon sequencing of microbial communities across the range of microenvironments in OHK to describe the microbial diversity present and to gain insight into the cycling of iron, oxygen, and carbon in this ecosystem. These analyses suggest that productivity at OHK is based on aerobic iron-oxidizing Gallionellaceae. In contrast to other BIF analog sites, Cyanobacteria, anoxygenic phototrophs, and iron-reducing micro-organisms are present at only low abundances. These observations support a hypothesis where low growth yields and the high stoichiometry of iron oxidized per carbon fixed by aerobic iron-oxidizing chemoautotrophs like Gallionellaceae result in accumulation of iron oxide phases without stoichiometric buildup of organic matter. This system supports little dissimilatory iron reduction, further setting OHK apart from other process analog sites where iron oxidation is primarily driven by phototrophic organisms. This positions OHK as a study area where the controls on primary productivity in iron-rich environments can be further elucidated. When compared with geological data, the metabolisms and mineralogy at OHK are most similar to specific BIF occurrences deposited after the Great Oxygenation Event, and generally discordant with those that accumulated before it.
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Affiliation(s)
- L M Ward
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - A Idei
- Department of Biology, Tokyo Metropolitan University, Tokyo, Japan
| | - S Terajima
- Department of Geosciences, Tohoku University, Sendai City, Japan
| | - T Kakegawa
- Department of Geosciences, Tohoku University, Sendai City, Japan
| | - W W Fischer
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - S E McGlynn
- Department of Biology, Tokyo Metropolitan University, Tokyo, Japan
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Blue Marble Space Institute of Science, Seattle, WA, USA
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Percak-Dennett E, He S, Converse B, Konishi H, Xu H, Corcoran A, Noguera D, Chan C, Bhattacharyya A, Borch T, Boyd E, Roden EE. Microbial acceleration of aerobic pyrite oxidation at circumneutral pH. GEOBIOLOGY 2017; 15:690-703. [PMID: 28452176 DOI: 10.1111/gbi.12241] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Accepted: 03/22/2017] [Indexed: 06/07/2023]
Abstract
Pyrite (FeS2 ) is the most abundant sulfide mineral on Earth and represents a significant reservoir of reduced iron and sulfur both today and in the geologic past. In modern environments, oxidative transformations of pyrite and other metal sulfides play a key role in terrestrial element partitioning with broad impacts to contaminant mobility and the formation of acid mine drainage systems. Although the role of aerobic micro-organisms in pyrite oxidation under acidic-pH conditions is well known, to date there is very little known about the capacity for aerobic micro-organisms to oxidize pyrite at circumneutral pH. Here, we describe two enrichment cultures, obtained from pyrite-bearing subsurface sediments, that were capable of sustained cell growth linked to pyrite oxidation and sulfate generation at neutral pH. The cultures were dominated by two Rhizobiales species (Bradyrhizobium sp. and Mesorhizobium sp.) and a Ralstonia species. Shotgun metagenomic sequencing and genome reconstruction indicated the presence of Fe and S oxidation pathways in these organisms, and the presence of a complete Calvin-Benson-Bassham CO2 fixation system in the Bradyrhizobium sp. Oxidation of pyrite resulted in thin (30-50 nm) coatings of amorphous Fe(III) oxide on the pyrite surface, with no other secondary Fe or S phases detected by electron microscopy or X-ray absorption spectroscopy. Rates of microbial pyrite oxidation were approximately one order of magnitude higher than abiotic rates. These results demonstrate the ability of aerobic microbial activity to accelerate pyrite oxidation and expand the potential contribution of micro-organisms to continental sulfide mineral weathering around the time of the Great Oxidation Event to include neutral-pH environments. In addition, our findings have direct implications for the geochemistry of modern sedimentary environments, including stimulation of the early stages of acid mine drainage formation and mobilization of pyrite-associated metals.
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Affiliation(s)
- E Percak-Dennett
- Department of Geoscience, NASA Astrobiology Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - S He
- Department of Geoscience, NASA Astrobiology Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - B Converse
- Department of Geoscience, NASA Astrobiology Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - H Konishi
- Department of Geoscience, NASA Astrobiology Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - H Xu
- Department of Geoscience, NASA Astrobiology Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - A Corcoran
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - D Noguera
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - C Chan
- Department of Geological Sciences, University of Delaware, Newark, DE, USA
| | - A Bhattacharyya
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - T Borch
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - E Boyd
- Department of Microbiology & Immunology, Montana State University, Bozeman, MT, USA
| | - E E Roden
- Department of Geoscience, NASA Astrobiology Institute, University of Wisconsin-Madison, Madison, WI, USA
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Enrichment and Physiological Characterization of a Cold-Adapted Nitrite-Oxidizing Nitrotoga sp. from an Eelgrass Sediment. Appl Environ Microbiol 2017; 83:AEM.00549-17. [PMID: 28500038 DOI: 10.1128/aem.00549-17] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 05/02/2017] [Indexed: 12/26/2022] Open
Abstract
Nitrite-oxidizing bacteria (NOB) are responsible for the second step of nitrification in natural and engineered ecosystems. The recently discovered genus Nitrotoga belongs to the Betaproteobacteria and potentially has high environmental importance. Although environmental clones affiliated with Nitrotoga are widely distributed, the limited number of cultivated Nitrotoga spp. results in a poor understanding of their ecophysiological features. In this study, we successfully enriched the nonmarine cold-adapted Nitrotoga sp. strain AM1 from coastal sand in an eelgrass zone and investigated its physiological characteristics. Multistep-enrichment approaches led to an increase in the abundance of AM1 to approximately 80% of the total bacterial population. AM1 was the only detectable NOB in the bacterial community. The 16S rRNA gene sequence of AM1 was 99.6% identical to that of "Candidatus Nitrotoga arctica," which was enriched from permafrost-affected soil. The highest nitrogen oxidation rate of AM1 was observed at 16°C. The half-saturation constant (Km ) and the generation time were determined to be 25 μM NO2- and 54 h, respectively. The nitrite oxidation rate of AM1 was stimulated at concentrations of <30 mM NH4Cl but completely inhibited at 50 mM NH4Cl. AM1 can grow well under specific environmental conditions, such as low temperature and in the presence of a relatively high concentration of free ammonia. These results help improve our comprehension of the functional importance of NitrotogaIMPORTANCE Nitrite-oxidizing bacteria (NOB) are key players in the second step of nitrification, which is an important process of the nitrogen cycle. Recent studies have suggested that the organisms of the novel NOB genus Nitrotoga were widely distributed and played a functional role in natural and engineered ecosystems. However, only a few Nitrotoga enrichments have been obtained, and little is known about their ecology and physiology. In this study, we successfully enriched a Nitrotoga sp. from sand in a shallow coastal marine ecosystem and undertook a physiological characterization. The laboratory experiments showed that the Nitrotoga enrichment culture could adapt not only to low temperature but also to relatively high concentrations of free ammonia. The determination of as-yet-unknown unique characteristics of Nitrotoga contributes to the improvement of our insights into the microbiology of nitrification.
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A universal assay for the detection of siderophore activity in natural waters. Biometals 2016; 29:1085-1095. [PMID: 27815738 DOI: 10.1007/s10534-016-9979-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 10/28/2016] [Indexed: 10/20/2022]
Abstract
Siderophores, a family of biogenic metal chelating agents, play critical roles in the biogeochemical cycling of Fe and other metals by facilitating their solubilization and uptake in circumneutral to alkaline oxic environments. However, because of their small concentrations (ca. nM) and large number of molecular structures, siderophore detection and quantification in environmental samples requires specialized equipment and expertise, and often requires pre-concentration of samples, which may introduce significant bias. The "universal" CAS assay, which was originally designed for use in bacterial cultures, quantifies the iron chelating function of a pool of siderophores but only at concentrations (>2 µM) well above the concentrations estimated to be present in marine, freshwater, and soil samples. In this manuscript, we present a high sensitivity modification of this universal assay (HS-CAS) suitable for detecting and quantifying siderophore activity in the nM concentration range, allowing for direct quantitation of siderophore reactivity in transparent aqueous samples.
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Orenia metallireducens sp. nov. Strain Z6, a Novel Metal-Reducing Member of the Phylum Firmicutes from the Deep Subsurface. Appl Environ Microbiol 2016; 82:6440-6453. [PMID: 27565620 DOI: 10.1128/aem.02382-16] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 08/19/2016] [Indexed: 12/11/2022] Open
Abstract
A novel halophilic and metal-reducing bacterium, Orenia metallireducens strain Z6, was isolated from briny groundwater extracted from a 2.02 km-deep borehole in the Illinois Basin, IL. This organism shared 96% 16S rRNA gene similarity with Orenia marismortui but demonstrated physiological properties previously unknown for this genus. In addition to exhibiting a fermentative metabolism typical of the genus Orenia, strain Z6 reduces various metal oxides [Fe(III), Mn(IV), Co(III), and Cr(VI)], using H2 as the electron donor. Strain Z6 actively reduced ferrihydrite over broad ranges of pH (6 to 9.6), salinity (0.4 to 3.5 M NaCl), and temperature (20 to 60°C). At pH 6.5, strain Z6 also reduced more crystalline iron oxides, such as lepidocrocite (γ-FeOOH), goethite (α-FeOOH), and hematite (α-Fe2O3). Analysis of X-ray absorption fine structure (XAFS) following Fe(III) reduction by strain Z6 revealed spectra from ferrous secondary mineral phases consistent with the precipitation of vivianite [Fe3(PO4)2] and siderite (FeCO3). The draft genome assembled for strain Z6 is 3.47 Mb in size and contains 3,269 protein-coding genes. Unlike the well-understood iron-reducing Shewanella and Geobacter species, this organism lacks the c-type cytochromes for typical Fe(III) reduction. Strain Z6 represents the first bacterial species in the genus Orenia (order Halanaerobiales) reported to reduce ferric iron minerals and other metal oxides. This microbe expands both the phylogenetic and physiological scopes of iron-reducing microorganisms known to inhabit the deep subsurface and suggests new mechanisms for microbial iron reduction. These distinctions from other Orenia spp. support the designation of strain Z6 as a new species, Orenia metallireducens sp. nov. IMPORTANCE A novel iron-reducing species, Orenia metallireducens sp. nov., strain Z6, was isolated from groundwater collected from a geological formation located 2.02 km below land surface in the Illinois Basin, USA. Phylogenetic, physiologic, and genomic analyses of strain Z6 found it to have unique properties for iron reducers, including (i) active microbial iron-reducing capacity under broad ranges of temperatures (20 to 60°C), pHs (6 to 9.6), and salinities (0.4 to 3.5 M NaCl), (ii) lack of c-type cytochromes typically affiliated with iron reduction in Geobacter and Shewanella species, and (iii) being the only member of the Halanaerobiales capable of reducing crystalline goethite and hematite. This study expands the scope of phylogenetic affiliations, metabolic capacities, and catalytic mechanisms for iron-reducing microbes.
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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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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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Xiao E, Krumins V, Tang S, Xiao T, Ning Z, Lan X, Sun W. Correlating microbial community profiles with geochemical conditions in a watershed heavily contaminated by an antimony tailing pond. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2016; 215:141-153. [PMID: 27182975 DOI: 10.1016/j.envpol.2016.04.087] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 04/22/2016] [Accepted: 04/25/2016] [Indexed: 06/05/2023]
Abstract
Mining activities have introduced various pollutants to surrounding aquatic and terrestrial environments, causing adverse impacts to the environment. Indigenous microbial communities are responsible for the biogeochemical cycling of pollutants in diverse environments, indicating the potential for bioremediation of such pollutants. Antimony (Sb) has been extensively mined in China and Sb contamination in mining areas has been frequently encountered. To date, however, the microbial composition and structure in response to Sb contamination has remained overlooked. Sb and As frequently co-occur in sulfide-rich ores, and co-contamination of Sb and As is observed in some mining areas. We characterized, for the first time, the microbial community profiles and their responses to Sb and As pollution from a watershed heavily contaminated by Sb tailing pond in Southwest China. The indigenous microbial communities were profiled by high-throughput sequencing from 16 sediment samples (535,390 valid reads). The comprehensive geochemical data (specifically, physical-chemical properties and different Sb and As extraction fractions) were obtained from river water and sediments at different depths as well. Canonical correspondence analysis (CCA) demonstrated that a suite of in situ geochemical and physical factors significantly structured the overall microbial community compositions. Further, we found significant correlations between individual phylotypes (bacterial genera) and the geochemical fractions of Sb and As by Spearman rank correlation. A number of taxonomic groups were positively correlated with the Sb and As extractable fractions and various Sb and As species in sediment, suggesting potential roles of these phylotypes in Sb biogeochemical cycling.
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Affiliation(s)
- Enzong Xiao
- State Key Laboratory of Environmental Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Valdis Krumins
- Department of Environmental Sciences, Rutgers University, New Brunswick, NJ 08901, USA
| | - Song Tang
- School of Environment and Sustainability, University of Saskatchewan, Saskatoon S7N5B3, Canada
| | - Tangfu Xiao
- State Key Laboratory of Environmental Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; Innovation Center and Key Laboratory of Waters Safety & Protection in the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China.
| | - Zengping Ning
- State Key Laboratory of Environmental Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
| | - Xiaolong Lan
- State Key Laboratory of Environmental Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weimin Sun
- Guangdong Institute of Eco-environment and Soil Sciences, Guangzhou 510650, China; Department of Microbiology and Biochemistry, Rutgers University, New Brunswick, NJ 08901, USA.
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Kikuchi S, Makita H, Konno U, Shiraishi F, Ijiri A, Takai K, Maeda M, Takahashi Y. Limited reduction of ferrihydrite encrusted by goethite in freshwater sediment. GEOBIOLOGY 2016; 14:374-389. [PMID: 27027643 DOI: 10.1111/gbi.12181] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 01/18/2016] [Indexed: 06/05/2023]
Abstract
Many physical and chemical processes control the extent of Fe(III) oxyhydroxide reduction by dissimilatory Fe(III)-reducing bacteria. The surface precipitation of secondary Fe minerals on Fe(III) oxyhydroxides limits the extent of microbial Fe(III) reduction, but this phenomenon has not yet been observed in nature. This paper reports the observation of secondary Fe-mineral (goethite) encrustation on ferrihydrite surface within freshwater sediment up to 10 cm deep. The sediment surface was characterized by the predominance of ferrihydrites with biogenic stalks and sheaths. An Fe(II)-oxidizing bacterium (Gallionellaceae) was detected by 16S rRNA gene analysis at sediment depths of 1 and 2 cm. Fe(2+) concentration in the sediment pore water was relatively higher at 2-4 cm depths. The 16S rRNA genes affiliated with dissimilatory Fe(III)-reducing bacteria were detected at 1, 2, and 4 cm depths. The results of the Fe K-edge extended X-ray absorption fine structure (EXAFS) analysis suggested the presence of goethite and siderite at depths below 3 cm. However, the change in the Fe-mineral composition was restricted to sediment depths between 3 and 4 cm, despite the presence of abundant ferrihydrite at depths below 4 cm. An increase in CH4 concentration was observed at deeper than 6 cm. Stable isotopic analysis of CH4 in the pore water indicated that acetoclastic CH4 occurred at depths below 7 cm. Transmission electron microscope observations suggested the presence of goethite and siderite on stalks and sheaths at depths below 3 cm. Results from conversion electron yield EXAFS analysis suggested that goethite dominated at 10 cm depth, thereby indicating that ferrihydrite was encrusted by goethite at this depth. Moreover, the incomplete reduction of ferrihydrite below depths of 4 cm was not due to the lack of organic carbon, but was possibly due to the surface encrustation of goethite on ferrihydrite.
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Affiliation(s)
- S Kikuchi
- Department of Earth and Planetary Systems Science, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
- Project Team for Development of New-Generation Research Protocol for Submarine Resources, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - H Makita
- Department of Subsurface Geobiological Analysis and Research (d-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - U Konno
- Department of Subsurface Geobiological Analysis and Research (d-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - F Shiraishi
- Department of Earth and Planetary Systems Science, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - A Ijiri
- Kochi Institute for Core Sample Research, Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi, Japan
| | - K Takai
- Department of Subsurface Geobiological Analysis and Research (d-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - M Maeda
- Department of Technical Center, Hiroshima University, Higashi-Hiroshima, Japan
| | - Y Takahashi
- Department of Earth and Planetary Systems Science, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
- Department of Earth and Planetary Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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Fortney NW, He S, Converse BJ, Beard BL, Johnson CM, Boyd ES, Roden EE. Microbial Fe(III) oxide reduction potential in Chocolate Pots hot spring, Yellowstone National Park. GEOBIOLOGY 2016; 14:255-275. [PMID: 26750514 DOI: 10.1111/gbi.12173] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 11/10/2015] [Indexed: 06/05/2023]
Abstract
Chocolate Pots hot springs (CP) is a unique, circumneutral pH, iron-rich, geothermal feature in Yellowstone National Park. Prior research at CP has focused on photosynthetically driven Fe(II) oxidation as a model for mineralization of microbial mats and deposition of Archean banded iron formations. However, geochemical and stable Fe isotopic data have suggested that dissimilatory microbial iron reduction (DIR) may be active within CP deposits. In this study, the potential for microbial reduction of native CP Fe(III) oxides was investigated, using a combination of cultivation dependent and independent approaches, to assess the potential involvement of DIR in Fe redox cycling and associated stable Fe isotope fractionation in the CP hot springs. Endogenous microbial communities were able to reduce native CP Fe(III) oxides, as documented by most probable number enumerations and enrichment culture studies. Enrichment cultures demonstrated sustained DIR driven by oxidation of acetate, lactate, and H2 . Inhibitor studies and molecular analyses indicate that sulfate reduction did not contribute to observed rates of DIR in the enrichment cultures through abiotic reaction pathways. Enrichment cultures produced isotopically light Fe(II) during DIR relative to the bulk solid-phase Fe(III) oxides. Pyrosequencing of 16S rRNA genes from enrichment cultures showed dominant sequences closely affiliated with Geobacter metallireducens, a mesophilic Fe(III) oxide reducer. Shotgun metagenomic analysis of enrichment cultures confirmed the presence of a dominant G. metallireducens-like population and other less dominant populations from the phylum Ignavibacteriae, which appear to be capable of DIR. Gene (protein) searches revealed the presence of heat-shock proteins that may be involved in increased thermotolerance in the organisms present in the enrichments as well as porin-cytochrome complexes previously shown to be involved in extracellular electron transport. This analysis offers the first detailed insight into how DIR may impact the Fe geochemistry and isotope composition of a Fe-rich, circumneutral pH geothermal environment.
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Affiliation(s)
- N W Fortney
- Department of Geoscience, NASA Astrobiology Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - S He
- Department of Geoscience, NASA Astrobiology Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - B J Converse
- Department of Geoscience, NASA Astrobiology Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - B L Beard
- Department of Geoscience, NASA Astrobiology Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - C M Johnson
- Department of Geoscience, NASA Astrobiology Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - E S Boyd
- Department of Microbiology and Immunology, NASA Astrobiology Institute, Montana State University, Bozeman, MT, USA
| | - E E Roden
- Department of Geoscience, NASA Astrobiology Institute, University of Wisconsin-Madison, Madison, WI, USA
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Hüpeden J, Wegen S, Off S, Lücker S, Bedarf Y, Daims H, Kühn C, Spieck E. Relative Abundance of Nitrotoga spp. in a Biofilter of a Cold-Freshwater Aquaculture Plant Appears To Be Stimulated by Slightly Acidic pH. Appl Environ Microbiol 2016; 82:1838-45. [PMID: 26746710 PMCID: PMC4784051 DOI: 10.1128/aem.03163-15] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 12/31/2015] [Indexed: 12/22/2022] Open
Abstract
The functioning of recirculation aquaculture systems (RAS) is essential to maintain water quality for fish health, and one crucial process here is nitrification. The investigated RAS was connected to a rainbow trout production system and operated at an average temperature of 13°C and pH 6.8. Community analyses of the nitrifying biofilm revealed a coexistence of Nitrospira and Nitrotoga, and it is hypothesized that a slightly acidic pH in combination with lower temperatures favors the growth of the latter. Modification of the standard cultivation approach toward lower pH values of 5.7 to 6.0 resulted in the successful enrichment (99% purity) of Nitrotoga sp. strain HW29, which had a 16S rRNA sequence similarity of 99.0% to Nitrotoga arctica. Reference cultures of Nitrospira defluvii and the novel Nitrotoga sp. HW29 were used to confirm differentiation of these nitrite oxidizers in distinct ecological niches. Nitrotoga sp. HW29 revealed pH and temperature optima of 6.8 and 22°C, respectively, whereas Nitrospira defluvii displayed the highest nitrite oxidation rate at pH 7.3 and 32°C. We report here the occurrence of Nitrotoga as one of the main nitrite-oxidizing bacteria in freshwater aquaculture systems and indicate that a slightly acidic pH, in addition to temperatures below 20°C, can be applied as a selective isolation criterion for this microorganism.
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Affiliation(s)
- Jennifer Hüpeden
- Biocenter Klein Flottbek, Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Simone Wegen
- Biocenter Klein Flottbek, Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Sandra Off
- Biocenter Klein Flottbek, Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Sebastian Lücker
- Department of Microbiology, Faculty of Science, Radboud University, Nijmegen, The Netherlands Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Yvonne Bedarf
- Biocenter Klein Flottbek, Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Holger Daims
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Carsten Kühn
- State Research Centre of Agriculture and Fisheries Mecklenburg-Vorpommern, Institute of Fisheries, Rostock, Germany
| | - Eva Spieck
- Biocenter Klein Flottbek, Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
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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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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: 43] [Impact Index Per Article: 4.8] [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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Emerson D, Scott JJ, Benes J, Bowden WB. Microbial iron oxidation in the Arctic tundra and its implications for biogeochemical cycling. Appl Environ Microbiol 2015; 81:8066-75. [PMID: 26386054 PMCID: PMC4651080 DOI: 10.1128/aem.02832-15] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 09/01/2015] [Indexed: 11/20/2022] Open
Abstract
The role that neutrophilic iron-oxidizing bacteria play in the Arctic tundra is unknown. This study surveyed chemosynthetic iron-oxidizing communities at the North Slope of Alaska near Toolik Field Station (TFS) at Toolik Lake (lat 68.63, long -149.60). Microbial iron mats were common in submerged habitats with stationary or slowly flowing water, and their greatest areal extent is in coating plant stems and sediments in wet sedge meadows. Some Fe-oxidizing bacteria (FeOB) produce easily recognized sheath or stalk morphotypes that were present and dominant in all the mats we observed. The cool water temperatures (9 to 11°C) and reduced pH (5.0 to 6.6) at all sites kinetically favor microbial iron oxidation. A microbial survey of five sites based on 16S rRNA genes found a predominance of Proteobacteria, with Betaproteobacteria and members of the family Comamonadaceae being the most prevalent operational taxonomic units (OTUs). In relative abundance, clades of lithotrophic FeOB composed 5 to 10% of the communities. OTUs related to cyanobacteria and chloroplasts accounted for 3 to 25% of the communities. Oxygen profiles showed evidence for oxygenic photosynthesis at the surface of some mats, indicating the coexistence of photosynthetic and FeOB populations. The relative abundance of OTUs belonging to putative Fe-reducing bacteria (FeRB) averaged around 11% in the sampled iron mats. Mats incubated anaerobically with 10 mM acetate rapidly initiated Fe reduction, indicating that active iron cycling is likely. The prevalence of iron mats on the tundra might impact the carbon cycle through lithoautotrophic chemosynthesis, anaerobic respiration of organic carbon coupled to iron reduction, and the suppression of methanogenesis, and it potentially influences phosphorus dynamics through the adsorption of phosphorus to iron oxides.
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Affiliation(s)
- David Emerson
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, USA
| | - Jarrod J Scott
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, USA
| | - Joshua Benes
- Rubenstein School of Environment and Natural Resources, University of Vermont, Burlington, Vermont, USA
| | - William B Bowden
- Rubenstein School of Environment and Natural Resources, University of Vermont, Burlington, Vermont, USA
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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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42
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Xiong MY, Shelobolina ES, Roden EE. Potential for microbial oxidation of ferrous iron in basaltic glass. ASTROBIOLOGY 2015; 15:331-340. [PMID: 25915449 DOI: 10.1089/ast.2014.1233] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Basaltic glass (BG) is an amorphous ferrous iron [Fe(II)]-containing material present in basaltic rocks, which are abundant on rocky planets such as Earth and Mars. Previous research has suggested that Fe(II) in BG can serve as an energy source for chemolithotrophic microbial metabolism, which has important ramifications for potential past and present microbial life on Mars. However, to date there has been no direct demonstration of microbially catalyzed oxidation of Fe(II) in BG. In this study, three different culture systems were used to investigate the potential for microbial oxidation of Fe(II) in BG, including (1) the chemolithoautotrophic Fe(II)-oxidizing, nitrate-reducing "Straub culture"; (2) the mixotrophic Fe(II)-oxidizing, nitrate-reducing organism Desulfitobacterium frappieri strain G2; and (3) indigenous microorganisms from a streambed Fe seep in Wisconsin. The BG employed consisted of clay and silt-sized particles of freshly quenched lava from the TEB flow in Kilauea, Hawaii. Soluble Fe(II) or chemically reduced NAu-2 smectite (RS) were employed as positive controls to verify Fe(II) oxidation activity in the culture systems. All three systems demonstrated oxidation of soluble Fe(II) and/or structural Fe(II) in RS, whereas no oxidation of Fe(II) in BG material was observed. The inability of the Straub culture to oxidize Fe(II) in BG was particularly surprising, as this culture can oxidize other insoluble Fe(II)-bearing minerals such as biotite, magnetite, and siderite. Although the reason for the resistance of the BG toward enzymatic oxidation remains unknown, it seems possible that the absence of distinct crystal faces or edge sites in the amorphous glass renders the material resistant to such attack. These findings have implications with regard to the idea that Fe(II)-Si-rich phases in basalt rocks could provide a basis for chemolithotrophic microbial life on Mars, specifically in neutral-pH environments where acid-promoted mineral dissolution and utilization of dissolved Fe(II) as an energy source is not likely to take place.
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Affiliation(s)
- Mai Yia Xiong
- Department of Geoscience, University of Wisconsin, and NASA Astrobiology Institute, University of Wisconsin, Madison, Wisconsin
| | - Evgenya S Shelobolina
- Department of Geoscience, University of Wisconsin, and NASA Astrobiology Institute, University of Wisconsin, Madison, Wisconsin
| | - Eric E Roden
- Department of Geoscience, University of Wisconsin, and NASA Astrobiology Institute, University of Wisconsin, Madison, Wisconsin
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Microbial iron mats at the Mid-Atlantic Ridge and evidence that Zetaproteobacteria may be restricted to iron-oxidizing marine systems. PLoS One 2015; 10:e0119284. [PMID: 25760332 PMCID: PMC4356598 DOI: 10.1371/journal.pone.0119284] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 01/26/2015] [Indexed: 12/02/2022] Open
Abstract
Chemolithoautotrophic iron-oxidizing bacteria play an essential role in the global iron cycle. Thus far, the majority of marine iron-oxidizing bacteria have been identified as Zetaproteobacteria, a novel class within the phylum Proteobacteria. Marine iron-oxidizing microbial communities have been found associated with volcanically active seamounts, crustal spreading centers, and coastal waters. However, little is known about the presence and diversity of iron-oxidizing communities at hydrothermal systems along the slow crustal spreading center of the Mid-Atlantic Ridge. From October to November 2012, samples were collected from rust-colored mats at three well-known hydrothermal vent systems on the Mid-Atlantic Ridge (Rainbow, Trans-Atlantic Geotraverse, and Snake Pit) using the ROV Jason II. The goal of these efforts was to determine if iron-oxidizing Zetaproteobacteria were present at sites proximal to black smoker vent fields. Small, diffuse flow venting areas with high iron(II) concentrations and rust-colored microbial mats were observed at all three sites proximal to black smoker chimneys. A novel, syringe-based precision sampler was used to collect discrete microbial iron mat samples at the three sites. The presence of Zetaproteobacteria was confirmed using a combination of 16S rRNA pyrosequencing and single-cell sorting, while light micros-copy revealed a variety of iron-oxyhydroxide structures, indicating that active iron-oxidizing communities exist along the Mid-Atlantic Ridge. Sequencing analysis suggests that these iron mats contain cosmopolitan representatives of Zetaproteobacteria, but also exhibit diversity that may be uncommon at other iron-rich marine sites studied to date. A meta-analysis of publically available data encompassing a variety of aquatic habitats indicates that Zetaproteobacteria are rare if an iron source is not readily available. This work adds to the growing understanding of Zetaproteobacteria ecology and suggests that this organism is likely locally restricted to iron-rich marine environments but may exhibit wide-scale geographic distribution, further underscoring the importance of Zetaproteobacteria in global iron cycling.
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MacDonald DJ, Findlay AJ, McAllister SM, Barnett JM, Hredzak-Showalter P, Krepski ST, Cone SG, Scott J, Bennett SK, Chan CS, Emerson D, Luther Iii GW. Using in situ voltammetry as a tool to identify and characterize habitats of iron-oxidizing bacteria: from fresh water wetlands to hydrothermal vent sites. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2014; 16:2117-2126. [PMID: 24924809 DOI: 10.1039/c4em00073k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Iron-oxidizing bacteria (FeOB) likely play a large role in the biogeochemistry of iron, making the detection and understanding of the biogeochemical processes FeOB are involved in of critical importance. By deploying our in situ voltammetry system, we are able to measure a variety of redox species, specifically Fe(ii) and O2, simultaneously. This technique provides significant advantages in both characterizing the environments in which microaerophilic FeOB are found, and finding diverse conditions in which FeOB could potentially thrive. Described here are four environments with different salinities [one fresh groundwater seep site, one beach-groundwater mixing site, one hydrothermal vent site (Mid-Atlantic Ridge), and one estuary (Chesapeake Bay)] where in situ voltammetry was deployed, and where the presence of FeOB were confirmed by either culturing methods or molecular data. The sites varied in both O2 and Fe(ii) content with O2 ranging from below the 3 μM detection limit of the electrodes at the Chesapeake Bay suboxic zone, to as high 150 μM O2 at the vent site. In addition, a range of Fe(ii) concentrations supported FeOB communities, from 3 μM Fe(ii) in the Chesapeake Bay to 300 μM in the beach aquifer. In situ electrochemistry provides the means to quickly measure these redox gradients at appropriate resolution, making it possible in real time to detect niches likely inhabited by microaerophilic FeOB, then accurately sample for proof of FeOB presence and activity. This study demonstrates the utility of this approach while also greatly expanding our knowledge of FeOB habitats.
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Affiliation(s)
- Daniel J MacDonald
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA.
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Schmidt B, Sánchez LA, Fretschner T, Kreps G, Ferrero MA, Siñeriz F, Szewzyk U. Isolation of Sphaerotilus-Leptothrix strains from iron bacteria communities in Tierra del Fuego wetlands. FEMS Microbiol Ecol 2014; 90:454-66. [PMID: 25098830 DOI: 10.1111/1574-6941.12406] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 01/27/2014] [Accepted: 08/03/2014] [Indexed: 11/29/2022] Open
Abstract
Sheath-forming iron- and manganese-depositing bacteria belonging to the Sphaerotilus-Leptothrix group (SLG) are widespread in natural and artificial water systems. Known requirements for their growth include the presence of organic substrates and molecular oxygen. High concentrations of reduced iron or manganese, although not necessary for most species, make their growth a noticeable phenomenon. Such microbial communities have been studied mostly in the Northern Hemisphere. Here, we present descriptions of diverse ochre-depositing microbial communities in Tierra del Fuego, Argentina, using a combined approach of microscopical examination, clone library construction and cultivation focused on SLG bacteria. To date, only few SLG type strains are available. The present work increases the number and diversity of cultivated SLG bacteria by obtaining isolates from biofilms and sediment samples of wetlands in Tierra del Fuego. Thirty isolates were selected based on morphological features such as sheath formation and iron/manganese deposition. Five operational taxonomic units (OTUs) were deduced. Sequencing of 16S rRNA genes showed that one OTU is identical to the Leptothrix mobilis Feox-1(T) -sequence while the four remaining OTUs show similarity values related to previously described type strains. Similarity values ranged from 96.5% to 98.8%, indicating possible new species and subspecies.
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Affiliation(s)
- Bertram Schmidt
- Umweltmikrobiologie, Technische Universität Berlin, Berlin, Germany
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46
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Quaiser A, Bodi X, Dufresne A, Naquin D, Francez AJ, Dheilly A, Coudouel S, Pedrot M, Vandenkoornhuyse P. Unraveling the stratification of an iron-oxidizing microbial mat by metatranscriptomics. PLoS One 2014; 9:e102561. [PMID: 25033299 PMCID: PMC4102501 DOI: 10.1371/journal.pone.0102561] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 06/19/2014] [Indexed: 02/02/2023] Open
Abstract
A metatranscriptomic approach was used to study community gene expression in a naturally occurring iron-rich microbial mat. Total microbial community RNA was reversely transcribed and sequenced by pyrosequencing. Characterization of expressed gene sequences provided accurate and detailed information of the composition of the transcriptionally active community and revealed phylogenetic and functional stratifications within the mat. Comparison of 16S rRNA reads and delineation of OTUs showed significantly lower values of metatranscriptomic-based richness and diversity in the upper parts of the mat than in the deeper regions. Taxonomic affiliation of rRNA sequences and mRNA genome recruitments indicated that iron-oxidizing bacteria affiliated to the genus Leptothrix, dominated the community in the upper layers of the mat. Surprisingly, type I methanotrophs contributed to the majority of the sequences in the deep layers of the mat. Analysis of mRNA expression patterns showed that genes encoding the three subunits of the particulate methane monooxygenase (pmoCAB) were the most highly expressed in our dataset. These results provide strong hints that iron-oxidation and methane-oxidation occur simultaneously in microbial mats and that both groups of microorganisms are major players in the functioning of this ecosystem.
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Affiliation(s)
- Achim Quaiser
- Université de Rennes 1, CNRS UMR6553 EcoBio, Rennes, France
- * E-mail:
| | - Xavier Bodi
- Université de Rennes 1, CNRS UMR6553 EcoBio, Rennes, France
| | | | - Delphine Naquin
- CNRS FRC3115 Centre de Recherches de Gif-sur-Yvette, Gif sur Yvette, France
| | | | - Alexandra Dheilly
- Université de Rennes 1, CNRS UMS3343 OSUR, Plateforme génomique environnementale et fonctionnelle, Rennes, France
| | - Sophie Coudouel
- Université de Rennes 1, CNRS UMS3343 OSUR, Plateforme génomique environnementale et fonctionnelle, Rennes, France
| | - Mathieu Pedrot
- Université de Rennes 1, CNRS UMR6118 Géosciences, Rennes, France
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47
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Li J, Sun W, Wang S, Sun Z, Lin S, Peng X. Bacteria diversity, distribution and insight into their role in S and Fe biogeochemical cycling during black shale weathering. Environ Microbiol 2014; 16:3533-47. [DOI: 10.1111/1462-2920.12536] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2013] [Accepted: 06/09/2014] [Indexed: 11/26/2022]
Affiliation(s)
- Jiwei Li
- Sanya Institute of Deep-Sea Science and Engineering; Chinese Academy of Sciences; Sanya 572000 China
| | - Weimin Sun
- Department of Environmental Science; Rutgers University; New Brunswick NJ 08901 USA
| | - Shiming Wang
- Faculty of Geosciences and Environmental Engineering; Southwest Jiaotong University; Chengdu 610031 China
| | - Zhilei Sun
- Department of Marine Mineral Resources; Qingdao Institute of Marine Geology; Qingdao 266071 China
| | - Sixiang Lin
- Faculty of Geosciences and Environmental Engineering; Southwest Jiaotong University; Chengdu 610031 China
| | - Xiaotong Peng
- Sanya Institute of Deep-Sea Science and Engineering; Chinese Academy of Sciences; Sanya 572000 China
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Brantner JS, Senko JM. Response of soil-associated microbial communities to intrusion of coal mine-derived acid mine drainage. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:8556-8563. [PMID: 24971467 DOI: 10.1021/es502261u] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A system has been identified in which coal mine-derived acid mine drainage (AMD) flows as a 0.5-cm-deep sheet over the terrestrial surface. This flow regime enhances the activities of Fe(II) oxidizing bacteria, which catalyze the oxidative precipitation of Fe from AMD. These activities give rise to Fe(III) (hydr)oxide-rich deposits (referred to as an iron mound) overlying formerly pristine soil. This iron mound has developed with no human intervention, indicating that microbiological activities associated with iron mounds may be exploited as an inexpensive and sustainable approach to remove Fe(II) from AMD. To evaluate the changes in microbial activities and communities that occur when AMD infiltrates initially pristine soil, we incubated AMD-unimpacted soil with site AMD. Continuous exposure of soil to AMD induced progressively greater rates of Fe(II) biooxidation. The development of Fe(II) oxidizing activities was enhanced by inoculation of soil with microorganisms associated with mature iron mound sediment. Evaluation of pyrosequencing-derived 16S rRNA gene sequences recovered from incubations revealed the development of microbial community characteristics that were similar to those of the mature iron mound sediment. Our results indicate that upon mixing of AMD with pristine soil, microbial communities develop that mediate rapid oxidative precipitation of Fe from AMD.
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Affiliation(s)
- Justin S Brantner
- Department of Biology, ‡Integrated Biosciences Program, and §Department of Geosciences, The University of Akron , Akron, Ohio 44325, United States
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49
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Fleming EJ, Cetinić I, Chan CS, Whitney King D, Emerson D. Ecological succession among iron-oxidizing bacteria. ISME JOURNAL 2013; 8:804-15. [PMID: 24225888 DOI: 10.1038/ismej.2013.197] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 09/02/2013] [Accepted: 09/22/2013] [Indexed: 11/09/2022]
Abstract
Despite over 125 years of study, the factors that dictate species dominance in neutrophilic iron-oxidizing bacterial (FeOB) communities remain unknown. In a freshwater wetland, we documented a clear ecological succession coupled with niche separation between the helical stalk-forming Gallionellales (for example, Gallionella ferruginea) and tubular sheath-forming Leptothrix ochracea. Changes in the iron-seep community were documented using microscopy and cultivation-independent methods. Quantification of Fe-oxyhydroxide morphotypes by light microscopy was coupled with species-specific fluorescent in situ hybridization (FISH) probes using a protocol that minimized background fluorescence caused by the Fe-oxyhydroxides. Together with scanning electron microscopy, these techniques all indicated that Gallionellales dominated during early spring, with L. ochracea becoming more abundant for the remainder of the year. Analysis of tagged pyrosequencing reads of the small subunit ribosomal RNA gene (SSU rRNA) collected during seasonal progression supported a clear Gallionellales to L. ochracea transition, and community structure grouped according to observed dominant FeOB forms. Axis of redundancy analysis of physicochemical parameters collected from iron mats during the season, plotted with FeOB abundance, corroborated several field and microscopy-based observations and uncovered several unanticipated relationships. On the basis of these relationships, we conclude that the ecological niche of the stalk-forming Gallionellales is in waters with low organic carbon and steep redoxclines, and the sheath-forming L. ochracea is abundant in waters that contain high concentrations of complex organic carbon, high Fe and Mn content and gentle redoxclines. Finally, these findings identify a largely unexplored relationship between FeOB and organic carbon.
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Affiliation(s)
- Emily J Fleming
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Ivona Cetinić
- University of Maine, Darling Marine Center, Walpole, ME, USA
| | - Clara S Chan
- Department of Geological Sciences, University of Delaware, Newark, DE, USA
| | - D Whitney King
- Department of Chemistry, Colby College, Waterville, ME, USA
| | - David Emerson
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
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50
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Lee JS, McBeth JM, Ray RI, Little BJ, Emerson D. Iron cycling at corroding carbon steel surfaces. BIOFOULING 2013; 29:1243-52. [PMID: 24093730 PMCID: PMC3827670 DOI: 10.1080/08927014.2013.836184] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 08/15/2013] [Indexed: 06/02/2023]
Abstract
Surfaces of carbon steel (CS) exposed to mixed cultures of iron-oxidizing bacteria (FeOB) and dissimilatory iron-reducing bacteria (FeRB) in seawater media under aerobic conditions were rougher than surfaces of CS exposed to pure cultures of either type of microorganism. The roughened surface, demonstrated by profilometry, is an indication of loss of metal from the surface. In the presence of CS, aerobically grown FeOB produced tight, twisted helical stalks encrusted with iron oxides. When CS was exposed anaerobically in the presence of FeRB, some surface oxides were removed. However, when the same FeOB and FeRB were grown together in an aerobic medium, FeOB stalks were less encrusted with iron oxides and appeared less tightly coiled. These observations suggest that iron oxides on the stalks were reduced and solubilized by the FeRB. Roughened surfaces of CS and denuded stalks were replicated with culture combinations of different species of FeOB and FeRB under three experimental conditions. Measurements of electrochemical polarization resistance established different rates of corrosion of CS in aerobic and anaerobic media, but could not differentiate rate differences between sterile controls and inoculated exposures for a given bulk concentration of dissolved oxygen. Similarly, total iron in the electrolyte could not be used to differentiate treatments. The experiments demonstrate the potential for iron cycling (oxidation and reduction) on corroding CS in aerobic seawater media.
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Affiliation(s)
- Jason S. Lee
- Naval Research Laboratory, Stennis Space Center, MS, USA
| | - Joyce M. McBeth
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Richard I. Ray
- Naval Research Laboratory, Stennis Space Center, MS, USA
| | | | - David Emerson
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
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