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Ye J, Hu A, Gao C, Li F, Li L, Guo Y, Ren G, Li B, Rensing C, Nealson KH, Zhou S, Xiong Y. Abiotic Methane Production Driven by Ubiquitous Non-Fenton-Type Reactive Oxygen Species. Angew Chem Int Ed Engl 2024:e202403884. [PMID: 38489233 DOI: 10.1002/anie.202403884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 03/15/2024] [Accepted: 03/15/2024] [Indexed: 03/17/2024]
Abstract
Abiotic CH4 production driven by Fenton-type reactive oxygen species (ROS) has been confirmed to be an indispensable component of the atmospheric CH4 budget. While the chemical reactions independent of Fenton chemistry to ROS are ubiquitous in nature, it remains unknown whether the produced ROS can drive abiotic CH4 production. Here, we first demonstrated the abiotic CH4 production at the soil-water interface under illumination. Leveraging this finding, polymeric carbon nitrides (CNx) as a typical analogue of natural geobattery material and dimethyl sulfoxide (DMSO) as a natural methyl donor were used to unravel the underlying mechanisms. We revealed that the ROS, photocatalytically produced by CNx, can oxidize DMSO into CH4 with a high selectivity of 91.5 %. Such an abiotic CH4 production process was further expanded to various non-Fenton-type reaction systems, such as electrocatalysis, pyrocatalysis and sonocatalysis. This work provides insights into the geochemical cycle of abiotic CH4, and offers a new route to CH4 production via integrated energy development.
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Affiliation(s)
- Jie Ye
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Andong Hu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chao Gao
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, 230026, China
| | - Fengqi Li
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lei Li
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yulin Guo
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Guoping Ren
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Bing Li
- Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Christopher Rensing
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Kenneth H Nealson
- Department of Earth Science, University of Southern California, Los Angeles, California, 90089, United States
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yujie Xiong
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, 230026, China
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2
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Van Den Berghe M, Walworth NG, Dalvie NC, Dupont CL, Springer M, Andrews MG, Romaniello SJ, Hutchins DA, Montserrat F, Silver PA, Nealson KH. Microbial Catalysis for CO 2 Sequestration: A Geobiological Approach. Cold Spring Harb Perspect Biol 2023:a041673. [PMID: 37788887 DOI: 10.1101/cshperspect.a041673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
One of the greatest threats facing the planet is the continued increase in excess greenhouse gasses, with CO2 being the primary driver due to its rapid increase in only a century. Excess CO2 is exacerbating known climate tipping points that will have cascading local and global effects including loss of biodiversity, global warming, and climate migration. However, global reduction of CO2 emissions is not enough. Carbon dioxide removal (CDR) will also be needed to avoid the catastrophic effects of global warming. Although the drawdown and storage of CO2 occur naturally via the coupling of the silicate and carbonate cycles, they operate over geological timescales (thousands of years). Here, we suggest that microbes can be used to accelerate this process, perhaps by orders of magnitude, while simultaneously producing potentially valuable by-products. This could provide both a sustainable pathway for global drawdown of CO2 and an environmentally benign biosynthesis of materials. We discuss several different approaches, all of which involve enhancing the rate of silicate weathering. We use the silicate mineral olivine as a case study because of its favorable weathering properties, global abundance, and growing interest in CDR applications. Extensive research is needed to determine both the upper limit of the rate of silicate dissolution and its potential to economically scale to draw down significant amounts (Mt/Gt) of CO2 Other industrial processes have successfully cultivated microbial consortia to provide valuable services at scale (e.g., wastewater treatment, anaerobic digestion, fermentation), and we argue that similar economies of scale could be achieved from this research.
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Affiliation(s)
| | - Nathan G Walworth
- Vesta, San Francisco, California 94114, USA
- University of Southern California, Los Angeles, California 90007, USA
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Neil C Dalvie
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Chris L Dupont
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, California 92037, USA
- Department of Human Biology and Genomic Medicine, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Michael Springer
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | | | | | - David A Hutchins
- University of Southern California, Los Angeles, California 90007, USA
| | | | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Kenneth H Nealson
- Vesta, San Francisco, California 94114, USA
- University of Southern California, Los Angeles, California 90007, USA
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3
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Thompson J, Barr C, Babcock-Adams L, Bird L, La Cava E, Garber A, Hongoh Y, Liu M, Nealson KH, Okamoto A, Repeta D, Suzuki S, Tacto C, Tashjian M, Merino N. Insights into the physiological and genomic characterization of three bacterial isolates from a highly alkaline, terrestrial serpentinizing system. Front Microbiol 2023; 14:1179857. [PMID: 37520355 PMCID: PMC10373932 DOI: 10.3389/fmicb.2023.1179857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 05/23/2023] [Indexed: 08/01/2023] Open
Abstract
The terrestrial serpentinite-hosted ecosystem known as "The Cedars" is home to a diverse microbial community persisting under highly alkaline (pH ~ 12) and reducing (Eh < -550 mV) conditions. This extreme environment presents particular difficulties for microbial life, and efforts to isolate microorganisms from The Cedars over the past decade have remained challenging. Herein, we report the initial physiological assessment and/or full genomic characterization of three isolates: Paenibacillus sp. Cedars ('Paeni-Cedars'), Alishewanella sp. BS5-314 ('Ali-BS5-314'), and Anaerobacillus sp. CMMVII ('Anaero-CMMVII'). Paeni-Cedars is a Gram-positive, rod-shaped, mesophilic facultative anaerobe that grows between pH 7-10 (minimum pH tested was 7), temperatures 20-40°C, and 0-3% NaCl concentration. The addition of 10-20 mM CaCl2 enhanced growth, and iron reduction was observed in the following order, 2-line ferrihydrite > magnetite > serpentinite ~ chromite ~ hematite. Genome analysis identified genes for flavin-mediated iron reduction and synthesis of a bacillibactin-like, catechol-type siderophore. Ali-BS5-314 is a Gram-negative, rod-shaped, mesophilic, facultative anaerobic alkaliphile that grows between pH 10-12 and temperatures 10-40°C, with limited growth observed 1-5% NaCl. Nitrate is used as a terminal electron acceptor under anaerobic conditions, which was corroborated by genome analysis. The Ali-BS5-314 genome also includes genes for benzoate-like compound metabolism. Anaero-CMMVII remained difficult to cultivate for physiological studies; however, growth was observed between pH 9-12, with the addition of 0.01-1% yeast extract. Anaero-CMMVII is a probable oxygen-tolerant anaerobic alkaliphile with hydrogenotrophic respiration coupled with nitrate reduction, as determined by genome analysis. Based on single-copy genes, ANI, AAI and dDDH analyses, Paeni-Cedars and Ali-BS5-314 are related to other species (P. glucanolyticus and A. aestuarii, respectively), and Anaero-CMMVII represents a new species. The characterization of these three isolates demonstrate the range of ecophysiological adaptations and metabolisms present in serpentinite-hosted ecosystems, including mineral reduction, alkaliphily, and siderophore production.
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Affiliation(s)
- Jaclyn Thompson
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Casey Barr
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Lydia Babcock-Adams
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Lina Bird
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, United States
| | - Eugenio La Cava
- National Institute for Materials Science, Tsukuba, Ibaraki, Japan
| | - Arkadiy Garber
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ, United States
| | - Yuichi Hongoh
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Mark Liu
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Kenneth H. Nealson
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Akihiro Okamoto
- Research Center for Macromolecules and Biomaterials, National Institute for Materials Science, Tsukuba, Japan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido, Japan
- Graduate School of Science and Technology, University of Tsukuba, Tsukuba, Japan
| | - Daniel Repeta
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Shino Suzuki
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, Sagamihara, Kanagawa, Japan
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), JAMSTEC, Yokosuka, Kanagawa, Japan
| | - Clarissa Tacto
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Michelle Tashjian
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Nancy Merino
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, United States
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4
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Nealson KH. Measuring the pulse of our planet. Proc Natl Acad Sci U S A 2023; 120:e2308206120. [PMID: 37343052 PMCID: PMC10319026 DOI: 10.1073/pnas.2308206120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/23/2023] Open
Affiliation(s)
- Kenneth H. Nealson
- Department of Earth Sciences and Biological Sciences, University of Southern California, Dornsife College, Los Angeles, CA90089
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5
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Chen S, Chen J, Zhang L, Huang S, Liu X, Yang Y, Luan T, Zhou S, Nealson KH, Rensing C. Biophotoelectrochemical process co-driven by dead microalgae and live bacteria. ISME J 2023; 17:712-719. [PMID: 36823233 PMCID: PMC10119253 DOI: 10.1038/s41396-023-01383-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 02/08/2023] [Accepted: 02/10/2023] [Indexed: 02/25/2023]
Abstract
Anaerobic reduction processes in natural waters can be promoted by dead microalgae that have been attributed to nutrient substances provided by the decomposition of dead microalgae for other microorganisms. However, previous reports have not considered that dead microalgae may also serve as photosensitizers to drive microbial reduction processes. Here we demonstrate a photoelectric synergistic linkage between dead microalgae and bacteria capable of extracellular electron transfer (EET). Illumination of dead Raphidocelis subcapitata resulted in two-fold increase in the rate of anaerobic bioreduction by pure Geobacter sulfurreducens, suggesting that photoelectrons generated from the illuminated dead microalgae were transferred to the EET-capable microorganisms. Similar phenomena were observed in NO3- reduction driven by irradiated dead Chlorella vulgaris and living Shewanella oneidensis, and Cr(VI) reduction driven by irradiated dead Raphidocelis subcapitata and living Bacillus subtilis. Enhancement of bioreduction was also seen when the killed microalgae were illuminated in mixed-culture lake water, suggesting that EET-capable bacteria were naturally present and this phenomenon is common in post-bloom systems. The intracellular ferredoxin-NADP+-reductase is inactivated in the dead microalgae, allowing the production and extracellular transfer of photoelectrons. The use of mutant strains confirmed that the electron transport pathway requires multiheme cytochromes. Taken together, these results suggest a heretofore overlooked biophotoelectrochemical process jointly mediated by illumination of dead microalgae and live EET-capable bacteria in natural ecosystems, which may add an important component in the energetics of bioreduction phenomena particularly in microalgae-enriched environments.
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Affiliation(s)
- Shanshan Chen
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, China
| | - Jin Chen
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lanlan Zhang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, China
| | - Shaofu Huang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xing Liu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuting Yang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, China
| | - Tiangang Luan
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, China
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China.
| | - Kenneth H Nealson
- Department of Earth Science, University of Southern California, Los Angeles, CA, USA
| | - Christopher Rensing
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
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6
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Liu X, Ye Y, Zhang Z, Rensing C, Zhou S, Nealson KH. Prophage Induction Causes Geobacter Electroactive Biofilm Decay. Environ Sci Technol 2023; 57:6196-6204. [PMID: 36997849 DOI: 10.1021/acs.est.2c08443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Sustaining a metabolically active electroactive biofilm (EAB) is essential for the high efficiency and durable operation of microbial fuel cells (MFCs). However, EABs usually decay during long-term operation, and, until now, the causes remain unknown. Here, we report that lysogenic phages can cause EAB decay in Geobacter sulfurreducens fuel cells. A cross-streak agar assay and bioinformatic analysis revealed the presence of prophages on the G. sulfurreducens genome, and a mitomycin C induction assay revealed the lysogenic to lytic transition of those prophages, resulting in a progressive decay in both current generation and the EAB. Furthermore, the addition of phages purified from decayed EAB resulted in accelerated decay of the EAB, thereafter contributing to a faster decline in current generation; otherwise, deleting prophage-related genes rescued the decay process. Our study provides the first evidence of an interaction between phages and electroactive bacteria and suggests that attack by phages is a primary cause of EAB decay, having significant implications in bioelectrochemical systems.
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Affiliation(s)
- Xing Liu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yin Ye
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhishuai Zhang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Christopher Rensing
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Kenneth H Nealson
- Department of Earth Science, University of Southern California, Los Angeles, California 90089, United States
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7
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Huang L, Liu X, Rensing C, Yuan Y, Zhou S, Nealson KH. Light-independent anaerobic microbial oxidation of manganese driven by an electrosyntrophic coculture. ISME J 2023; 17:163-171. [PMID: 36261509 PMCID: PMC9751303 DOI: 10.1038/s41396-022-01335-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 10/08/2022] [Accepted: 10/11/2022] [Indexed: 11/05/2022]
Abstract
Anaerobic microbial manganese oxidation (AMMO) has been considered an ancient biological metabolism for Mn element cycling on Archaean Earth before the presence of oxygen. A light-dependent AMMO was recently observed under strictly anoxic conditions, providing a new proxy for the interpretation of the evolution of oxygenic photosynthesis. However, the feasibility of biotic Mn(II) oxidation in dark geological habitats that must have been abundant remains unknown. Therefore, we discovered that it would be possible to achieve AMMO in a light-independent electrosyntrophic coculture between Rhodopseudomonas palustris and Geobacter metallireducens. Transmission electron microscopy analysis revealed insoluble particle formation in the coculture with Mn(II) addition. X-ray diffraction and X-ray photoelectron spectroscopy analysis verified that these particles were a mixture of MnO2 and Mn3O4. The absence of Mn oxides in either of the monocultures indicated that the Mn(II)-oxidizing activity was induced via electrosyntrophic interactions. Radical quenching and isotopic experiments demonstrated that hydroxyl radicals (•OH) produced from H2O dissociation by R. palustris in the coculture contributed to Mn(II) oxidation. All these findings suggest a new, symbiosis-dependent and light-independent AMMO route, with potential importance to the evolution of oxygenic photosynthesis and the biogeochemical cycling of manganese on Archaean and modern Earth.
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Affiliation(s)
- Lingyan Huang
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, China
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xing Liu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Christopher Rensing
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yong Yuan
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, China.
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kenneth H Nealson
- Department of Earth Science, University of Southern California, Los Angeles, CA, USA
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8
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Wang Y, You LX, Zhong HL, Wu GK, Li YP, Yang XJ, Wang AJ, Nealson KH, Herzberg M, Rensing C. Au(III)-induced extracellular electron transfer by Burkholderia contaminans ZCC for the bio-recovery of gold nanoparticles. Environ Res 2022; 210:112910. [PMID: 35151659 DOI: 10.1016/j.envres.2022.112910] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 01/15/2022] [Accepted: 02/05/2022] [Indexed: 06/14/2023]
Abstract
The biorecovery of gold (Au) by microbial reduction has received increasing attention, however, the biomolecules involved and the mechanisms by which they operate to produce Au nanoparticles have been not resolved. Here we report that Burkholderia contaminans ZCC is capable of reduction of Au(III) to Au nanoparticles on the cell surface. Exposure of B. contaminans ZCC to Au(III) led to significant changes in the functional group of cell proteins, with approximately 11.1% of the (C-C/C-H) bonds being converted to CO (8.1%) and C-OH (3.0%) bonds and 29.4% of the CO bonds being converted to (C-OH/C-O-C/P-O-C) bonds, respectively. In response to Au(III), B. contaminans ZCC also displayed the ability of extracellular electron transfer (EET) via membrane proteins and could produce reduced riboflavin as verified by electrochemical and liquid chromatography-mass spectrometric results, but did not do so without Au(III) being present. Addition of exogenous reduced riboflavin to the medium suggested that B. contaminans ZCC could utilize indirect EET via riboflavin to enhance the rate of reduction of Au(III). Transcriptional analysis of the riboflavin genes (ribBDEFH) supported the view of the importance of riboflavin in the reduction of Au(III) and its importance in the biorecovery of gold.
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Affiliation(s)
- Yi Wang
- College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua, 321004, PR China
| | - Le-Xing You
- College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua, 321004, PR China.
| | - Hong-Lin Zhong
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, PR China
| | - Gao-Kai Wu
- College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua, 321004, PR China
| | - Yuan-Ping Li
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, PR China
| | - Xiao-Jun Yang
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, PR China
| | - Ai-Jun Wang
- College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua, 321004, PR China
| | - Kenneth H Nealson
- Department of Earth Science, University of Southern California, Los Angeles, CA, USA
| | - Martin Herzberg
- Molecular Microbiology, Institute for Biology/Microbiology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle/Saale, Germany
| | - Christopher Rensing
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, PR China.
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9
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Barr CR, Bedrossian M, Lohmann KJ, Nealson KH. Magnetotactic bacteria: concepts, conundrums, and insights from a novel in situ approach using digital holographic microscopy (DHM). J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2022; 208:107-124. [DOI: 10.1007/s00359-022-01543-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 12/09/2021] [Accepted: 12/11/2021] [Indexed: 11/25/2022]
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10
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Van Den Berghe M, Merino N, Nealson KH, West AJ. Silicate minerals as a direct source of limiting nutrients: Siderophore synthesis and uptake promote ferric iron bioavailability from olivine and microbial growth. Geobiology 2021; 19:618-630. [PMID: 34105248 DOI: 10.1111/gbi.12457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 05/22/2021] [Indexed: 06/12/2023]
Abstract
Iron is a micronutrient critical to fundamental biological processes including respiration and photosynthesis, and it can therefore impact primary and heterotrophic productivity. Yet in oxic environments, iron is highly insoluble, rendering it, in principle, unavailable as a nutrient for biological growth. Life has "solved" this problem via the invention of iron chelates, known as siderophores, that keep iron available for microbial productivity. In this work, we examined the impact of siderophore synthesis on the speciation, mobility, and bioavailability of iron from rock-forming silicate minerals-shedding new light on the mechanisms by which microbes use mineral substrates to support primary productivity, as well as the consequent effects on silicate dissolution. Growth experiments were performed with Shewanella oneidensis MR-1 in an oxic, iron-depleted minimal medium, amended with olivine minerals as the sole source of iron. Experiments included the wild-type strain MR-1, and a siderophore synthesis gene deletion mutant strain (ΔMR-1). Relative to MR-1, ΔMR-1 exhibited a very pronounced growth penalty and an extended lag phase. However, substantial growth of ΔMR-1, comparable to MR-1 growth, was observed when the mutant strain was provided with siderophores in the form of either filtrate from a well-grown MR-1 culture, or commercially available deferoxamine. These observations suggest that siderophores are critical for S. oneidensis to acquire iron from olivine. Growth-limiting concentrations of deferoxamine amendments were observed to be ≤5-10 µM, concentrations significantly lower than previously recorded as necessary to impact mineral dissolution rates. X-ray photoelectric spectroscopy analyses of the incubated olivine surfaces suggest that siderophores deplete mineral surface layers of ferric iron. Combined, these results demonstrate that low micromolar concentrations of siderophores can effectively mobilize iron bound within silicate minerals, supporting very significant biological growth in limiting environments. The specific mechanism would involve siderophores removing a protective layer of nanometer-thick iron oxides, enhancing silicate dissolution and nutrient bioavailability.
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Affiliation(s)
- Martin Van Den Berghe
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
| | - Nancy Merino
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Biosciences and Biotechnology division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Kenneth H Nealson
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
| | - A Joshua West
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
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11
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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12
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Bird LJ, Kuenen JG, Osburn MR, Tomioka N, Ishii S, Barr C, Nealson KH, Suzuki S. Serpentinimonas gen. nov., Serpentinimonas raichei sp. nov., Serpentinimonas barnesii sp. nov. and Serpentinimonas maccroryi sp. nov., hyperalkaliphilic and facultative autotrophic bacteria isolated from terrestrial serpentinizing springs. Int J Syst Evol Microbiol 2021; 71:004945. [PMID: 34379584 PMCID: PMC8513617 DOI: 10.1099/ijsem.0.004945] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 07/02/2021] [Indexed: 11/18/2022] Open
Abstract
Three highly alkaliphilic bacterial strains designated as A1T, H1T and B1T were isolated from two highly alkaline springs at The Cedars, a terrestrial serpentinizing site. Cells from all strains were motile, Gram-negative and rod-shaped. Strains A1T, H1T and B1T were mesophilic (optimum, 30 °C), highly alkaliphilic (optimum, pH 11) and facultatively autotrophic. Major cellular fatty acids were saturated and monounsaturated hexadecenoic and octadecanoic acids. The genome size of strains A1T, H1T and B1T was 2 574 013, 2 475 906 and 2 623 236 bp, and the G+C content was 66.0, 66.2 and 66.1 mol%, respectively. Analysis of the 16S rRNA genes showed the highest similarity to the genera Malikia (95.1-96.4 %), Macromonas (93.0-93.6 %) and Hydrogenophaga (93.0-96.6 %) in the family Comamonadaceae. Phylogenetic analysis based on 16S rRNA gene and phylogenomic analysis based on core gene sequences revealed that the isolated strains diverged from the related species, forming a distinct branch. Average amino acid identity values of strains A1T, H1T and B1T against the genomes of related members in this family were below 67 %, which is below the suggested threshold for genera boundaries. Average nucleotide identity by blast values and digital DNA-DNA hybridization among the three strains were below 92.0 and 46.6 % respectively, which are below the suggested thresholds for species boundaries. Based on phylogenetic, genomic and phenotypic characterization, we propose Serpentinimonas gen. nov., Serpentinimonas raichei sp. nov. (type strain A1T=NBRC 111848T=DSM 103917T), Serpentinimonas barnesii sp. nov. (type strain H1T= NBRC 111849T=DSM 103920T) and Serpentinimonas maccroryi sp. nov. (type strain B1T=NBRC 111850T=DSM 103919T) belonging to the family Comamonadaceae. We have designated Serpentinimonas raichei the type species for the genus because it is the dominant species in The Cedars springs.
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Affiliation(s)
- Lina J. Bird
- Center for Bio/Molecular Science and Engineering Naval Research Lab, 4555 Overlook Ave S.W., Washington DC 20375, USA
- Department of Earth Sciences, University of Southern California, 35 W. 37th St. SHS 560, Los Angeles, California 90089, USA
| | - J. Gijs Kuenen
- Department of Earth Sciences, University of Southern California, 35 W. 37th St. SHS 560, Los Angeles, California 90089, USA
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629HZ, Delft, Netherlands
| | - Magdalena R. Osburn
- Department of Earth and Planetary Sciences, Weinberg College of Arts & Sciences. Northwestern University Evanston, Evanston, USA
| | - Naotaka Tomioka
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Monobe B200, Nankoku, Kochi 783-8502, Japan
| | - Shun’ichi Ishii
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Monobe B200, Nankoku, Kochi 783-8502, Japan
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), JAMSTEC, Natsushima 2-15, Yokosuka, Kanagawa 237-0061, Japan
| | - Casey Barr
- Department of Earth Sciences, University of Southern California, 35 W. 37th St. SHS 560, Los Angeles, California 90089, USA
| | - Kenneth H. Nealson
- Department of Earth Sciences, University of Southern California, 35 W. 37th St. SHS 560, Los Angeles, California 90089, USA
| | - Shino Suzuki
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Monobe B200, Nankoku, Kochi 783-8502, Japan
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), JAMSTEC, Natsushima 2-15, Yokosuka, Kanagawa 237-0061, Japan
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), 3-1-1 Yoshinodai, Chuo-ku, Sagamihara, Kanagawa 252-5210, Japan
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13
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Liu X, Zhan J, Liu L, Gan F, Ye J, Nealson KH, Rensing C, Zhou S. In Situ Spectroelectrochemical Characterization Reveals Cytochrome-Mediated Electric Syntrophy in Geobacter Coculture. Environ Sci Technol 2021; 55:10142-10151. [PMID: 34196176 DOI: 10.1021/acs.est.1c00356] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Direct interspecies electron transfer (DIET) between microbial species prevails in some key microbial consortia. However, the electron transfer mechanism(s) in these consortia is controversial due to lack of efficient characterization methods. Here, we provide an in situ anaerobic spectroelectrochemical coculture cell (in situ ASCC) to induce the formation of DIET coculture biofilm on the interdigitated microelectrode arrays and characterize the electron transfer directly. Two typical Geobacter DIET cocultures, Geobacter metallireducens and wild-type Geobacter sulfurreducens (G.m&G.s) and G. metallireducens and a G. sulfurreducens strain deficient in citrate synthase (G.m&G.s-ΔgltA), were selected. In situ Raman and electrochemical Fourier transform infrared (FTIR) spectroscopy indicated that cytochromes are abundant in the electric syntrophic coculture. Cyclic voltammetry and potential step experiment revealed a diffusion-controlled electron transfer process and the electrochemical gating measurements further demonstrated a cytochrome-mediated electron transfer in the DIET coculture. Furthermore, the G.m&G.s-ΔgltA coculture displayed a higher redox conductivity than the G.m&G.s coculture, consistent with the existence of an intimate and efficient electrical connection between these two species. Our findings provide the first report of a redox-gradient-driven electron transport facilitated by c-type cytochromes in DIET coculture, supporting the model that DIET is mediated by cytochromes and suggest a platform to explore the other DIET consortia.
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Affiliation(s)
- Xing Liu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ji Zhan
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lu Liu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Feiting Gan
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jie Ye
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Kenneth H Nealson
- Department of Earth Science, University of Southern California, Los Angeles, California 90007, United States
| | - Christopher Rensing
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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14
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Liu X, Huang L, Rensing C, Ye J, Nealson KH, Zhou S. Syntrophic interspecies electron transfer drives carbon fixation and growth by Rhodopseudomonas palustris under dark, anoxic conditions. Sci Adv 2021; 7:7/27/eabh1852. [PMID: 34215588 DOI: 10.1126/sciadv.abh1852] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 05/20/2021] [Indexed: 06/13/2023]
Abstract
In natural anoxic environments, anoxygenic photosynthetic bacteria fix CO2 by photoheterotrophy, photoautotrophy, or syntrophic anaerobic photosynthesis. Here, we describe electroautotrophy, a previously unidentified dark CO2 fixation mode enabled by the electrosyntrophic interaction between Geobacter metallireducens and Rhodopseudomonas palustris. After an electrosyntrophic coculture is formed, electrons are transferred either directly or indirectly (via electron shuttles) from G. metallireducens to R. palustris, thereby providing reducing power and energy for the dark CO2 fixation. Transcriptomic analyses demonstrated the high expression of genes encoding for the extracellular electron transfer pathway in G. metallireducens and the Calvin-Benson-Bassham carbon fixation cycle in R. palustris Given that sediments constitute one of the most ubiquitous and abundant niches on Earth and that, at depth, most of the sedimentary niche is both anoxic and dark, dark carbon fixation provides a metabolic window for the survival of anoxygenic phototrophs, as well as an as-yet unappreciated contribution to the global carbon cycle.
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Affiliation(s)
- Xing Liu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lingyan Huang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Christopher Rensing
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jie Ye
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kenneth H Nealson
- Department of Earth Science, University of Southern California, Los Angeles, CA, USA.
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China.
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15
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Merino N, Kawai M, Boyd ES, Colman DR, McGlynn SE, Nealson KH, Kurokawa K, Hongoh Y. Single-Cell Genomics of Novel Actinobacteria With the Wood-Ljungdahl Pathway Discovered in a Serpentinizing System. Front Microbiol 2020; 11:1031. [PMID: 32655506 PMCID: PMC7325909 DOI: 10.3389/fmicb.2020.01031] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 04/27/2020] [Indexed: 01/04/2023] Open
Abstract
Serpentinite-hosted systems represent modern-day analogs of early Earth environments. In these systems, water-rock interactions generate highly alkaline and reducing fluids that can contain hydrogen, methane, and low-molecular-weight hydrocarbons-potent reductants capable of fueling microbial metabolism. In this study, we investigated the microbiota of Hakuba Happo hot springs (∼50°C; pH∼10.5-11), located in Nagano (Japan), which are impacted by the serpentinization process. Analysis of the 16S rRNA gene amplicon sequences revealed that the bacterial community comprises Nitrospirae (47%), "Parcubacteria" (19%), Deinococcus-Thermus (16%), and Actinobacteria (9%), among others. Notably, only 57 amplicon sequence variants (ASV) were detected, and fifteen of these accounted for 90% of the amplicons. Among the abundant ASVs, an early-branching, uncultivated actinobacterial clade identified as RBG-16-55-12 in the SILVA database was detected. Ten single-cell genomes (average pairwise nucleotide identity: 0.98-1.00; estimated completeness: 33-93%; estimated genome size: ∼2.3 Mb) that affiliated with this clade were obtained. Taxonomic classification using single copy genes indicates that the genomes belong to the actinobacterial class-level clade UBA1414 in the Genome Taxonomy Database. Based on metabolic pathway predictions, these actinobacteria are anaerobes, capable of glycolysis, dissimilatory nitrate reduction and CO2 fixation via the Wood-Ljungdahl (WL) pathway. Several other genomes within UBA1414 and two related class-level clades also encode the WL pathway, which has not yet been reported for the Actinobacteria phylum. For the Hakuba actinobacterium, the energy metabolism related to the WL pathway is likely supported by a combination of the Rnf complex, group 3b and 3d [NiFe]-hydrogenases, [FeFe]-hydrogenases, and V-type (H+/Na+ pump) ATPase. The genomes also harbor a form IV ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) complex, also known as a RubisCO-like protein, and contain signatures of interactions with viruses, including clustered regularly interspaced short palindromic repeat (CRISPR) regions and several phage integrases. This is the first report and detailed genome analysis of a bacterium within the Actinobacteria phylum capable of utilizing the WL pathway. The Hakuba actinobacterium is a member of the clade UBA1414/RBG-16-55-12, formerly within the group "OPB41." We propose to name this bacterium 'Candidatus Hakubanella thermoalkaliphilus.'
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Affiliation(s)
- Nancy Merino
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.,Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States.,Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Mikihiko Kawai
- School of Life Sciences and Technology, Tokyo Institute of Technology, Tokyo, Japan.,Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Eric S Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - Daniel R Colman
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - Shawn E McGlynn
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.,Biofunctional Catalyst Research Team, RIKEN Center for Sustainable Resource Science, Saitama, Japan.,Blue Marble Space Institute of Science, Seattle, WA, United States
| | - Kenneth H Nealson
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Ken Kurokawa
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.,Department of Informatics, National Institute of Genetics, Shizuoka, Japan
| | - Yuichi Hongoh
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.,School of Life Sciences and Technology, Tokyo Institute of Technology, Tokyo, Japan
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16
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Affiliation(s)
- Kenneth H Nealson
- University of Southern California, Department of Earth Science and Biological Sciences, Los Angeles, CA
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17
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Garber AI, Nealson KH, Okamoto A, McAllister SM, Chan CS, Barco RA, Merino N. FeGenie: A Comprehensive Tool for the Identification of Iron Genes and Iron Gene Neighborhoods in Genome and Metagenome Assemblies. Front Microbiol 2020; 11:37. [PMID: 32082281 PMCID: PMC7005843 DOI: 10.3389/fmicb.2020.00037] [Citation(s) in RCA: 150] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 01/09/2020] [Indexed: 01/15/2023] Open
Abstract
Iron is a micronutrient for nearly all life on Earth. It can be used as an electron donor and electron acceptor by iron-oxidizing and iron-reducing microorganisms and is used in a variety of biological processes, including photosynthesis and respiration. While it is the fourth most abundant metal in the Earth's crust, iron is often limiting for growth in oxic environments because it is readily oxidized and precipitated. Much of our understanding of how microorganisms compete for and utilize iron is based on laboratory experiments. However, the advent of next-generation sequencing and surge in publicly available sequence data has made it possible to probe the structure and function of microbial communities in the environment. To bridge the gap between our understanding of iron acquisition, iron redox cycling, iron storage, and magnetosome formation in model microorganisms and the plethora of sequence data available from environmental studies, we have created a comprehensive database of hidden Markov models (HMMs) based on genes related to iron acquisition, storage, and reduction/oxidation in Bacteria and Archaea. Along with this database, we present FeGenie, a bioinformatics tool that accepts genome and metagenome assemblies as input and uses our comprehensive HMM database to annotate provided datasets with respect to iron-related genes and gene neighborhood. An important contribution of this tool is the efficient identification of genes involved in iron oxidation and dissimilatory iron reduction, which have been largely overlooked by standard annotation pipelines. We validated FeGenie against a selected set of 28 isolate genomes and showcase its utility in exploring iron genes present in 27 metagenomes, 4 isolate genomes from human oral biofilms, and 17 genomes from candidate organisms, including members of the candidate phyla radiation. We show that FeGenie accurately identifies iron genes in isolates. Furthermore, analysis of metagenomes using FeGenie demonstrates that the iron gene repertoire and abundance of each environment is correlated with iron richness. While this tool will not replace the reliability of culture-dependent analyses of microbial physiology, it provides reliable predictions derived from the most up-to-date genetic markers. FeGenie's database will be maintained and continually updated as new genes are discovered. FeGenie is freely available: https://github.com/Arkadiy-Garber/FeGenie.
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Affiliation(s)
- Arkadiy I. Garber
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
- Department of Earth Sciences, University of Delaware, Newark, DE, United States
| | - Kenneth H. Nealson
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Akihiro Okamoto
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science, Tsukuba, Japan
| | - Sean M. McAllister
- School of Marine Science and Policy, University of Delaware, Newark, DE, United States
| | - Clara S. Chan
- Department of Earth Sciences, University of Delaware, Newark, DE, United States
- School of Marine Science and Policy, University of Delaware, Newark, DE, United States
| | - Roman A. Barco
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Nancy Merino
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, United States
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18
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Lam BR, Barge LM, Noell AC, Nealson KH. Detecting Endogenous Microbial Metabolism and Differentiating Between Abiotic and Biotic Signals Observed by Bioelectrochemical Systems in Soils. Astrobiology 2020; 20:39-52. [PMID: 31560219 DOI: 10.1089/ast.2018.1892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Unambiguous detection of chemical and physical signatures of microbial life on Mars or other solar system bodies requires differentiation between signals produced by biotic and abiotic processes; instruments aimed at generalized in situ extant life detection would therefore increase the science return of a life-detection mission. Here, we investigate Bioelectrochemical Systems (BES) as a technique to measure microbial metabolism (which produces electrical current and redox changes) and distinguish between potential abiotic and biotic responses in environmental samples. Samples from inhabited niches should contain everything necessary to produce current, that is, catalysts (microorganisms) and fuel (nutrients). BES can also probe for inactive organisms in less energetically rich areas by adding a fuel to drive metabolism. A commercial potting soil and a Mars simulant soil were inoculated in the anodic chamber of microbial fuel cells, and current was monitored over time. Addition of a fuel (electron donor) source was tested for metabolic stimulation of endogenous microbes. Redox reactions between Mars simulant soil and the introduced electron donor (lactate) produced false-positive results, emphasizing the importance of careful interpretation of signals obtained. The addition of lactate to both soils resulted in enhanced biologically produced current, allowing stimulation and detection of dormant microbes. Our results demonstrate that BES provide an approach to detect metabolism in samples without prior knowledge of the organisms present, and that thorough electrochemical analyses and experimental design are necessary to determine if signals are biotic.
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Affiliation(s)
- Bonita R Lam
- Department of Biological Sciences, University of Southern California, Los Angeles, California
| | - Laura M Barge
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California
| | - Aaron C Noell
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California
| | - Kenneth H Nealson
- Department of Biological Sciences, University of Southern California, Los Angeles, California
- Department of Earth Sciences, University of Southern California, Los Angeles, California
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19
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Lam BR, Barr CR, Rowe AR, Nealson KH. Differences in Applied Redox Potential on Cathodes Enrich for Diverse Electrochemically Active Microbial Isolates From a Marine Sediment. Front Microbiol 2019; 10:1979. [PMID: 31555224 PMCID: PMC6724507 DOI: 10.3389/fmicb.2019.01979] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 08/12/2019] [Indexed: 01/21/2023] Open
Abstract
The diversity of microbially mediated redox processes that occur in marine sediments is likely underestimated, especially with respect to the metabolisms that involve solid substrate electron donors or acceptors. Though electrochemical studies that utilize poised potential electrodes as a surrogate for solid substrate or mineral interactions have shed some much needed light on these areas, these studies have traditionally been limited to one redox potential or metabolic condition. This work seeks to uncover the diversity of microbes capable of accepting cathodic electrons from a marine sediment utilizing a range of redox potentials, by coupling electrochemical enrichment approaches to microbial cultivation and isolation techniques. Five lab-scale three-electrode electrochemical systems were constructed, using electrodes that were initially incubated in marine sediment at cathodic or electron-donating voltages (five redox potentials between -400 and -750 mV versus Ag/AgCl) as energy sources for enrichment. Electron uptake was monitored in the laboratory bioreactors and linked to the reduction of supplied terminal electron acceptors (nitrate or sulfate). Enriched communities exhibited differences in community structure dependent on poised redox potential and terminal electron acceptor used. Further cultivation of microbes was conducted using media with reduced iron (Fe0, FeCl2) and sulfur (S0) compounds as electron donors, resulting in the isolation of six electrochemically active strains. The isolates belong to the genera Vallitalea of the Clostridia, Arcobacter of the Epsilonproteobacteria, Desulfovibrio of the Deltaproteobacteria, and Vibrio and Marinobacter of the Gammaproteobacteria. Electrochemical characterization of the isolates with cyclic voltammetry yielded a wide range of midpoint potentials (99.20 to -389.1 mV versus Ag/AgCl), indicating diverse metabolic pathways likely support the observed electron uptake. Our work demonstrates culturing under various electrochemical and geochemical regimes allows for enhanced cultivation of diverse cathode-oxidizing microbes from one environmental system. Understanding the mechanisms of solid substrate oxidation from environmental microbes will further elucidation of the ecological relevance of these electron transfer interactions with implications for microbe-electrode technologies.
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Affiliation(s)
- Bonita R. Lam
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Casey R. Barr
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Annette R. Rowe
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, United States
| | - Kenneth H. Nealson
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
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20
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Torres MA, Dong S, Nealson KH, West AJ. The kinetics of siderophore-mediated olivine dissolution. Geobiology 2019; 17:401-416. [PMID: 30734464 DOI: 10.1111/gbi.12332] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 12/18/2018] [Accepted: 01/05/2019] [Indexed: 05/28/2023]
Abstract
Silicate minerals represent an important reservoir of nutrients at Earth's surface and a source of alkalinity that modulates long-term geochemical cycles. Due to the slow kinetics of primary silicate mineral dissolution and the potential for nutrient immobilization by secondary mineral precipitation, the bioavailability of many silicate-bound nutrients may be limited by the ability of micro-organisms to actively scavenge these nutrients via redox alteration and/or organic ligand production. In this study, we use targeted laboratory experiments with olivine and the siderophore deferoxamine B to explore how microbial ligands affect nutrient (Fe) release and the overall rate of mineral dissolution. Our results show that olivine dissolution rates are accelerated in the presence of micromolar concentrations of deferoxamine B. Based on the non-linear decrease in rates with time and formation of a Fe3+ -ligand complex, we attribute this acceleration in dissolution rates to the removal of an oxidized surface coating that forms during the dissolution of olivine at circum-neutral pH in the presence of O2 and the absence of organic ligands. While increases in dissolution rates are observed with micromolar concentrations of siderophores, it remains unclear whether such conditions could be realized in natural environments due to the strong physiological control on microbial siderophore production. So, to contextualize our experimental results, we also developed a feedback model, which considers how microbial physiology and ligand-promoted mineral dissolution kinetics interact to control the extent of biotic enhancement of dissolution rates expected for different environments. The model predicts that physiological feedbacks severely limit the extent to which dissolution rates may be enhanced by microbial activity, though the rate of physical transport modulates this limitation.
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Affiliation(s)
- Mark A Torres
- Department of Earth Sciences, University of Southern California, Los Angeles, California
| | - Sijia Dong
- Department of Earth Sciences, University of Southern California, Los Angeles, California
| | - Kenneth H Nealson
- Department of Earth Sciences, University of Southern California, Los Angeles, California
| | - A Joshua West
- Department of Earth Sciences, University of Southern California, Los Angeles, California
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21
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Fu Y, Zhang Y, Li B, Liang D, Lu S, Xiang Y, Xie B, Liu H, Nealson KH. Extracellular electron transfer of Shewanella oneidensis MR-1 for cathodic hydrogen evolution reaction. Electrochim Acta 2019. [DOI: 10.1016/j.electacta.2019.03.085] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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22
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Suzuki S, Nealson KH, Ishii S. Genomic and in-situ Transcriptomic Characterization of the Candidate Phylum NPL-UPL2 From Highly Alkaline Highly Reducing Serpentinized Groundwater. Front Microbiol 2018; 9:3141. [PMID: 30619209 PMCID: PMC6305446 DOI: 10.3389/fmicb.2018.03141] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 12/04/2018] [Indexed: 12/05/2022] Open
Abstract
Serpentinization is a process whereby water interacts with reduced mantle rock called peridotite to produce a new suite of minerals (e.g., serpentine), a highly alkaline fluid, and hydrogen. In previous reports, we identified abundance of microbes of the candidate phylum NPL-UPA2 in a serpentinization site called The Cedars. Here, we report the first metagenome assembled genome (MAG) of the candidate phylum as well as the in-situ gene expression. The MAG of the phylum NPL-UPA2, named Unc8, is only about 1 Mbp and its biosynthetic properties suggest it should be capable of independent growth. In keeping with the highly reducing niche of Unc8, its genome encodes none of the known oxidative stress response genes including superoxide dismutases. With regard to energy metabolism, the MAG of Unc8 encodes all enzymes for Wood-Ljungdahl acetogenesis pathway, a ferredoxin:NAD+ oxidoreductase (Rnf) and electron carriers for flavin-based electron bifurcation (Etf, Hdr). Furthermore, the transcriptome of Unc8 in the waters of The Cedars showed enhanced levels of gene expression in the key enzymes of the Wood-Ljungdahl pathway [e.g., Carbon monoxide dehydrogenase /Acetyl-CoA synthase complex (CODH/ACS), Rnf, Acetyl-CoA synthetase (Acd)], which indicated that the Unc8 is an acetogen. However, the MAG of Unc8 encoded no well-known hydrogenase genes, suggesting that the energy metabolism of Unc8 might be focused on CO as the carbon and energy sources for the acetate formation. Given that CO could be supplied via abiotic reaction associated with deep subsurface serpentinization, while available CO2 would be at extremely low concentrations in this high pH environment, CO-associated metabolism could provide advantageous approach. The CODH/ACS in Unc8 is a Bacteria/Archaea hybrid type of six-subunit complex and the electron carriers, Etf and Hdr, showed the highest similarity to those in Archaea, suggesting that archaeal methanogenic energy metabolism was incorporated into the bacterial acetogenesis in NPL-UPA2. Given that serpentinization systems are viewed as potential habitats for early life, and that acetogenesis via the Wood-Ljungdahl pathway is proposed as an energy metabolism of Last Universal Common Ancestor, a phylogenetically distinct acetogen from an early earth analog site may provide important insights in primordial lithotrophs and their habitat.
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Affiliation(s)
- Shino Suzuki
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology, Nankoku, Japan.,Department of Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, United States.,Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Kenneth H Nealson
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Shun'ichi Ishii
- Department of Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, United States.,R&D Center for Submarine Resources, JAMSTEC, Nankoku, Japan
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23
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Affiliation(s)
- David Bermudes
- Center for Great Lakes Studies, University of Wisconsin-Milwaukee, 600 East Greenfield Avenue, Milwaukee, Wisconsin 53204
| | - Valerie L. Gerlach
- Marquette University, Department of Chemistry, Milwaukee, Wisconsin 53233
| | - Kenneth H. Nealson
- Center for Great Lakes Studies, University of Wisconsin-Milwaukee, 600 East Greenfield Avenue, Milwaukee, Wisconsin 53204
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24
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Affiliation(s)
- David Bermudes
- University of Wisconsin-Milwaukee, Center for Great Lakes Studies, 600 East Greenfield Avenue, Milwaukee, Wisconsin 53204
| | | | - Kenneth H. Nealson
- University of Wisconsin-Milwaukee, Center for Great Lakes Studies, 600 East Greenfield Avenue, Milwaukee, Wisconsin 53204
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25
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Lam BR, Rowe AR, Nealson KH. Variation in electrode redox potential selects for different microorganisms under cathodic current flow from electrodes in marine sediments. Environ Microbiol 2018; 20:2270-2287. [PMID: 29786168 DOI: 10.1111/1462-2920.14275] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 05/07/2018] [Accepted: 05/08/2018] [Indexed: 12/20/2022]
Abstract
Extracellular electron transport (EET) is a microbial process that allows microorganisms to transport electrons to and from insoluble substrates outside of the cell. Although progress has been made in understanding how microbes transfer electrons to insoluble substrates, the process of receiving electrons has largely remained unexplored. We investigated redox potentials favourable for donating electrons to dissolved and insoluble components in Catalina Harbor marine sediment by combining electrochemical techniques with geochemistry and molecular methods. Working electrodes buried in sediment microcosms were poised at seven redox potentials between -300 and -750 mV versus Ag/AgCl using a three-electrode system. In electrode biofilms recovered after 2-month incubations, overall community diversity increased with more negative redox potentials. Abundances of known EET-capable groups (e.g., Alteromonadales and Desulfuromonadales) varied with redox potential. Motility and chemotaxis genes were found in greater abundance in electrode communities, suggesting a possible selective advantage of these pathways for colonization and utilization of the electrode. Our enrichments demonstrated the validity of this approach in capturing groups known, as well as novel groups (e.g., Campylobacterales) that perform EET. The diverse nature of the enriched cathode communities suggest that insoluble substrate oxidation may be a critical, although poorly described microbial metabolic process in marine sediment.
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Affiliation(s)
- Bonita R Lam
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Annette R Rowe
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Kenneth H Nealson
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.,Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
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26
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Okamoto A, Rowe A, Deng X, Nealson KH. Self-standing Electrochemical Set-up to Enrich Anode-respiring Bacteria On-site. J Vis Exp 2018. [PMID: 30102275 DOI: 10.3791/57632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Anaerobic respiration coupled with electron transport to insoluble minerals (referred to as extracellular electron transport [EET]) is thought to be critical for microbial energy production and persistence in many subsurface environments, especially those lacking soluble terminal electron acceptors. While EET-capable microbes have been successfully isolated from various environments, the diversity of bacteria capable of EET is still poorly understood, especially in difficult-to-sample, low energy or extreme environments, such as many subsurface ecosystems. Here, we describe an on-site electrochemical system to enrich EET-capable bacteria using an anode as a respiratory terminal electron acceptor. This anode is connected to a cathode capable of catalyzing abiotic oxygen reduction. Comparing this approach with electrocultivation methods that use a potentiostat for poising the electrode potential, the two-electrode system does not require an external power source. We present an example of our on-site enrichment utilized in an alkaline pond at the Cedars, a terrestrial serpentinization site in Northern California. Prior attempts to cultivate mineral reducing bacteria were unsuccessful, which is likely due to the low-biomass nature of this site and/or the low relative abundance of metal reducing microbes. Prior to implementing our two-electrode enrichment, we measured the vertical profile of dissolved oxygen concentration. This allowed us to place the carbon felt anode and platinum-electroplated carbon felt cathode at depths that would support anaerobic and aerobic processes, respectively. Following on-site incubation, we further enriched the anodic electrode in the laboratory and confirmed a distinct microbial community compared to the surface-attached or biofilm communities normally observed at the Cedars. This enrichment subsequently led to the isolation of the first electrogenic microbe from the Cedars. This method of on-site microbial enrichment has the potential to greatly enhance the isolation of EET-capable bacteria from low biomass or difficult to sample habitats.
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Affiliation(s)
- Akihiro Okamoto
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science;
| | - Annette Rowe
- Department of Earth Sciences, University of Southern California
| | - Xiao Deng
- Department of Applied Chemistry, The University of Tokyo
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27
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Deng X, Dohmae N, Nealson KH, Hashimoto K, Okamoto A. Multi-heme cytochromes provide a pathway for survival in energy-limited environments. Sci Adv 2018; 4:eaao5682. [PMID: 29464208 PMCID: PMC5815863 DOI: 10.1126/sciadv.aao5682] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 01/12/2018] [Indexed: 05/22/2023]
Abstract
Bacterial reduction of oxidized sulfur species (OSS) is critical for energy production in anaerobic marine subsurfaces. In organic-poor sediments, H2 has been considered as a major energy source for bacterial respiration. We identified outer-membrane cytochromes (OMCs) that are broadly conserved in sediment OSS-respiring bacteria and enable cells to directly use electrons from insoluble minerals via extracellular electron transport. Biochemical, transcriptomic, and microscopic analyses revealed that the identified OMCs were highly expressed on the surface of cells and nanofilaments in response to electron donor limitation. This electron uptake mechanism provides sufficient but minimum energy to drive the reduction of sulfate and other OSS. These results suggest a widespread mechanism for survival of OSS-respiring bacteria via electron uptake from solid minerals in energy-poor marine sediments.
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Affiliation(s)
- Xiao Deng
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Tokyo 113-8656, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kenneth H. Nealson
- Department of Earth and Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Kazuhito Hashimoto
- Interfacial Energy Conversion Group, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
| | - Akihiro Okamoto
- Interfacial Energy Conversion Group, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
- Corresponding author.
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28
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Robador A, LaRowe DE, Finkel SE, Amend JP, Nealson KH. Changes in Microbial Energy Metabolism Measured by Nanocalorimetry during Growth Phase Transitions. Front Microbiol 2018; 9:109. [PMID: 29449836 PMCID: PMC5800293 DOI: 10.3389/fmicb.2018.00109] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 01/17/2018] [Indexed: 11/13/2022] Open
Abstract
Calorimetric measurements of the change in heat due to microbial metabolic activity convey information about the kinetics, as well as the thermodynamics, of all chemical reactions taking place in a cell. Calorimetric measurements of heat production made on bacterial cultures have recorded the energy yields of all co-occurring microbial metabolic reactions, but this is a complex, composite signal that is difficult to interpret. Here we show that nanocalorimetry can be used in combination with enumeration of viable cell counts, oxygen consumption rates, cellular protein content, and thermodynamic calculations to assess catabolic rates of an isolate of Shewanella oneidensis MR-1 and infer what fraction of the chemical energy is assimilated by the culture into biomass and what fraction is dissipated in the form of heat under different limiting conditions. In particular, our results demonstrate that catabolic rates are not necessarily coupled to rates of cell division, but rather, to physiological rearrangements of S. oneidensis MR-1 upon growth phase transitions. In addition, we conclude that the heat released by growing microorganisms can be measured in order to understand the physiochemical nature of the energy transformation and dissipation associated with microbial metabolic activity in conditions approaching those found in natural systems.
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Affiliation(s)
- Alberto Robador
- Center for Dark Energy Biosphere Investigations, University of Southern California, Los Angeles, CA, United States.,Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States.,Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Douglas E LaRowe
- Center for Dark Energy Biosphere Investigations, University of Southern California, Los Angeles, CA, United States.,Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Steven E Finkel
- Center for Dark Energy Biosphere Investigations, University of Southern California, Los Angeles, CA, United States.,Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Jan P Amend
- Center for Dark Energy Biosphere Investigations, University of Southern California, Los Angeles, CA, United States.,Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States.,Marine and Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Kenneth H Nealson
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States.,Marine and Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
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29
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Harris HW, Sánchez-Andrea I, McLean JS, Salas EC, Tran W, El-Naggar MY, Nealson KH. Redox Sensing within the Genus Shewanella. Front Microbiol 2018; 8:2568. [PMID: 29422884 PMCID: PMC5789149 DOI: 10.3389/fmicb.2017.02568] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 12/11/2017] [Indexed: 11/28/2022] Open
Abstract
A novel bacterial behavior called congregation was recently described in Shewanella oneidensis MR-1 as the accumulation of cells around insoluble electron acceptors (IEA). It is the result of a series of “run-and-reversal” events enabled by modulation of swimming speed and direction. The model proposed that the swimming cells constantly sense their surroundings with specialized outer membrane cytochromes capable of extracellular electron transport (EET). Up to this point, neither the congregation nor attachment behavior have been studied in any other strains. In this study, the wild type of S. oneidensis MR-1 and several deletion mutants as well as eight other Shewanella strains (Shewanella putrefaciens CN32, S. sp. ANA-3, S. sp. W3-18-1, Shewanella amazonensis SB2B, Shewanella loihica PV-4, Shewanella denitrificans OS217, Shewanella baltica OS155, and Shewanella frigidimarina NCIMB400) were screened for the ability to congregate. To monitor congregation and attachment, specialized cell-tracking techniques, as well as a novel cell accumulation after photo-bleaching (CAAP) confocal microscopy technique were utilized in this study. We found a strong correlation between the ability of strain MR-1 to accumulate on mineral surface and the presence of key EET genes such as mtrBC/omcA (SO_1778, SO_1776, and SO_1779) and gene coding for methyl-accepting protein (MCPs) with Ca+ channel chemotaxis receptor (Cache) domain (SO_2240). These EET and taxis genes were previously identified as essential for characteristic run and reversal swimming around IEA surfaces. CN32, ANA-3, and PV-4 congregated around both Fe(OH)3 and MnO2. Two other Shewanella spp. showed preferences for one oxide over the other: preferences that correlated with the metal content of the environments from which the strains were isolated: e.g., W3-18-1, which was isolated from an iron-rich habitat congregated and attached preferentially to Fe(OH)3, while SB2B, which was isolated from a MnO2-rich environment, preferred MnO2.
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Affiliation(s)
- Howard W Harris
- Department of Earth Sciences, Biological Sciences and Physics, University of Southern California, Los Angeles, CA, United States
| | | | - Jeffrey S McLean
- Department of Periodontics, University of Washington, Seattle, WA, United States.,Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, CA, United States
| | | | - William Tran
- Department of Earth Sciences, Biological Sciences and Physics, University of Southern California, Los Angeles, CA, United States
| | - Mohamed Y El-Naggar
- Department of Earth Sciences, Biological Sciences and Physics, University of Southern California, Los Angeles, CA, United States
| | - Kenneth H Nealson
- Department of Earth Sciences, Biological Sciences and Physics, University of Southern California, Los Angeles, CA, United States
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30
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Ishii S, Suzuki S, Yamanaka Y, Wu A, Nealson KH, Bretschger O. Population dynamics of electrogenic microbial communities in microbial fuel cells started with three different inoculum sources. Bioelectrochemistry 2017. [DOI: 10.1016/j.bioelechem.2017.06.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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31
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Abstract
Electromicrobiology is the domain of those prokaryotes able to interact with charged electrodes, using them as electron donors and/or electron acceptors. This is performed via a process called extracellular electron transport, in which outer membrane cytochromes are used to oxidize and/or reduce otherwise unavailable insoluble electron acceptors. EET‐capable bacteria can thus be used for a variety of purposes, ranging from small power sources, water reclamation, to pollution remediation and electrosynthesis. Because the study of EET‐capable bacteria is in its nascent phase, the applications are mostly in developmental stages, but the potential for significant contributions to environmental quality is high and moving forward.
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Affiliation(s)
- Kenneth H Nealson
- Department of Earth Science and Biological Sciences, University of Southern California, 835 W. 37th Street, SHS Rm 560, Los Angeles, CA, 90089, USA
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32
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Rowe AR, Yoshimura M, LaRowe DE, Bird LJ, Amend JP, Hashimoto K, Nealson KH, Okamoto A. In situ
electrochemical enrichment and isolation of a magnetite-reducing bacterium from a high pH serpentinizing spring. Environ Microbiol 2017; 19:2272-2285. [DOI: 10.1111/1462-2920.13723] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 03/05/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Annette R. Rowe
- Department of Earth Sciences; University of Southern California; Los Angeles CA 90089 USA
| | - Miho Yoshimura
- Department of Applied and Chemical Engineering; University of Tokyo; Tokyo Japan
| | - Doug E. LaRowe
- Department of Earth Sciences; University of Southern California; Los Angeles CA 90089 USA
| | - Lina J. Bird
- Department of Earth Sciences; University of Southern California; Los Angeles CA 90089 USA
| | - Jan P. Amend
- Department of Earth Sciences; University of Southern California; Los Angeles CA 90089 USA
- Department of Biological Sciences; University of Southern California; Los Angeles CA 90089 USA
| | - Kazuhito Hashimoto
- Center for Green Research on Energy and Environmental Materials; National Institute for Material Sciences; Tsukuba Ibaraki 305-0047 Japan
| | - Kenneth H. Nealson
- Department of Earth Sciences; University of Southern California; Los Angeles CA 90089 USA
| | - Akihiro Okamoto
- Center for Green Research on Energy and Environmental Materials; National Institute for Material Sciences; Tsukuba Ibaraki 305-0047 Japan
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33
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Ding M, Shiu HY, Li SL, Lee CK, Wang G, Wu H, Weiss NO, Young TD, Weiss PS, Wong GCL, Nealson KH, Huang Y, Duan X. Nanoelectronic Investigation Reveals the Electrochemical Basis of Electrical Conductivity in Shewanella and Geobacter. ACS Nano 2016; 10:9919-9926. [PMID: 27787972 DOI: 10.1021/acsnano.6b03655] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The electrical conductivity measured in Shewanella and Geobacter spp. is an intriguing physical property that is the fundamental basis for possible extracellular electron transport (EET) pathways. There is considerable debate regarding the origins of the electrical conductivity reported in these microbial cellular structures, which is essential for deciphering the EET mechanism. Here, we report systematic on-chip nanoelectronic investigations of both Shewanella and Geobacter spp. under physiological conditions to elucidate the complex basis of electrical conductivity of both individual microbial cells and biofilms. Concurrent electrical and electrochemical measurements of living Shewanella at both few-cell and the biofilm levels indicate that the apparent electrical conductivity can be traced to electrochemical-based electron transfer at the cell/electrode interface. We further show that similar results and conclusions apply to the Geobacter spp. Taken together, our study offers important insights into previously proposed physical models regarding microbial conductivities as well as EET pathways for Shewanella and Geobacter spp.
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Affiliation(s)
| | | | - Shiue-Lin Li
- Department of Earth Sciences and Biological Sciences, University of Southern California , Los Angeles, California 90089, United States
| | | | | | | | | | | | | | | | - Kenneth H Nealson
- Department of Earth Sciences and Biological Sciences, University of Southern California , Los Angeles, California 90089, United States
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34
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Lee CK, Kim AJ, Santos GS, Lai PY, Lee SY, Qiao DF, Anda JD, Young TD, Chen Y, Rowe AR, Nealson KH, Weiss PS, Wong GCL. Evolution of Cell Size Homeostasis and Growth Rate Diversity during Initial Surface Colonization of Shewanella oneidensis. ACS Nano 2016; 10:9183-9192. [PMID: 27571459 DOI: 10.1021/acsnano.6b05123] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Cell size control and homeostasis are fundamental features of bacterial metabolism. Recent work suggests that cells add a constant size between birth and division ("adder" model). However, it is not known how cell size homeostasis is influenced by the existence of heterogeneous microenvironments, such as those during biofilm formation. Shewanella oneidensis MR-1 can use diverse energy sources on a range of surfaces via extracellular electron transport (EET), which can impact growth, metabolism, and size diversity. Here, we track bacterial surface communities at single-cell resolution to show that not only do bacterial motility appendages influence the transition from two- to three-dimensional biofilm growth and control postdivisional cell fates, they strongly impact cell size homeostasis. For every generation, we find that the average growth rate for cells that stay on the surface and continue to divide (nondetaching population) and that for cells that detach before their next division (detaching population) are roughly constant. However, the growth rate distribution is narrow for the nondetaching population, but broad for the detaching population in each generation. Interestingly, the appendage deletion mutants (ΔpilA, ΔmshA-D, Δflg) have significantly broader growth rate distributions than that of the wild type for both detaching and nondetaching populations, which suggests that Shewanella appendages are important for sensing and integrating environmental inputs that contribute to size homeostasis. Moreover, our results suggest multiplexing of appendages for sensing and motility functions contributes to cell size dysregulation. These results can potentially provide a framework for generating metabolic diversity in S. oneidensis populations to optimize EET in heterogeneous environments.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Annette R Rowe
- Department of Earth Sciences & Biological Sciences, University of Southern California , Los Angeles, California 90089, United States
| | - Kenneth H Nealson
- Department of Earth Sciences & Biological Sciences, University of Southern California , Los Angeles, California 90089, United States
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35
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Bennett RR, Lee CK, De Anda J, Nealson KH, Yildiz FH, O'Toole GA, Wong GCL, Golestanian R. Species-dependent hydrodynamics of flagellum-tethered bacteria in early biofilm development. J R Soc Interface 2016; 13:20150966. [PMID: 26864892 DOI: 10.1098/rsif.2015.0966] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Monotrichous bacteria on surfaces exhibit complex spinning movements. Such spinning motility is often a part of the surface detachment launch sequence of these cells. To understand the impact of spinning motility on bacterial surface interactions, we develop a hydrodynamic model of a surface-bound bacterium, which reproduces behaviours that we observe in Pseudomonas aeruginosa, Shewanella oneidensis and Vibrio cholerae, and provides a detailed dictionary for connecting observed spinning behaviour to bacteria-surface interactions. Our findings indicate that the fraction of the flagellar filament adhered to the surface, the rotation torque of this appendage, the flexibility of the flagellar hook and the shape of the bacterial cell dictate the likelihood that a microbe will detach and the optimum orientation that it should have during detachment. These findings are important for understanding species-specific reversible attachment, the key transition event between the planktonic and biofilm lifestyle for motile, rod-shaped organisms.
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Affiliation(s)
- Rachel R Bennett
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford OX1 3NP, UK Department of Physics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Calvin K Lee
- Department of Bioengineering, Department of Chemistry and Biochemistry, California NanoSystems Institute, University of California, Los Angeles, CA 90095-1600, USA
| | - Jaime De Anda
- Department of Bioengineering, Department of Chemistry and Biochemistry, California NanoSystems Institute, University of California, Los Angeles, CA 90095-1600, USA
| | - Kenneth H Nealson
- Departments of Earth Sciences and Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Fitnat H Yildiz
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, CA 95064, USA
| | - George A O'Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Gerard C L Wong
- Department of Bioengineering, Department of Chemistry and Biochemistry, California NanoSystems Institute, University of California, Los Angeles, CA 90095-1600, USA
| | - Ramin Golestanian
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford OX1 3NP, UK
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36
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Abstract
Electromicrobiology is a subdiscipline of microbiology that involves extracellular electron transfer (EET) to (or from) insoluble electron active redox compounds located outside the outer membrane of the cell. These interactions can often be studied using electrochemical techniques which have provided novel insights into microbial physiology in recent years. The mechanisms (and variations) of outward EET are well understood for two model systems, Shewanella and Geobacter, both of which employ multihaem cytochromes to provide an electron conduit to the cell exterior. In contrast, little is known of the intricacies of inward EET, even in these model systems. Given the number of labs now working on EET, it seems likely that most of the mechanistic details will be understood in a few years for the model systems, and the many applications of electromicrobiology will continue to move forward. But emerging work, using electrodes as electron acceptors and donors is providing an abundance of new types of microbes capable of EET inward and/or outward: microbes that are clearly different from our known systems. The extent of this very diverse, and perhaps widely distributed and biogeochemically important ability needs to be determined to understand the mechanisms, importance, and raison d'etre of EET for microbial biology.
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Affiliation(s)
- Kenneth H Nealson
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
| | - Annette R Rowe
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
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37
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Cámara B, Suzuki S, Nealson KH, Wierzchos J, Ascaso C, Artieda O, de los Ríos A. Ignimbrite textural properties as determinants of endolithic colonization patterns from hyper-arid Atacama Desert. Int Microbiol 2016; 17:235-47. [PMID: 26421739 DOI: 10.2436/20.1501.01.226] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 12/15/2014] [Indexed: 11/15/2022]
Abstract
This study explores the photosynthetic microbial colonization of rhyolitic ignimbrites in Lomas de Tilocalar, a hyper-arid region of the Atacama Desert, Chile. Colonization appeared in the form of a green layer a few millimeters beneath the ignimbrite surface. Some ignimbrite rocks revealed two distinct micromorphological areas of identical mineralogical and chemical composition but different textural properties. According to texture, colonization patterns varied in terms of the extension and depth of colonization. The diversity of photosynthetic microorganisms was assessed by denaturing gradient gel electrophoresis (DGGE) of the 23S rRNA gene and by generating clone libraries of the 16S rRNA gene. We observed a low diversity of photosynthetic microorganisms colonizing the ignimbrite microhabitat. Most rRNA gene sequences recovered greatly resembled those of Chroococcidiopsis hypolith clones from arid deserts. These results point to highly restrictive conditions of the hyper-arid Atacama Desert conditioning the diversity of cyanobacteria, and suggest that microbial colonization and composition patterns might be determined by the microscale physico-chemical properties of the ignimbrite rocks.
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Affiliation(s)
| | | | - Kenneth H Nealson
- J. Craig Venter Institute, La Jolla, CA, USA.,University of Southern California, Los Angeles, CA, USA
| | | | - Carmen Ascaso
- National Museum of Natural Sciences-CSIC, Madrid, Spain
| | - Octavio Artieda
- Department of Plant Biology, Ecology and Earth Sciences. University of Extremadura, Plasencia, Spain
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Johnson JE, Savalia P, Davis R, Kocar BD, Webb SM, Nealson KH, Fischer WW. Real-Time Manganese Phase Dynamics during Biological and Abiotic Manganese Oxide Reduction. Environ Sci Technol 2016; 50:4248-58. [PMID: 27018915 PMCID: PMC5502836 DOI: 10.1021/acs.est.5b04834] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Manganese oxides are often highly reactive and easily reduced, both abiotically, by a variety of inorganic chemical species, and biologically during anaerobic respiration by microbes. To evaluate the reaction mechanisms of these different reduction routes and their potential lasting products, we measured the sequence progression of microbial manganese(IV) oxide reduction mediated by chemical species (sulfide and ferrous iron) and the common metal-reducing microbe Shewanella oneidensis MR-1 under several endmember conditions, using synchrotron X-ray spectroscopic measurements complemented by X-ray diffraction and Raman spectroscopy on precipitates collected throughout the reaction. Crystalline or potentially long-lived phases produced in these experiments included manganese(II)-phosphate, manganese(II)-carbonate, and manganese(III)-oxyhydroxides. Major controls on the formation of these discrete phases were alkalinity production and solution conditions such as inorganic carbon and phosphate availability. The formation of a long-lived Mn(III) oxide appears to depend on aqueous Mn(2+) production and the relative proportion of electron donors and electron acceptors in the system. These real-time measurements identify mineralogical products during Mn(IV) oxide reduction, contribute to understanding the mechanism of various Mn(IV) oxide reduction pathways, and assist in interpreting the processes occurring actively in manganese-rich environments and recorded in the geologic record of manganese-rich strata.
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Affiliation(s)
- Jena E. Johnson
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California 91125, United States
- Corresponding Author:
| | - Pratixa Savalia
- University of Southern California, Los Angeles, California 90089, United States
| | - Ryan Davis
- Stanford Synchrotron Radiation Lightsource, Menlo Park, California 94025, United States
| | - Benjamin D. Kocar
- Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Samuel M. Webb
- Stanford Synchrotron Radiation Lightsource, Menlo Park, California 94025, United States
| | - Kenneth H. Nealson
- University of Southern California, Los Angeles, California 90089, United States
| | - Woodward W. Fischer
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California 91125, United States
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Robador A, LaRowe DE, Jungbluth SP, Lin HT, Rappé MS, Nealson KH, Amend JP. Nanocalorimetric Characterization of Microbial Activity in Deep Subsurface Oceanic Crustal Fluids. Front Microbiol 2016; 7:454. [PMID: 27092118 PMCID: PMC4820435 DOI: 10.3389/fmicb.2016.00454] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 03/21/2016] [Indexed: 11/30/2022] Open
Abstract
Although fluids within the upper oceanic basaltic crust harbor a substantial fraction of the total prokaryotic cells on Earth, the energy needs of this microbial population are unknown. In this study, a nanocalorimeter (sensitivity down to 1.2 nW ml(-1)) was used to measure the enthalpy of microbially catalyzed reactions as a function of temperature in samples from two distinct crustal fluid aquifers. Microorganisms in unamended, warm (63°C) and geochemically altered anoxic fluids taken from 292 meters sub-basement (msb) near the Juan de Fuca Ridge produced 267.3 mJ of heat over the course of 97 h during a step-wise isothermal scan from 35.5 to 85.0°C. Most of this heat signal likely stems from the germination of thermophilic endospores (6.66 × 10(4) cells ml(-1) FLUID) and their subsequent metabolic activity at temperatures greater than 50°C. The average cellular energy consumption (5.68 pW cell(-1)) reveals the high metabolic potential of a dormant community transported by fluids circulating through the ocean crust. By contrast, samples taken from 293 msb from cooler (3.8°C), relatively unaltered oxic fluids, produced 12.8 mJ of heat over the course of 14 h as temperature ramped from 34.8 to 43.0°C. Corresponding cell-specific energy turnover rates (0.18 pW cell(-1)) were converted to oxygen uptake rates of 24.5 nmol O2 ml(-1) FLUID d(-1), validating previous model predictions of microbial activity in this environment. Given that the investigated fluids are characteristic of expansive areas of the upper oceanic crust, the measured metabolic heat rates can be used to constrain boundaries of habitability and microbial activity in the oceanic crust.
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Affiliation(s)
- Alberto Robador
- Center for Dark Energy Biosphere Investigations, NASA Astrobiology Institute, University of Southern California, Los AngelesCA, USA
| | - Douglas E. LaRowe
- Department of Earth Sciences, University of Southern California, Los AngelesCA, USA
| | - Sean P. Jungbluth
- Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, HonoluluHI, USA
- Hawaii Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, KaneoheHI, USA
| | - Huei-Ting Lin
- Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, HonoluluHI, USA
| | - Michael S. Rappé
- Hawaii Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, KaneoheHI, USA
| | - Kenneth H. Nealson
- Department of Earth Sciences, University of Southern California, Los AngelesCA, USA
- Department of Biological Sciences, University of Southern California, Los AngelesCA, USA
| | - Jan P. Amend
- Department of Earth Sciences, University of Southern California, Los AngelesCA, USA
- Department of Biological Sciences, University of Southern California, Los AngelesCA, USA
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Wei H, Dai J, Xia M, Romine MF, Shi L, Beliav A, Tiedje JM, Nealson KH, Fredrickson JK, Zhou J, Qiu D. Functional roles of CymA and NapC in reduction of nitrate and nitrite by Shewanella putrefaciens W3-18-1. Microbiology (Reading) 2016; 162:930-941. [PMID: 27010745 DOI: 10.1099/mic.0.000285] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Shewanella putrefaciens W3-18-1 harbours two periplasmic nitrate reductase (Nap) gene clusters, NapC-associated nap-alpha (napEDABC) and CymA-dependent nap-beta (napDAGHB), for dissimilatory nitrate respiration. CymA is a member of the NapC/NirT quinol dehydrogenase family and acts as a hub to support different respiratory pathways, including those on iron [Fe(III)] and manganese [Mn(III, IV)] (hydr)oxide, nitrate, nitrite, fumarate and arsenate in Shewanella strains. However, in our analysis it was shown that another NapC/NirT family protein, NapC, was only involved in nitrate reduction, although both CymA and NapC can transfer quinol-derived electrons to a periplasmic terminal reductase or an electron acceptor. Furthermore, our results showed that NapC could only interact specifically with the Nap-alpha nitrate reductase while CymA could interact promiscuously with Nap-alpha, Nap-beta and the NrfA nitrite reductase for nitrate and nitrite reduction. To further explore the difference in specificity, site-directed mutagenesis on both CymA and NapC was conducted and the phenotypic changes in nitrate and nitrite reduction were tested. Our analyses demonstrated that the Lys-91 residue played a key role in nitrate reduction for quinol oxidation and the Asp-166 residue might influence the maturation of CymA. The Asp-97 residue might be one of the key factors that influence the interaction of CymA with the cytochromes NapB and NrfA.
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Affiliation(s)
- Hehong Wei
- Institute of hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Jingcheng Dai
- Institute of hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
| | - Ming Xia
- Institute of hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | | | - Liang Shi
- Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Alex Beliav
- Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
| | - Kenneth H Nealson
- Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | | | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Plant Biology and Microbiology, University of Oklahoma, OK, Norman, OK 73019, USA
| | - Dongru Qiu
- Institute of hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
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Kan J, Clingenpeel S, Dow CL, McDermott TR, Macur RE, Inskeep WP, Nealson KH. Geochemistry and Mixing Drive the Spatial Distribution of Free-Living Archaea and Bacteria in Yellowstone Lake. Front Microbiol 2016; 7:210. [PMID: 26973602 PMCID: PMC4770039 DOI: 10.3389/fmicb.2016.00210] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 02/08/2016] [Indexed: 11/13/2022] Open
Abstract
Yellowstone Lake, the largest subalpine lake in the United States, harbors great novelty and diversity of Bacteria and Archaea. Size-fractionated water samples (0.1–0.8, 0.8–3.0, and 3.0–20 μm) were collected from surface photic zone, deep mixing zone, and vent fluids at different locations in the lake by using a remotely operated vehicle (ROV). Quantification with real-time PCR indicated that Bacteria dominated free-living microorganisms with Bacteria/Archaea ratios ranging from 4037:1 (surface water) to 25:1 (vent water). Microbial population structures (both Bacteria and Archaea) were assessed using 454-FLX sequencing with a total of 662,302 pyrosequencing reads for V1 and V2 regions of 16S rRNA genes. Non-metric multidimensional scaling (NMDS) analyses indicated that strong spatial distribution patterns existed from surface to deep vents for free-living Archaea and Bacteria in the lake. Along with pH, major vent-associated geochemical constituents including CH4, CO2, H2, DIC (dissolved inorganic carbon), DOC (dissolved organic carbon), SO42-, O2 and metals were likely the major drivers for microbial population structures, however, mixing events occurring in the lake also impacted the distribution patterns. Distinct Bacteria and Archaea were present among size fractions, and bigger size fractions included particle-associated microbes (> 3 μm) and contained higher predicted operational taxonomic unit richness and microbial diversities (genus level) than free-living ones (<0.8 μm). Our study represents the first attempt at addressing the spatial distribution of Bacteria and Archaea in Yellowstone Lake, and our results highlight the variable contribution of Archaea and Bacteria to the hydrogeochemical-relevant metabolism of hydrogen, carbon, nitrogen, and sulfur.
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Affiliation(s)
- Jinjun Kan
- Stroud Water Research Center, Avondale PA, USA
| | | | | | - Timothy R McDermott
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman MT, USA
| | - Richard E Macur
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman MT, USA
| | - William P Inskeep
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman MT, USA
| | - Kenneth H Nealson
- Department of Earth Sciences, University of Southern California, Los Angeles CA, USA
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Luo S, Guo W, Nealson KH, Feng X, He Z. ¹³C Pathway Analysis for the Role of Formate in Electricity Generation by Shewanella Oneidensis MR-1 Using Lactate in Microbial Fuel Cells. Sci Rep 2016; 6:20941. [PMID: 26868848 PMCID: PMC4751489 DOI: 10.1038/srep20941] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 01/14/2016] [Indexed: 12/16/2022] Open
Abstract
Microbial fuel cell (MFC) is a promising technology for direct electricity generation from organics by microorganisms. The type of electron donors fed into MFCs affects the electrical performance, and mechanistic understanding of such effects is important to optimize the MFC performance. In this study, we used a model organism in MFCs, Shewanella oneidensis MR-1, and (13)C pathway analysis to investigate the role of formate in electricity generation and the related microbial metabolism. Our results indicated a synergistic effect of formate and lactate on electricity generation, and extra formate addition on the original lactate resulted in more electrical output than using formate or lactate as a sole electron donor. Based on the (13)C tracer analysis, we discovered decoupled cell growth and electricity generation in S. oneidensis MR-1 during co-utilization of lactate and formate (i.e., while the lactate was mainly metabolized to support the cell growth, the formate was oxidized to release electrons for higher electricity generation). To our best knowledge, this is the first time that (13)C tracer analysis was applied to study microbial metabolism in MFCs and it was demonstrated to be a valuable tool to understand the metabolic pathways affected by electron donors in the selected electrochemically-active microorganisms.
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Affiliation(s)
- Shuai Luo
- Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Weihua Guo
- Department of Biological Systems Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Kenneth H Nealson
- Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Xueyang Feng
- Department of Biological Systems Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Zhen He
- Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
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Thacher R, Hsu L, Ravindran V, Nealson KH, Pirbazari M. Modeling the transport and bioreduction of hexavalent chromium in aquifers: Influence of natural organic matter. Chem Eng Sci 2015. [DOI: 10.1016/j.ces.2015.08.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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44
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Li SL, Nealson KH. Enriching distinctive microbial communities from marine sediments via an electrochemical-sulfide-oxidizing process on carbon electrodes. Front Microbiol 2015; 6:111. [PMID: 25741331 PMCID: PMC4330880 DOI: 10.3389/fmicb.2015.00111] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Accepted: 01/29/2015] [Indexed: 11/13/2022] Open
Abstract
Sulfide is a common product of marine anaerobic respiration, and a potent reactant biologically and geochemically. Here we demonstrate the impact on microbial communities with the removal of sulfide via electrochemical methods. The use of differential pulse voltammetry revealed that the oxidation of soluble sulfide was seen at +30 mV (vs. SHE) at all pH ranges tested (from pH = 4 to 8), while non-ionized sulfide, which dominated at pH = 4 was poorly oxidized via this process. Two mixed cultures (CAT and LA) were enriched from two different marine sediments (from Catalina Island, CAT; from the Port of Los Angeles, LA) in serum bottles using a seawater medium supplemented with lactate, sulfate, and yeast extract, to obtain abundant biomass. Both CAT and LA cultures were inoculated in electrochemical cells (using yeast-extract-free seawater medium as an electrolyte) equipped with carbon-felt electrodes. In both cases, when potentials of +630 or +130 mV (vs. SHE) were applied, currents were consistently higher at +630 then at +130 mV, indicating more sulfide being oxidized at the higher potential. In addition, higher organic-acid and sulfate conversion rates were found at +630 mV with CAT, while no significant differences were found with LA at different potentials. The results of microbial-community analyses revealed a decrease in diversity for both CAT and LA after electrochemical incubation. In addition, some bacteria (e.g., Clostridium and Arcobacter) not well-known to be capable of extracellular electron transfer, were found to be dominant in the electrochemical cells. Thus, even though the different mixed cultures have different tolerances for sulfide, electrochemical-sulfide removal can lead to major population changes.
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Affiliation(s)
- Shiue-Lin Li
- Department of Earth Science, University of Southern California Los Angeles, CA, USA
| | - Kenneth H Nealson
- Department of Earth Science, University of Southern California Los Angeles, CA, USA
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45
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Affiliation(s)
- Kenneth H Nealson
- Wrigley Professor of Environmental Sciences, University of Southern California, Los Angeles, CA, USA
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46
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Rowe AR, Chellamuthu P, Lam B, Okamoto A, Nealson KH. Marine sediments microbes capable of electrode oxidation as a surrogate for lithotrophic insoluble substrate metabolism. Front Microbiol 2015; 5:784. [PMID: 25642220 PMCID: PMC4294203 DOI: 10.3389/fmicb.2014.00784] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Accepted: 12/21/2014] [Indexed: 11/13/2022] Open
Abstract
Little is known about the importance and/or mechanisms of biological mineral oxidation in sediments, partially due to the difficulties associated with culturing mineral-oxidizing microbes. We demonstrate that electrochemical enrichment is a feasible approach for isolation of microbes capable of gaining electrons from insoluble minerals. To this end we constructed sediment microcosms and incubated electrodes at various controlled redox potentials. Negative current production was observed in incubations and increased as redox potential decreased (tested −50 to −400 mV vs. Ag/AgCl). Electrode-associated biomass responded to the addition of nitrate and ferric iron as terminal electron acceptors in secondary sediment-free enrichments. Elemental sulfur, elemental iron and amorphous iron sulfide enrichments derived from electrode biomass demonstrated products indicative of sulfur or iron oxidation. The microbes isolated from these enrichments belong to the genera Halomonas, Idiomarina, Marinobacter, and Pseudomonas of the Gammaproteobacteria, and Thalassospira and Thioclava from the Alphaproteobacteria. Chronoamperometry data demonstrates sustained electrode oxidation from these isolates in the absence of alternate electron sources. Cyclic voltammetry demonstrated the variability in dominant electron transfer modes or interactions with electrodes (i.e., biofilm, planktonic or mediator facilitated) and the wide range of midpoint potentials observed for each microbe (from 8 to −295 mV vs. Ag/AgCl). The diversity of extracellular electron transfer mechanisms observed in one sediment and one redox condition, illustrates the potential importance and abundance of these interactions. This approach has promise for increasing our understanding the extent and diversity of microbe mineral interactions, as well as increasing the repository of microbes available for electrochemical applications.
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Affiliation(s)
- Annette R Rowe
- Department of Earth Sciences, University of Southern California, Los Angeles Los Angeles, CA, USA
| | - Prithiviraj Chellamuthu
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles Los Angeles, CA, USA
| | - Bonita Lam
- Department Marine and Environmental Biology, University of Southern California, Los Angeles Los Angeles, CA, USA
| | - Akihiro Okamoto
- Department of Applied Chemistry, University of Tokyo Tokyo, Japan
| | - Kenneth H Nealson
- Department of Earth Sciences, University of Southern California, Los Angeles Los Angeles, CA, USA ; Department of Molecular and Computational Biology, University of Southern California, Los Angeles Los Angeles, CA, USA ; Department Marine and Environmental Biology, University of Southern California, Los Angeles Los Angeles, CA, USA
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Okamoto A, Hashimoto K, Nealson KH. Flavin Redox Bifurcation as a Mechanism for Controlling the Direction of Electron Flow during Extracellular Electron Transfer. Angew Chem Int Ed Engl 2014; 53:10988-91. [DOI: 10.1002/anie.201407004] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Indexed: 11/12/2022]
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Okamoto A, Nakamura R, Nealson KH, Hashimoto K. Bound Flavin Model Suggests Similar Electron-Transfer Mechanisms inShewanellaandGeobacter. ChemElectroChem 2014. [DOI: 10.1002/celc.201402151] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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49
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Ishii S, Suzuki S, Norden-Krichmar TM, Phan T, Wanger G, Nealson KH, Sekiguchi Y, Gorby YA, Bretschger O. Microbial population and functional dynamics associated with surface potential and carbon metabolism. ISME J 2014; 8:963-78. [PMID: 24351938 PMCID: PMC3996694 DOI: 10.1038/ismej.2013.217] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 09/04/2013] [Accepted: 11/02/2013] [Indexed: 11/08/2022]
Abstract
Microbial extracellular electron transfer (EET) to solid surfaces is an important reaction for metal reduction occurring in various anoxic environments. However, it is challenging to accurately characterize EET-active microbial communities and each member's contribution to EET reactions because of changes in composition and concentrations of electron donors and solid-phase acceptors. Here, we used bioelectrochemical systems to systematically evaluate the synergistic effects of carbon source and surface redox potential on EET-active microbial community development, metabolic networks and overall electron transfer rates. The results indicate that faster biocatalytic rates were observed under electropositive electrode surface potential conditions, and under fatty acid-fed conditions. Temporal 16S rRNA-based microbial community analyses showed that Geobacter phylotypes were highly diverse and apparently dependent on surface potentials. The well-known electrogenic microbes affiliated with the Geobacter metallireducens clade were associated with lower surface potentials and less current generation, whereas Geobacter subsurface clades 1 and 2 were associated with higher surface potentials and greater current generation. An association was also observed between specific fermentative phylotypes and Geobacter phylotypes at specific surface potentials. When sugars were present, Tolumonas and Aeromonas phylotypes were preferentially associated with lower surface potentials, whereas Lactococcus phylotypes were found to be closely associated with Geobacter subsurface clades 1 and 2 phylotypes under higher surface potential conditions. Collectively, these results suggest that surface potentials provide a strong selective pressure, at the species and strain level, for both solid surface respirators and fermentative microbes throughout the EET-active community development.
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Affiliation(s)
- Shun'ichi Ishii
- J. Craig Venter Institute, La Jolla, CA, USA
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
- Japan Society for the Promotion of Science (JSPS), Chiyoda-ku, Tokyo, Japan
| | | | | | - Tony Phan
- J. Craig Venter Institute, La Jolla, CA, USA
| | - Greg Wanger
- J. Craig Venter Institute, La Jolla, CA, USA
| | - Kenneth H Nealson
- J. Craig Venter Institute, La Jolla, CA, USA
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
| | - Yuji Sekiguchi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Yuri A Gorby
- J. Craig Venter Institute, La Jolla, CA, USA
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
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Jang JK, Kan J, Bretschger O, Gorby YA, Hsu L, Kim BH, Nealson KH. Electricity Generation by Microbial Fuel Cell Using Microorganisms as Catalyst in Cathode. J Microbiol Biotechnol 2013; 23:1765-73. [DOI: 10.4014/jmb.1310.10117] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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