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Qiao J, Chen M, Zhong S, Tong H, Li F. Soil Humic Acid Stimulates Potentially Active Dissimilatory Arsenate-Reducing Bacteria in Flooded Paddy Soil as Revealed by Metagenomic Stable Isotope Probing. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:2303-2312. [PMID: 38263620 DOI: 10.1021/acs.est.3c07753] [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: 01/25/2024]
Abstract
Dissimilatory arsenate reduction contributes a large proportion of arsenic flux from flooded paddy soil, which is closely linked to soil organic carbon input and efflux. Humic acid (HA) represents a natural ingredient in soil and is shown to enhance microbial arsenate respiration to promote arsenic mobility. However, the community and function profiles of metabolically active arsenate-respiring bacteria and their interactions with HA in paddy soil remain unclear. To probe this linkage, we performed a genome-centric comparison of potentially active arsenate-respiring bacteria in anaerobic microcosms amended with 13C-lactate and HA by combining stable-isotope probing with genome-resolved metagenomics. Indeed, HA greatly accelerated the microbial reduction of arsenate to arsenite. Enrichment of bacteria that harbor arsenate-respiring reductase genes (arrA) in HA-enriched 13C-DNA was confirmed by metagenomic binning, which are affiliated with Firmicutes (mainly Desulfitobacterium, Bacillus, Brevibacillus, and Clostridia) and Acidobacteria. Characterization of reference extracellular electron transfer (EET)-related genes in these arrA-harboring bacteria supports the presence of EET-like genes, with partial electron-transport chain genes identified. This suggests that Gram-positive Firmicutes- and Acidobacteria-related members may harbor unspecified EET-associated genes involved in metal reduction. Our findings highlight the link between soil HA and potentially active arsenate-respiring bacteria, which can be considered when using HA for arsenic removal.
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Affiliation(s)
- Jiangtao Qiao
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, China
| | - Manjia Chen
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, China
| | - Songxiong Zhong
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, China
| | - Hui Tong
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, China
| | - Fangbai Li
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, China
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Runge EA, Mansor M, Kappler A, Duda JP. Microbial biosignatures in ancient deep-sea hydrothermal sulfides. GEOBIOLOGY 2023; 21:355-377. [PMID: 36524457 DOI: 10.1111/gbi.12539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 11/03/2022] [Accepted: 12/03/2022] [Indexed: 06/17/2023]
Abstract
Deep-sea hydrothermal systems provide ideal conditions for prebiotic reactions and ancient metabolic pathways and, therefore, might have played a pivotal role in the emergence of life. To understand this role better, it is paramount to examine fundamental interactions between hydrothermal processes, non-living matter, and microbial life in deep time. However, the distribution and diversity of microbial communities in ancient deep-sea hydrothermal systems are still poorly constrained, so evolutionary, and ecological relationships remain unclear. One important reason is an insufficient understanding of the formation of diagnostic microbial biosignatures in such settings and their preservation through geological time. This contribution centers around microbial biosignatures in Precambrian deep-sea hydrothermal sulfide deposits. Intending to provide a valuable resource for scientists from across the natural sciences whose research is concerned with the origins of life, we first introduce different types of biosignatures that can be preserved over geological timescales (rock fabrics and textures, microfossils, mineral precipitates, carbonaceous matter, trace metal, and isotope geochemical signatures). We then review selected reports of biosignatures from Precambrian deep-sea hydrothermal sulfide deposits and discuss their geobiological significance. Our survey highlights that Precambrian hydrothermal sulfide deposits potentially encode valuable information on environmental conditions, the presence and nature of microbial life, and the complex interactions between fluids, micro-organisms, and minerals. It further emphasizes that the geobiological interpretation of these records is challenging and requires the concerted application of analytical and experimental methods from various fields, including geology, mineralogy, geochemistry, and microbiology. Well-orchestrated multidisciplinary studies allow us to understand the formation and preservation of microbial biosignatures in deep-sea hydrothermal sulfide systems and thus help unravel the fundamental geobiology of ancient settings. This, in turn, is critical for reconstructing life's emergence and early evolution on Earth and the search for life elsewhere in the universe.
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Affiliation(s)
- Eric Alexander Runge
- Sedimentology and Organic Geochemistry, Department of Geosciences, Tübingen University, Tübingen, Germany
| | - Muammar Mansor
- Geomicrobiology, Department of Geosciences, Tübingen University, Tübingen, Germany
| | - Andreas Kappler
- Geomicrobiology, Department of Geosciences, Tübingen University, Tübingen, Germany
- Cluster of Excellence EXC 2124, Controlling Microbes to Fight Infection, Tübingen, Germany
| | - Jan-Peter Duda
- Sedimentology and Organic Geochemistry, Department of Geosciences, Tübingen University, Tübingen, Germany
- Geobiology, Geoscience Center, Göttingen University, Göttingen, Germany
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Zhang HS, Feng QD, Zhang DY, Zhu GL, Yang L. Bacterial community structure in geothermal springs on the northern edge of Qinghai-Tibet plateau. Front Microbiol 2023; 13:994179. [PMID: 37180363 PMCID: PMC10172933 DOI: 10.3389/fmicb.2022.994179] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 12/13/2022] [Indexed: 03/19/2023] Open
Abstract
Introduction:In order to reveal the composition of the subsurface hydrothermal bacterial community in the zones of magmatic tectonics and their response to heat storage environments.Methods:In this study, we performed hydrochemical analysis and regional sequencing of the 16S rRNA microbial V4-V5 region in 7 Pleistocene and Lower Neogene hot water samples from the Gonghe basin.Results:Two geothermal hot spring reservoirs in the study area were found to be alkaline reducing environments with a mean temperature of 24.83°C and 69.28°C, respectively, and the major type of hydrochemistry was SO4-Cl·Na. The composition and structure of microorganisms in both types of geologic thermal storage were primarily controlled by temperature, reducing environment intensity, and hydrogeochemical processes. Only 195 ASVs were shared across different temperature environments, and the dominant bacterial genera in recent samples from temperate hot springs were Thermus and Hydrogenobacter, with both genera being typical of thermophiles. The correlation analysis showed that the overall level of relative abundance of the subsurface hot spring relied on a high temperature and a slightly alkaline reducing environment. Nearly all of the top 4 species in the abundance level (53.99% of total abundance) were positively correlated with temperature and pH, whereas they were negatively correlated with ORP (oxidation–reduction potential), nitrate, and bromine ions.Discussion:In general, the composition of bacteria in the groundwater in the study area was sensitive to the response of the thermal storage environment and also showed a relationship with geochemical processes, such as gypsum dissolution, mineral oxidation, etc.
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Zhang M, Guo H, Xia D, Dong Z, Liu X, Zhao W, Jia J, Yin X. Metagenomic insight of corn straw conditioning on substrates metabolism during coal anaerobic fermentation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 808:152220. [PMID: 34890652 DOI: 10.1016/j.scitotenv.2021.152220] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/14/2021] [Accepted: 12/02/2021] [Indexed: 06/13/2023]
Abstract
Increasing methane production from anaerobic digestion of coal is challenging. This study shows that the combined fermentation of coal and corn straw greatly enriched the substrates available to microorganisms. This was mainly manifested in the increased types and abundance of organic matter in the fermentation liquid, which enhanced methane production by 61%. Metagenomic analysis showed that the addition of corn straw enriched the abundance of Methanosarcina in the combined fermentation system and promoted the complementary advantages of the microorganisms. At the same time, the abundance of genes that convert glucose into acetic acid (K00927, K01689, K01905, etc.) in the combined fermentation system increased, which is conducive to acidification process and biomethane production. In addition, there were the two key methanogenic pathways, namely aceticlastic (57.1%-63.5%) and hydrogenotrophic (23.4%-25.1%) methanogenesis, identified in the single coal fermentation system and the combined coal and corn straw fermentation system. Combined fermentation enhanced the hydrogenotrophic and methylotrophic methanogenic pathways by increasing the gene abundance of K00200 (methane production from CO2 and oxidation of coenzyme M to CO2), K00440 (participates in the binding to other known physiological receptors with hydrogen as a donor), and K00577 (methyltransferase).
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Affiliation(s)
- Minglu Zhang
- School of Energy Science and Engineering, Henan Polytechnic University, Jiaozuo 454000, China
| | - Hongyu Guo
- School of Energy Science and Engineering, Henan Polytechnic University, Jiaozuo 454000, China.
| | - Daping Xia
- School of Energy Science and Engineering, Henan Polytechnic University, Jiaozuo 454000, China.
| | - Zhiwei Dong
- School of Energy Science and Engineering, Henan Polytechnic University, Jiaozuo 454000, China
| | - Xile Liu
- School of Geoscience and Surveying Engineering, China University of Mining &Technology, Beijing 100083, China
| | - Weizhong Zhao
- Institute of Resources and Environment, Henan Polytechnic University, Jiaozuo 454000, China
| | - Jianbo Jia
- College of Chemistry and Chemical Engineering, Henan Polytechnic University, Jiaozuo 454000, China
| | - Xiangju Yin
- School of Emergency Management, Henan Polytechnic University, Jiaozuo 454000, China.
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Xue X, Wang D, Yi X, Li Y, Han H. Simultaneously autotrophic denitrification and organics degradation in low-strength coal gasification wastewater (LSCGW) treatment via microelectrolysis-triggered Fe(II)/Fe(III) cycle. CHEMOSPHERE 2021; 278:130460. [PMID: 33838412 DOI: 10.1016/j.chemosphere.2021.130460] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 03/24/2021] [Accepted: 03/27/2021] [Indexed: 06/12/2023]
Abstract
The autotrophic iron-depended denitrification (AIDD), triggered by microelectrolysis, was established in the microelectrolysis-assistant up-flow anaerobic sludge blanket (MEA-UASB) with the purpose of low-strength coal gasification wastewater (LSCGW) treatment while control UASB operated in parallel. The results revealed that chemical oxygen demand (COD) removal efficiency and total nitrogen (TN) removal load at optimum current (2.5 A/m3) in MEA-UASB (83.2 ± 2.6% and 0.220 ± 0.010 kg N/m3·d) were 1.42-fold and 1.57-fold higher than those (58.5 ± 2.1% and 0.139 ± 0.011 kg N/m3·d) in UASB, verifying that AIDD and following dissimilatory iron reduction (DIR) process could offer the novel pathway to solve the electron donor-deficient and traditionally denitrification-infeasible problems. High-throughput 16S rRNA gene pyrosequencing shown that iron-oxidizing denitrifiers (Thiobacillus and Acidovorax species) and iron reducing bacteria (Geothrix and Ignavibacterium speices), acted as microbial iron cycle of contributors, were specially enriched at optimum operating condition. Additionally, the activities of microbial electron transfer chain, electron transporters (complex I, II, III and cytochrome c) and abundance of genes encoding important enzymes (narG, nirK/S, norB and nosZ) were remarkably promoted, suggesting that electron transport and consumption capacities were stimulated during denitrification process. This study could shed light on better understanding about microelectrolysis-triggered AIDD for treatment of refractory LSCGW and further widen its application potential in the future.
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Affiliation(s)
- Xiaofang Xue
- Department of Environmental Science and Engineering, College of Ecology and Environment, Hainan University, Haikou, 570228, China.
| | - Dexin Wang
- Department of Environmental Science and Engineering, College of Ecology and Environment, Hainan University, Haikou, 570228, China.
| | - Xuesong Yi
- Department of Environmental Science and Engineering, College of Ecology and Environment, Hainan University, Haikou, 570228, China.
| | - Yangyang Li
- Operation Services Division of Hospital Wastewater Treatment, General Affairs Department, Sanya Central Hospital, Sanya, 520000, China.
| | - Hongjun Han
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China.
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Zheng M, Han H, Shi J, Zhang Z, Ma W, Xu C. Metagenomic analysis of aromatic ring-cleavage mechanism in nano-Fe 3O 4@activated coke enhanced bio-system for coal pyrolysis wastewater treatment. JOURNAL OF HAZARDOUS MATERIALS 2021; 414:125387. [PMID: 33676245 DOI: 10.1016/j.jhazmat.2021.125387] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 01/25/2021] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
In current study, nano-Fe3O4@activated coke enhanced bio-system (FEBS) under limited-oxygen condition was applied for efficient treatment of aromatic organics in coal pyrolysis wastewater. Metagenomic analyses revealed functional microbiome linkages and mechanism involved in aromatic ring-cleavage. Based on biodegradation efficiency in different reactors, FEBS supplementation conferred the best organic removal (avg. 92.29%). It also showed a remarkable advantage in biodegradability maintenance (>40%) over control reactors. Metagenomics profiling revealed the degradation processes were driven by Fe3O4 redox reactions and microbial biofilm, while the suspended sludge was the principal force for aromatic mineralization. Based on the analysis of functional species and genes, most bacteria cleaved the benzene ring preferably through the aerobic pathways, mediated by catechol 1, 2-dioxygenase, catechol 2, 3-dioxygenase and protocatechuate 3, 4-dioxygenase (66-84%). Ecological network showed that Comamonas testosterone-centered microbiome and Azotobacter linked to the nitrogen (N)-heterocyclic ring-cleavage. Network linkage further demonstrated that Alicycliphilus and Acidovorax were the key tone taxa involved in benzene ring-cleavage. Finally, combined with analysis of degradation products, bacteria degraded N-heterocyclic ring containing organic aromatic compounds (quinoline) mainly through anaerobic processes, whereas cleavage of benzene ring preferred aerobic pathways. The enriched functional species were the primary reason for the enhanced biodegradation in FEBS.
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Affiliation(s)
- Mengqi Zheng
- School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Hongjun Han
- School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Jingxin Shi
- School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Zhengwen Zhang
- School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Wencheng Ma
- School of Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Chunyan Xu
- Harbin Gongchuang Environmental Protection Technology Company, Harbin, Heilongjiang 150090, China.
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High-Quality Draft Genome Sequence of the Siderophilic and Thermophilic Leptolyngbyaceae Cyanobacterium JSC-12. Microbiol Resour Announc 2021; 10:e0049521. [PMID: 34165332 PMCID: PMC8223812 DOI: 10.1128/mra.00495-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The siderophilic, thermophilic Leptolyngbyaceae cyanobacterium JSC-12 was isolated from a microbial mat in an iron-depositing hot spring. Here, we report the high-quality draft genome sequence of JSC-12, which may help elucidate the mechanisms of resistance to extreme iron concentrations in siderophilic cyanobacteria and lead to new remediation biotechnologies.
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8
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Nir I, Barak H, Kramarsky-Winter E, Kushmaro A, de Los Ríos A. Microscopic and biomolecular complementary approaches to characterize bioweathering processes at petroglyph sites from the Negev Desert, Israel. Environ Microbiol 2021; 24:967-980. [PMID: 34110072 DOI: 10.1111/1462-2920.15635] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 06/08/2021] [Indexed: 11/27/2022]
Abstract
Throughout the Negev Desert highlands, thousands of ancient petroglyphs sites are susceptible to deterioration processes that may result in the loss of this unique rock art. Therefore, the overarching goal of the current study was to characterize the composition, diversity and effects of microbial colonization of the rocks to find ways of protecting these unique treasures. The spatial organization of the microbial colonizers and their relationships with the lithic substrate were analysed using scanning electron microscopy. This approach revealed extensive epilithic and endolithic colonization and close microbial-mineral interactions. Shotgun sequencing analysis revealed various taxa from the archaea, bacteria and some eukaryotes. Metagenomic coding sequences (CDS) of these microbial lithobionts exhibited specific metabolic pathways involved in the rock elements' cycles and uptake processes. Thus, our results provide evidence for the potential participation of the microorganisms colonizing these rocks during different solubilization and mineralization processes. These damaging actions may contribute to the deterioration of this extraordinary rock art and thus threaten this valuable heritage. Shotgun metagenomic sequencing, in conjunction with the in situ scanning electron microscopy study, can thus be considered an effective strategy to understand the complexity of the weathering processes occurring at petroglyph sites and other cultural heritage assets.
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Affiliation(s)
- Irit Nir
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Be'er Sheva, 8410501, Israel
| | - Hana Barak
- Unit of Environmental Engineering, Ben-Gurion University of the Negev, Be'er Sheva, 8410501, Israel
| | - Esti Kramarsky-Winter
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Be'er Sheva, 8410501, Israel
| | - Ariel Kushmaro
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Be'er Sheva, 8410501, Israel.,The Ilse Katz Center for Meso and Nanoscale Science and Technology, Ben-Gurion University of the Negev, Be'er-Sheva, Israel
| | - Asunción de Los Ríos
- Department of Biogeochemistry and Microbial Ecology, National Museum of Natural Sciences (MNCN-CSIC), Madrid, Spain
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Friese A, Bauer K, Glombitza C, Ordoñez L, Ariztegui D, Heuer VB, Vuillemin A, Henny C, Nomosatryo S, Simister R, Wagner D, Bijaksana S, Vogel H, Melles M, Russell JM, Crowe SA, Kallmeyer J. Organic matter mineralization in modern and ancient ferruginous sediments. Nat Commun 2021; 12:2216. [PMID: 33850127 PMCID: PMC8044167 DOI: 10.1038/s41467-021-22453-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 03/15/2021] [Indexed: 02/02/2023] Open
Abstract
Deposition of ferruginous sediment was widespread during the Archaean and Proterozoic Eons, playing an important role in global biogeochemical cycling. Knowledge of organic matter mineralization in such sediment, however, remains mostly conceptual, as modern ferruginous analogs are largely unstudied. Here we show that in sediment of ferruginous Lake Towuti, Indonesia, methanogenesis dominates organic matter mineralization despite highly abundant reactive ferric iron phases like goethite that persist throughout the sediment. Ferric iron can thus be buried over geologic timescales even in the presence of labile organic carbon. Coexistence of ferric iron with millimolar concentrations of methane further demonstrates lack of iron-dependent methane oxidation. With negligible methane oxidation, methane diffuses from the sediment into overlying waters where it can be oxidized with oxygen or escape to the atmosphere. In low-oxygen ferruginous Archaean and Proterozoic oceans, therefore, sedimentary methane production was likely favored with strong potential to influence Earth's early climate.
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Affiliation(s)
- André Friese
- GFZ German Research Centre for Geosciences, Potsdam, Germany
| | - Kohen Bauer
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, Canada
| | - Clemens Glombitza
- ETH Zürich, Institute of Biogeochemistry and Pollutant Dynamics, Zürich, Switzerland
- Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
| | - Luis Ordoñez
- Department of Earth Sciences, University of Geneva, Geneva, Switzerland
| | - Daniel Ariztegui
- Department of Earth Sciences, University of Geneva, Geneva, Switzerland
| | - Verena B Heuer
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Aurèle Vuillemin
- GFZ German Research Centre for Geosciences, Potsdam, Germany
- Department of Earth & Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Cynthia Henny
- Research Center for Limnology, Indonesian Institute of Sciences (LIPI), Cibinong, Bogor, West Java, Indonesia
| | - Sulung Nomosatryo
- GFZ German Research Centre for Geosciences, Potsdam, Germany
- Research Center for Limnology, Indonesian Institute of Sciences (LIPI), Cibinong, Bogor, West Java, Indonesia
| | - Rachel Simister
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, Canada
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Potsdam, Germany
- Institute of Geosciences, University of Potsdam, Potsdam, Germany
| | - Satria Bijaksana
- Faculty of Mining and Petroleum Engineering, Institut Teknologi Bandung, Bandung, Jawa Barat, Indonesia
| | - Hendrik Vogel
- Institute of Geological Sciences & Oeschger Centre for Climate Change Research, University of Bern, Bern, Switzerland
| | - Martin Melles
- Institute of Geology and Mineralogy, University of Cologne, Cologne, Germany
| | - James M Russell
- Department of Earth, Environmental, and Planetary Sciences, Brown University, Providence, RI, USA
| | - Sean A Crowe
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada.
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, Canada.
| | - Jens Kallmeyer
- GFZ German Research Centre for Geosciences, Potsdam, Germany.
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Dissimilatory Iron-Reducing Microorganisms Are Present and Active in the Sediments of the Doce River and Tributaries Impacted by Iron Mine Tailings from the Collapsed Fundão Dam (Mariana, MG, Brazil). MINERALS 2021. [DOI: 10.3390/min11030244] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
On 5 November 2015, a large tailing deposit failed in Brazil, releasing an estimated 32.6 to 62 million m3 of iron mining tailings into the environment. Tailings from the Fundão Dam flowed down through the Gualaxo do Norte and Carmo riverbeds and floodplains and reached the Doce River. Since then, bottom sediments have become enriched in Fe(III) oxyhydroxides. Dissimilatory iron-reducing microorganisms (DIRMs) are anaerobes able to couple organic matter oxidation to Fe(III) reduction, producing CO2 and Fe(II), which can precipitate as magnetite (FeO·Fe2O3) and other Fe(II) minerals. In this work, we investigated the presence of DIRMs in affected and non-affected bottom sediments of the Gualaxo do Norte and Doce Rivers. The increase in Fe(II) concentrations in culture media over time indicated the presence of Fe(III)-reducing microorganisms in all sediments tested, which could reduce Fe(III) from both tailings and amorphous ferric oxyhydroxide. Half of our enrichment cultures converted amorphous Fe(III) oxyhydroxide into magnetite, which was characterized by X-ray diffraction, transmission electron microscopy, and magnetic measurements. The conversion of solid Fe(III) phases to soluble Fe(II) and/or magnetite is characteristic of DIRM cultures. The presence of DIRMs in the sediments of the Doce River and tributaries points to the possibility of reductive dissolution of goethite (α-FeOOH) and/or hematite (α-Fe2O3) from sediments, along with the consumption of organics, release of trace elements, and impairment of water quality.
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Suhadolnik MLS, Costa PS, Castro GM, Lobo FP, Nascimento AMA. Comprehensive insights into arsenic- and iron-redox genes, their taxonomy and associated environmental drivers deciphered by a meta-analysis. ENVIRONMENT INTERNATIONAL 2021; 146:106234. [PMID: 33181412 DOI: 10.1016/j.envint.2020.106234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/23/2020] [Accepted: 10/20/2020] [Indexed: 06/11/2023]
Abstract
In nature, arsenic (As) and iron (Fe) biotransformation are interconnected, influencing local As mobility and toxicity. While As- or Fe-metabolizing microorganisms are widely documented, knowledge concerning their cycling genes, associated with geophysicochemical data and taxonomic distribution, remains scarce. We performed a meta-analysis to explore the distribution and environmental importance of As- and Fe-redox genes (AsRGs and FeRGs) and predict their significant correlations and hosts. The most abundant and ubiquitous AsRGs and FeRGs were arsC and ccoN, respectively. The ccoN gene had the highest frequency at pH ≥ 9.1, in which dissolved Fe(II) is scarce, possibly contributing to enhanced host survival. Fe(III) oxidation genes iro and ccoN appear to be associated with As(V) detoxification in mesophilic environments. No correlation was observed between Fe(III) reduction gene omcB and arsenate reductase genes. Cytochromes with putative roles in Fe-redox reactions were identified (including yceJ and fbcH) and were significantly correlated with As(V) reduction genes under diverse geophysicochemical conditions. The taxonomies of AsRGs and FeRGs-carrying contigs revealed great diversity, among which various, such as Chlamydea (arsC) and Firmicutes (omcB), were previously undescribed. Nearly all (98.9%) of the AsRGs and FeRGs were not carried by any plasmid sequences. This meta-analysis expands our understanding of the global environmental, taxonomic and functional microbiome involved in As- and Fe-redox transformations. Moreover, these findings should help guide studies on putative in vivo functional roles of cytochromes in Fe-redox pathways.
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Affiliation(s)
- Maria Luíza S Suhadolnik
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - Patrícia S Costa
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - Giovanni M Castro
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - Francisco P Lobo
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - Andréa M A Nascimento
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil.
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12
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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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13
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Zheng M, Shi J, Xu C, Han Y, Zhang Z, Han H. Insights into electroactive biofilms for enhanced phenolic degradation of coal pyrolysis wastewater (CPW) by magnetic activated coke (MAC): Metagenomic analysis in attached biofilm and suspended sludge. JOURNAL OF HAZARDOUS MATERIALS 2020; 395:122688. [PMID: 32335283 DOI: 10.1016/j.jhazmat.2020.122688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/14/2020] [Accepted: 04/07/2020] [Indexed: 06/11/2023]
Abstract
To investigate the role of electroactive biofilms for enhanced phenolic degradation, lignite activated coke (LAC) and MAC were used as carriers in moving-bed biofilm reactor (MBBR) for CPW treatment. In contrast to activated sludge (AS) reactor, the carriers improved degradation performance of MBBR. Although two MBBRs exerted similar degradation capacity with over 92% of COD and 93% phenols removal under the highest phenolics concentration (500 mg/L), the effluent of MAC-based MBBR remained higher biodegradability (BOD5/COD = 0.34 vs 0.18) than that of LAC-based MBBR. Metagenomic analysis revealed that electroactive biofilms determined phenolic degradation of MAC-based MBBR. Primarily, Geobacter (17.33%) started Fe redox cycle on biofilms and developed syntrophy with Syntrophorhabdus (6.47%), which fermented phenols into easily biodegradable substrates. Subsequently, Ignavibacterium (3.38% to 2.52%) and Acidovorax (0.46% to 8.83%) conducted biological electricity from electroactive biofilms to suspended sludge. They synergized with dominated genus in suspended sludge, Alicycliphilus (19.56%) that accounted for phenolic oxidation and nitrate reduction. Consequently, the significantly advantage of Geobater and Syntrophorhabdus was the keystone reason for superior biodegradability maintenance of MAC-based MBBR.
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Affiliation(s)
- Mengqi Zheng
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Jingxin Shi
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Chunyan Xu
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Yuxing Han
- School of Engineering, South China Agriculture University, Guangzhou 510642, China.
| | - Zhengwen Zhang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Hongjun Han
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
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14
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Arbour TJ, Gilbert B, Banfield JF. Diverse Microorganisms in Sediment and Groundwater Are Implicated in Extracellular Redox Processes Based on Genomic Analysis of Bioanode Communities. Front Microbiol 2020; 11:1694. [PMID: 32849356 PMCID: PMC7399161 DOI: 10.3389/fmicb.2020.01694] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 06/29/2020] [Indexed: 11/17/2022] Open
Abstract
Extracellular electron transfer (EET) between microbes and iron minerals, and syntrophically between species, is a widespread process affecting biogeochemical cycles and microbial ecology. The distribution of this capacity among microbial taxa, and the thermodynamic controls on EET in complex microbial communities, are not fully known. Microbial electrochemical cells (MXCs), in which electrodes serve as the electron acceptor or donor, provide a powerful approach to enrich for organisms capable of EET and to study their metabolism. We used MXCs coupled with genome-resolved metagenomics to investigate the capacity for EET in microorganisms present in a well-studied aquifer near Rifle, CO. Electroactive biofilms were established and maintained for almost 4 years on anodes poised mostly at −0.2 to −0.25 V vs. SHE, a range that mimics the redox potential of iron-oxide minerals, using acetate as the sole carbon source. Here we report the metagenomic characterization of anode-biofilm and planktonic microbial communities from samples collected at timepoints across the study period. From two biofilm and 26 planktonic samples we reconstructed draft-quality and near-complete genomes for 84 bacteria and 2 archaea that represent the majority of organisms present. A novel Geobacter sp. with at least 72 putative multiheme c-type cytochromes (MHCs) was the dominant electrode-attached organism. However, a diverse range of other electrode-associated organisms also harbored putative MHCs with at least 10 heme-binding motifs, as well as porin-cytochrome complexes and e-pili, including Actinobacteria, Ignavibacteria, Chloroflexi, Acidobacteria, Firmicutes, Beta- and Gammaproteobacteria. Our results identify a small subset of the thousands of organisms previously detected in the Rifle aquifer that may have the potential to mediate mineral redox transformations.
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Affiliation(s)
- Tyler J Arbour
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, United States
| | - Benjamin Gilbert
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, United States.,Energy Geosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, United States.,Energy Geosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, United States
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15
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Dillon ML, Hawes I, Jungblut AD, Mackey TJ, Eisen JA, Doran PT, Sumner DY. Energetic and Environmental Constraints on the Community Structure of Benthic Microbial Mats in Lake Fryxell, Antarctica. FEMS Microbiol Ecol 2020; 96:fiz207. [PMID: 31905236 PMCID: PMC6974422 DOI: 10.1093/femsec/fiz207] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 01/03/2020] [Indexed: 11/13/2022] Open
Abstract
Ecological communities are regulated by the flow of energy through environments. Energy flow is typically limited by access to photosynthetically active radiation (PAR) and oxygen concentration (O2). The microbial mats growing on the bottom of Lake Fryxell, Antarctica, have well-defined environmental gradients in PAR and (O2). We analyzed the metagenomes of layers from these microbial mats to test the extent to which access to oxygen and light controls community structure. We found variation in the diversity and relative abundances of Archaea, Bacteria and Eukaryotes across three (O2) and PAR conditions: high (O2) and maximum PAR, variable (O2) with lower maximum PAR, and low (O2) and maximum PAR. We found distinct communities structured by the optimization of energy use on a millimeter-scale across these conditions. In mat layers where (O2) was saturated, PAR structured the community. In contrast, (O2) positively correlated with diversity and affected the distribution of dominant populations across the three habitats, suggesting that meter-scale diversity is structured by energy availability. Microbial communities changed across covarying gradients of PAR and (O2). The comprehensive metagenomic analysis suggests that the benthic microbial communities in Lake Fryxell are structured by energy flow across both meter- and millimeter-scales.
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Affiliation(s)
- Megan L Dillon
- Lawrence Berkeley National Laboratory Climate and Ecosystem Sciences Division 70A-2245B, One Cyclotron Rd Berkeley, CA 94720 510-486-5538
- Department of Earth and Planetary Sciences, University of California, Davis One Shields Ave Davis, CA 95616, USA
| | - Ian Hawes
- Coastal Marine Field Station, University of Waikato, 58 Cross Rd Sulphur Point Tauranga 3110, New Zealand
| | - Anne D Jungblut
- Life Sciences Department, Natural History Museum, Cromwell Rd South Kensington London SW7 5BD, UK
| | - Tyler J Mackey
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, 77 Massachusetts Ave Cambridge, MA 02139-4307, USA
| | - Jonathan A Eisen
- Department of Evolution and Ecology, University of California, Davis, One Shields Ave Davis, CA USA
| | - Peter T Doran
- Geology and Geophysics, Louisiana State University, E235 Howe Russell Kniffen Baton Rouge, LA 70803 USA
| | - Dawn Y Sumner
- Department of Earth and Planetary Sciences, University of California, Davis One Shields Ave Davis, CA 95616, USA
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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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A review of the mechanisms of mineral-based metabolism in early Earth analog rock-hosted hydrothermal ecosystems. World J Microbiol Biotechnol 2019; 35:29. [PMID: 30689069 DOI: 10.1007/s11274-019-2604-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 01/20/2019] [Indexed: 10/27/2022]
Abstract
Prior to the advent of oxygenic photosynthesis ~ 2.8-3.2 Ga, life was dependent on chemical energy captured from oxidation-reduction reactions involving minerals or substrates generated through interaction of water with minerals. Terrestrial hydrothermal environments host abundant and diverse non-photosynthetic communities and a variety of minerals that can sustain microbial metabolism. Minerals and substrates generated through interaction of minerals with water are differentially distributed in hot spring environments which, in turn, shapes the distribution of microbial life and the metabolic processes that support it. Emerging evidence suggests that terrestrial hydrothermal environments may have played a role in supporting the metabolism of the earliest forms of microbial life. It follows that these environments and their microbial inhabitants are increasingly being studied as analogs of early Earth ecosystems. Here we review current understanding of the processes that lead to variation in the availability of minerals or mineral-sourced substrates in terrestrial hydrothermal environments. In addition, we summarize proposed mechanisms of mineral substrate acquisition and metabolism in microbial cells inhabiting terrestrial hydrothermal environments, highlighting the importance of the dynamic interplay between biotic and abiotic reactions in influencing mineral substrate bioavailability. An emphasis is placed on mechanisms involved in the solubilization, acquisition, and metabolism of sulfur- and iron-bearing minerals, since these elements were likely integrated into the metabolism of the earliest anaerobic cells.
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18
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Thiel V, Garcia Costas AM, Fortney NW, Martinez JN, Tank M, Roden EE, Boyd ES, Ward DM, Hanada S, Bryant DA. " Candidatus Thermonerobacter thiotrophicus," A Non-phototrophic Member of the Bacteroidetes/Chlorobi With Dissimilatory Sulfur Metabolism in Hot Spring Mat Communities. Front Microbiol 2019; 9:3159. [PMID: 30687241 PMCID: PMC6338057 DOI: 10.3389/fmicb.2018.03159] [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] [Received: 10/16/2018] [Accepted: 12/05/2018] [Indexed: 12/31/2022] Open
Abstract
In this study we present evidence for a novel, thermophilic bacterium with dissimilatory sulfur metabolism, tentatively named “Candidatus Thermonerobacter thiotrophicus,” which is affiliated with the Bacteroides/Ignavibacteria/Chlorobi and which we predict to be a sulfate reducer. Dissimilatory sulfate reduction (DSR) is an important and ancient metabolic process for energy conservation with global importance for geochemical sulfur and carbon cycling. Characterized sulfate-reducing microorganisms (SRM) are found in a limited number of bacterial and archaeal phyla. However, based on highly diverse environmental dsrAB sequences, a variety of uncultivated and unidentified SRM must exist. The recent development of high-throughput sequencing methods allows the phylogenetic identification of some of these uncultured SRM. In this study, we identified a novel putative SRM inhabiting hot spring microbial mats that is a member of the OPB56 clade (“Ca. Kapabacteria”) within the Bacteroidetes/Chlorobi superphylum. Partial genomes for this new organism were retrieved from metagenomes from three different hot springs in Yellowstone National Park, United States, and Japan. Supporting the prediction of a sulfate-reducing metabolism for this organism during period of anoxia, diel metatranscriptomic analyses indicate highest relative transcript levels in situ for all DSR-related genes at night. The presence of terminal oxidases, which are transcribed during the day, further suggests that these organisms might also perform aerobic respiration. The relative phylogenetic proximity to the sulfur-oxidizing, chlorophototrophic Chlorobi further raises new questions about the evolution of dissimilatory sulfur metabolism.
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Affiliation(s)
- Vera Thiel
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
| | - Amaya M Garcia Costas
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States.,Department of Biology, Colorado State University-Pueblo, Pueblo, CO, United States
| | - Nathaniel W Fortney
- Department of Geoscience, University of Wisconsin-Madison, Madison, WI, United States
| | - Joval N Martinez
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan.,Department of Natural Sciences, University of St. La Salle, Bacolod, Philippines
| | - Marcus Tank
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
| | - Eric E Roden
- Department of Geoscience, University of Wisconsin-Madison, Madison, WI, United States
| | - Eric S Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - David M Ward
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, United States
| | - Satoshi Hanada
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States.,Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
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19
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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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20
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Borsodi AK, Anda D, Makk J, Krett G, Dobosy P, Büki G, Erőss A, Mádl-Szőnyi J. Biofilm forming bacteria and archaea in thermal karst springs of Gellért Hill discharge area (Hungary). J Basic Microbiol 2018; 58:928-937. [PMID: 30160784 DOI: 10.1002/jobm.201800138] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 06/13/2018] [Accepted: 06/24/2018] [Indexed: 12/20/2022]
Abstract
The Buda Thermal Karst System (BTKS) is an extensive active hypogenic cave system located beneath the residential area of the Hungarian capital. At the river Danube, several thermal springs discharge forming spring caves. To reveal and compare the morphological structure and prokaryotic diversity of reddish-brown biofilms developed on the carbonate rock surfaces of the springs, scanning electron microscopy (SEM), and molecular cloning were applied. Microbial networks formed by filamentous bacteria and other cells with mineral crystals embedded in extracellular polymeric substances were observed in the SEM images. Biofilms were dominated by prokaryotes belonging to phyla Proteobacteria, Chloroflexi and Nitrospirae (Bacteria) and Thaumarchaeota (Archaea) but their abundance showed differences according to the type of the host rock, geographic distance, and different water exchange. In addition, representatives of phyla Acidobacteria, Actinobacteria, Caldithrix, Cyanobacteria, Firmicutes Gemmatimonadetes, and several candidate divisions of Bacteria as well as Crenarchaeota and Euryarchaeota were detected in sample-dependent higher abundance. The results indicate that thermophilic, anaerobic sulfur-, sulfate-, nitrate-, and iron(III)-reducing chemoorganotrophic as well as sulfur-, ammonia-, and nitrite-oxidizing chemolithotrophic prokaryotes can interact in the studied biofilms adapted to the unique and extreme circumstances (e.g., aphotic and nearly anoxic conditions, oligotrophy, and radionuclide accumulation) in the thermal karst springs.
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Affiliation(s)
- Andrea K Borsodi
- Department of Microbiology, ELTE Eötvös Loránd University, Budapest, Hungary.,Danube Research Institute, MTA Centre for Ecological Research, Budapest, Hungary
| | - Dóra Anda
- Department of Microbiology, ELTE Eötvös Loránd University, Budapest, Hungary.,Danube Research Institute, MTA Centre for Ecological Research, Budapest, Hungary
| | - Judit Makk
- Department of Microbiology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Gergely Krett
- Department of Microbiology, ELTE Eötvös Loránd University, Budapest, Hungary.,Danube Research Institute, MTA Centre for Ecological Research, Budapest, Hungary
| | - Péter Dobosy
- Danube Research Institute, MTA Centre for Ecological Research, Budapest, Hungary
| | - Gabriella Büki
- Department of Microbiology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Anita Erőss
- Department of Physical and Applied Geology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Judit Mádl-Szőnyi
- Department of Physical and Applied Geology, ELTE Eötvös Loránd University, Budapest, Hungary
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21
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Amenabar MJ, Boyd ES. Mechanisms of Mineral Substrate Acquisition in a Thermoacidophile. Appl Environ Microbiol 2018; 84:e00334-18. [PMID: 29625980 PMCID: PMC5981063 DOI: 10.1128/aem.00334-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 04/02/2018] [Indexed: 01/01/2023] Open
Abstract
The thermoacidophile Acidianus is widely distributed in Yellowstone National Park hot springs that span large gradients in pH (1.60 to 4.84), temperature (42 to 90°C), and mineralogical composition. To characterize the potential role of flexibility in mineral-dependent energy metabolism in contributing to the widespread ecological distribution of this organism, we characterized the spectrum of minerals capable of supporting metabolism and the mechanisms that it uses to access these minerals. The energy metabolism of Acidianus strain DS80 was supported by elemental sulfur (S0), a variety of iron (hydr)oxides, and arsenic sulfide. Strain DS80 reduced, oxidized, and disproportionated S0 Cells growing via S0 reduction and disproportionation did not require direct access to the mineral to reduce it, whereas cells growing via S0 oxidation did require direct access, observations that are attributable to the role of H2S produced by S0 reduction/disproportionation in solubilizing and increasing the bioavailability of S0 Cells growing via iron (hydr)oxide reduction did not require access to the mineral, suggesting that the cells reduce Fe(III) that is being leached by the acidic growth medium. Cells growing via oxidation of arsenic sulfide with Fe(III) did not require access to the mineral to grow. The stoichiometry of reactants to products indicates that cells oxidize soluble As(III) released from oxidation of arsenic sulfide by aqueous Fe(III). Taken together, these observations underscore the importance of feedbacks between abiotic and biotic reactions in influencing the bioavailability of mineral substrates and defining ecological niches capable of supporting microbial metabolism.IMPORTANCE Mineral sources of electron donor and acceptor that support microbial metabolism are abundant in the natural environment. However, the spectrum of minerals capable of supporting a given microbial strain and the mechanisms that are used to access these minerals in support of microbial energy metabolism are often unknown, in particular among thermoacidophiles. Here, we show that the thermoacidophile Acidianus strain DS80 is adapted to use a variety of iron (hydro)oxide minerals, elemental sulfur, and arsenic sulfide to support growth. Cells rely on a complex interplay of abiologically and biologically catalyzed reactions that increase the solubility or bioavailability of minerals, thereby enabling their use in microbial metabolism.
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Affiliation(s)
- Maximiliano J Amenabar
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, USA
| | - Eric S Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, USA
- NASA Astrobiology Institute, Mountain View, California, USA
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22
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Stable Isotope Probing for Microbial Iron Reduction in Chocolate Pots Hot Spring, Yellowstone National Park. Appl Environ Microbiol 2018; 84:AEM.02894-17. [PMID: 29602784 DOI: 10.1128/aem.02894-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 03/26/2018] [Indexed: 11/20/2022] Open
Abstract
Chocolate Pots hot springs (CP) is a circumneutral-pH Fe-rich geothermal feature located in Yellowstone National Park. Previous Fe(III)-reducing enrichment culture studies with CP sediments identified close relatives of known dissimilatory Fe(III)-reducing bacterial (FeRB) taxa, including Geobacter and Melioribacter However, the abundances and activities of such organisms in the native microbial community are unknown. Here, we used stable isotope probing experiments combined with 16S rRNA gene amplicon and shotgun metagenomic sequencing to gain an understanding of the in situ Fe(III)-reducing microbial community at CP. Fe-Si oxide precipitates collected near the hot spring vent were incubated with unlabeled and 13C-labeled acetate to target active FeRB. We searched reconstructed genomes for homologs of genes involved in known extracellular electron transfer (EET) systems to identify the taxa involved in Fe redox transformations. Known FeRB taxa containing putative EET systems (Geobacter, Ignavibacteria) increased in abundance under acetate-amended conditions, whereas genomes related to Ignavibacterium and Thermodesulfovibrio that contained putative EET systems were recovered from incubations without electron donor. Our results suggest that FeRB play an active role in Fe redox cycling within Fe-Si oxide-rich deposits located at the hot spring vent.IMPORTANCE The identification of past near-surface hydrothermal environments on Mars emphasizes the importance of using modern Earth environments, such as CP, to gain insight into potential Fe-based microbial life on other rocky worlds, as well as ancient Fe-rich Earth ecosystems. By combining stable carbon isotope probing techniques and DNA sequencing technology, we gained insight into the pathways of microbial Fe redox cycling at CP. The results suggest that microbial Fe(III) oxide reduction is prominent in situ, with important implications for the generation of geochemical and stable Fe isotopic signatures of microbial Fe redox metabolism within Fe-rich circumneutral-pH thermal spring environments on Earth and Mars.
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Stern N, Mejia J, He S, Yang Y, Ginder-Vogel M, Roden EE. Dual Role of Humic Substances As Electron Donor and Shuttle for Dissimilatory Iron Reduction. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:5691-5699. [PMID: 29658273 PMCID: PMC6211804 DOI: 10.1021/acs.est.7b06574] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Dissimilatory iron-reducing bacteria (DIRB) are known to use humic substances (HS) as electron shuttles for dissimilatory iron reduction (DIR) by transferring electrons to HS-quinone moieties, which in turn rapidly reduce Fe(III) oxides. However, the potential for HS to serve as a source of organic carbon (OC) that can donate electrons for DIR is unknown. We studied whether humic acids (HA) and humins (HM) recovered from peat soil by sodium pyrophosphate extraction could serve as both electron shuttles and electron donors for DIR by freshwater sediment microorganisms. Both HA and HM served as electron shuttles in cultures amended with glucose. However, only HA served as an electron donor for DIR. Metagenomes from HA-containing cultures had an overrepresentation of genes involved in polysaccharide and to a lesser extent aromatic compound degradation, suggesting complex OC metabolism. Genomic searches for the porin-cytochrome complex involved in DIR resulted in matches to Ignavibacterium/Melioribacter, DIRB capable of polymeric OC metabolism. These results indicate that such taxa may have played a role in both DIR and decomposition of complex OC. Our results suggest that decomposition of HS coupled to DIR and other anaerobic pathways could play an important role in soil and sediment OC metabolism.
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Affiliation(s)
- Noah Stern
- Department of Civil and Environmental Engineering, Environmental Chemistry and Technology Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Jacqueline Mejia
- Department of Civil and Environmental Engineering, Environmental Chemistry and Technology Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Shaomei He
- Department of Geoscience, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Yu Yang
- Department of Civil and Environmental Engineering, University of Nevada-Reno, Reno, Nevada 89557, United States
| | - Matthew Ginder-Vogel
- Department of Civil and Environmental Engineering, Environmental Chemistry and Technology Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Eric E. Roden
- Department of Geoscience, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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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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