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Iizuka R, Hattori S, Kosaka Y, Masaki Y, Kawano Y, Ohtsu I, Hibbett D, Katayama Y, Yoshida M. Sulfur assimilation using gaseous carbonyl sulfide by the soil fungus Trichoderma harzianum. Appl Environ Microbiol 2024; 90:e0201523. [PMID: 38299812 PMCID: PMC10880591 DOI: 10.1128/aem.02015-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 01/03/2024] [Indexed: 02/02/2024] Open
Abstract
Fungi have the capacity to assimilate a diverse range of both inorganic and organic sulfur compounds. It has been recognized that all sulfur sources taken up by fungi are in soluble forms. In this study, we present evidence that fungi can utilize gaseous carbonyl sulfide (COS) for the assimilation of a sulfur compound. We found that the filamentous fungus Trichoderma harzianum strain THIF08, which has constitutively high COS-degrading activity, was able to grow with COS as the sole sulfur source. Cultivation with 34S-labeled COS revealed that sulfur atom from COS was incorporated into intracellular metabolites such as glutathione and ergothioneine. COS degradation by strain THIF08, in which as much of the moisture derived from the agar medium as possible was removed, indicated that gaseous COS was taken up directly into the cell. Escherichia coli transformed with a COS hydrolase (COSase) gene, which is clade D of the β-class carbonic anhydrase subfamily enzyme with high specificity for COS but low activity for CO2 hydration, showed that the COSase is involved in COS assimilation. Comparison of sulfur metabolites of strain THIF08 revealed a higher relative abundance of reduced sulfur compounds under the COS-supplemented condition than the sulfate-supplemented condition, suggesting that sulfur assimilation is more energetically efficient with COS than with sulfate because there is no redox change of sulfur. Phylogenetic analysis of the genes encoding COSase, which are distributed in a wide range of fungal taxa, suggests that the common ancestor of Ascomycota, Basidiomycota, and Mucoromycota acquired COSase at about 790-670 Ma.IMPORTANCEThe biological assimilation of gaseous CO2 and N2 involves essential processes known as carbon fixation and nitrogen fixation, respectively. In this study, we found that the fungus Trichoderma harzianum strain THIF08 can grow with gaseous carbonyl sulfide (COS), the most abundant and ubiquitous gaseous sulfur compound, as a sulfur source. When the fungus grew in these conditions, COS was assimilated into sulfur metabolites, and the key enzyme of this assimilation process is COS hydrolase (COSase), which specifically degrades COS. Moreover, the pathway was more energy efficient than the typical sulfate assimilation pathway. COSase genes are widely distributed in Ascomycota, Basidiomycota, and Mucoromycota and also occur in some Chytridiomycota, indicating that COS assimilation is widespread in fungi. Phylogenetic analysis of these genes revealed that the acquisition of COSase in filamentous fungi was estimated to have occurred at about 790-670 Ma, around the time that filamentous fungi transitioned to a terrestrial environment.
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Affiliation(s)
- Ryuka Iizuka
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Shohei Hattori
- International Center for Isotope Effects Research, School of Earth Sciences and Engineering, Nanjing University, Nanjing, Jiangsu, China
| | - Yusuke Kosaka
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Yoshihito Masaki
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Yusuke Kawano
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Euglena Co., Ltd., Minato‑ku, Tokyo, Japan
| | - Iwao Ohtsu
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Euglena Co., Ltd., Minato‑ku, Tokyo, Japan
| | - David Hibbett
- Department of Biology, Clark University, Worcester, Massachusetts, USA
| | - Yoko Katayama
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
- Independent Administrative Institution, Tokyo National Research Institute for Cultural Properties, Taito-ku, Tokyo, Japan
| | - Makoto Yoshida
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
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2
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Greening C, Grinter R. Microbial oxidation of atmospheric trace gases. Nat Rev Microbiol 2022; 20:513-528. [PMID: 35414013 DOI: 10.1038/s41579-022-00724-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2022] [Indexed: 02/06/2023]
Abstract
The atmosphere has recently been recognized as a major source of energy sustaining life. Diverse aerobic bacteria oxidize the three most abundant reduced trace gases in the atmosphere, namely hydrogen (H2), carbon monoxide (CO) and methane (CH4). This Review describes the taxonomic distribution, physiological role and biochemical basis of microbial oxidation of these atmospheric trace gases, as well as the ecological, environmental, medical and astrobiological importance of this process. Most soil bacteria and some archaea can survive by using atmospheric H2 and CO as alternative energy sources, as illustrated through genetic studies on Mycobacterium cells and Streptomyces spores. Certain specialist bacteria can also grow on air alone, as confirmed by the landmark characterization of Methylocapsa gorgona, which grows by simultaneously consuming atmospheric CH4, H2 and CO. Bacteria use high-affinity lineages of metalloenzymes, namely hydrogenases, CO dehydrogenases and methane monooxygenases, to utilize atmospheric trace gases for aerobic respiration and carbon fixation. More broadly, trace gas oxidizers enhance the biodiversity and resilience of soil and marine ecosystems, drive primary productivity in extreme environments such as Antarctic desert soils and perform critical regulatory services by mitigating anthropogenic emissions of greenhouse gases and toxic pollutants.
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Affiliation(s)
- Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia. .,Securing Antarctica's Environmental Future, Monash University, Clayton, Victoria, Australia. .,Centre to Impact AMR, Monash University, Clayton, Victoria, Australia.
| | - Rhys Grinter
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
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3
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Masaki Y, Iizuka R, Kato H, Kojima Y, Ogawa T, Yoshida M, Matsushita Y, Katayama Y. Fungal Carbonyl Sulfide Hydrolase of Trichoderma harzianum Strain THIF08 and Its Relationship with Clade D β-Carbonic Anhydrases. Microbes Environ 2021; 36. [PMID: 34024869 PMCID: PMC8209446 DOI: 10.1264/jsme2.me20058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Carbonyl sulfide (COS) is the most abundant and long-lived sulfur-containing gas in the atmosphere. Soil is the main sink of COS in the atmosphere and uptake is dominated by soil microorganisms; however, biochemical research has not yet been conducted on fungal COS degradation. COS hydrolase (COSase) was purified from Trichoderma harzianum strain THIF08, which degrades COS at concentrations higher than 10,000 parts per million by volume from atmospheric concentrations, and its gene cos (492 bp) was cloned. The recombinant protein purified from Escherichia coli expressing the cos gene converted COS to H2S. The deduced amino acid sequence of COSase (163 amino acids) was assigned to clade D in the phylogenetic tree of the β-carbonic anhydrase (β-CA) family, to which prokaryotic COSase and its structurally related enzymes belong. However, the COSase of strain THIF08 differed from the previously known prokaryotic COSase and its related enzymes due to its low reactivity to CO2 and inability to hydrolyze CS2. Sequence comparisons of the active site amino acids of clade D β-CA family enzymes suggested that various Ascomycota, particularly Sordariomycetes and Eurotiomycetes, possess similar enzymes to the COSase of strain THIF08 with >80% identity. These fungal COSase were phylogenetically distant to prokaryotic clade D β-CA family enzymes. These results suggest that various ascomycetes containing COSase contribute to the uptake of COS by soil.
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Affiliation(s)
- Yoshihito Masaki
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology
| | - Ryuka Iizuka
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology
| | - Hiromi Kato
- Graduate School of Life Sciences, Tohoku University
| | - Yuka Kojima
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology
| | - Takahiro Ogawa
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology
| | - Makoto Yoshida
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology
| | | | - Yoko Katayama
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology.,Independent Administrative Institution, Tokyo National Research Institute for Cultural Properties
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4
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Kato H, Ogawa T, Ohta H, Katayama Y. Enumeration of Chemoorganotrophic Carbonyl Sulfide (COS)-degrading Microorganisms by the Most Probable Number Method. Microbes Environ 2020; 35. [PMID: 32350165 PMCID: PMC7308577 DOI: 10.1264/jsme2.me19139] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Carbonyl sulfide (COS) is the most abundant sulfur compound in the atmosphere, and, thus, is important in the global sulfur cycle. Soil is a major sink of atmospheric COS and the numerical distribution of soil microorganisms that degrade COS is indispensable for estimating the COS-degrading potential of soil. However, difficulties are associated with counting COS-degrading microorganisms using culture-dependent approaches, such as the most probable number (MPN) method, because of the chemical hydrolysis of COS by water. We herein developed a two-step MPN method for COS-degrading microorganisms: the first step for chemoorganotrophic growth that supported a sufficient number of cells for COS degradation in the second step. Our new MPN analysis of various environmental samples revealed that the cell density of COS-degrading microorganisms in forest soils ranged between 106 and 108 MPN (g dry soil)–1, which was markedly higher than those in volcanic deposit and water samples, and strongly correlated with the rate of COS degradation in environmental samples. Numerically dominant COS degraders that were isolated from the MPN-positive culture were related to bacteria in the orders Bacillales and Actinomycetales. The present results provide numerical evidence for the ubiquity of COS-degrading microbes in natural environments.
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Affiliation(s)
- Hiromi Kato
- Graduate School of Life Sciences, Tohoku University
| | - Takahiro Ogawa
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology.,Present address: Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology
| | - Hiroyuki Ohta
- Department of Bioresource Science, Ibaraki University College of Agriculture
| | - Yoko Katayama
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology.,Independent Administrative Institution, Tokyo National Research Institute for Cultural Properties
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5
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Synthetic Methylotrophy in Yeasts: Towards a Circular Bioeconomy. Trends Biotechnol 2020; 39:348-358. [PMID: 33008643 DOI: 10.1016/j.tibtech.2020.08.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 08/07/2020] [Accepted: 08/24/2020] [Indexed: 01/04/2023]
Abstract
Mitigating climate change is a key driver for the development of sustainable and CO2-neutral production processes. In this regard, connecting carbon capture and utilization processes to derive microbial C1 fermentation substrates from CO2 is highly promising. This strategy uses methylotrophic microbes to unlock next-generation processes, converting CO2-derived methanol. Synthetic biology approaches in particular can empower synthetic methylotrophs to produce a variety of commodity chemicals. We believe that yeasts have outstanding potential for this purpose, because they are able to separate toxic intermediates and metabolic reactions in organelles. This compartmentalization can be harnessed to design superior synthetic methylotrophs, capable of utilizing methanol and other hitherto largely disregarded C1 compounds, thus supporting the establishment of a future circular economy.
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6
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Xia X, Zhang P, He L, Gao X, Li W, Zhou Y, Li Z, Li H, Yang L. Effects of tillage managements and maize straw returning on soil microbiome using 16S rDNA sequencing. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:765-777. [PMID: 30912294 DOI: 10.1111/jipb.12802] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 03/12/2019] [Indexed: 05/07/2023]
Abstract
Agricultural practices could affect bacterial diversity and community structure by altering soil physical and chemical properties. Straw returning and tillage practices are widely used in agriculture, however, the effects of these agricultural practices on microbiomes are still unclear. In the present study, we compared the 18 bacterial communities of soil with different straw returning and tillage treatment combinations. The V3-V4 regions of the 16S ribosomal RNA were amplified and analyzed by high-throughput sequencing technology. The results showed that the bacterial communities were consistently dominated by Acidobacteria, Proteobacteria, Actinobacteria, and Chloroflexi. Short-term straw returning and tillage practices significantly altered the diversity, relative abundance and functions of the soil microbiome. Soil subjected to rotary tillage and straw returning (RTS) combination possessed the highest bacterial diversity and lowest ratio of G+/G- bacteria, indicating that RTS could be an efficient integrated management system to improve microbiome in the short term. Double verifications based on relative abundance and network analysis, revealed close relationships of Mycobacterium and Methylibium with RTS, indicating they could serve as biomarkers for RTS. Investigating microbial changes under different agricultural practices will provide valuable foundations for land sustainable utilization and increase crop yields.
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Affiliation(s)
- Xinyao Xia
- Agricultural Big-Data Research Center, College of Plant Protection, Shandong Agricultural University, Taian, 271018, China
| | - Piaopiao Zhang
- Department of Clinical, Taishan Medical University, Taian, 271016, China
| | - Linlin He
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Xingxing Gao
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Weijun Li
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Yuanyuan Zhou
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Zongxin Li
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Hui Li
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Long Yang
- Agricultural Big-Data Research Center, College of Plant Protection, Shandong Agricultural University, Taian, 271018, China
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7
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Kitz F, Gómez-Brandón M, Eder B, Etemadi M, Spielmann FM, Hammerle A, Insam H, Wohlfahrt G. Soil carbonyl sulfide exchange in relation to microbial community composition: insights from a managed grassland soil amendment experiment. SOIL BIOLOGY & BIOCHEMISTRY 2019; 135:28-37. [PMID: 31579268 PMCID: PMC6774760 DOI: 10.1016/j.soilbio.2019.04.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The viability of carbonyl sulfide (COS) measurements for partitioning ecosystem-scale net carbon dioxide (CO2) fluxes into photosynthesis and respiration critically depends on our knowledge of non-leaf sinks and sources of COS in ecosystems. We combined soil gas exchange measurements of COS and CO2 with next-generation sequencing technology (NGS) to investigate the role of soil microbiota for soil COS exchange. We applied different treatments (litter and glucose addition, enzyme inhibition and gamma sterilization) to soil samples from a temperate grassland to manipulate microbial composition and activity. While untreated soil was characterized by consistent COS uptake, other treatments reduced COS uptake and even turned the soil into a net COS source. Removing biotic processes through sterilization led to positive or zero fluxes. We used NGS to link changes in the COS response to alterations in the microbial community composition, with bacterial data having a higher explanatory power for the measured COS fluxes than fungal data. We found that the genera Arthrobacter and Streptomyces were particularly abundant in samples exhibiting high COS emissions. Our results indicate co-occurring abiotic production and biotic consumption of COS in untreated soil, the latter linked to carbonic anhydrase activity, and a strong dependency of the COS flux on the activity, identity, abundance of and substrate available to microorganisms.
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Affiliation(s)
- Florian Kitz
- Department of Ecology, University of Innsbruck, Sternwartestraße 15, Innsbruck, Austria
| | - María Gómez-Brandón
- Department of Microbiology, University of Innsbruck, Technikerstraße 25, Innsbruck, Austria
| | - Bernhard Eder
- Department of Microbiology, University of Innsbruck, Technikerstraße 25, Innsbruck, Austria
| | - Mohammad Etemadi
- Department of Microbiology, University of Innsbruck, Technikerstraße 25, Innsbruck, Austria
| | - Felix M. Spielmann
- Department of Ecology, University of Innsbruck, Sternwartestraße 15, Innsbruck, Austria
| | - Albin Hammerle
- Department of Ecology, University of Innsbruck, Sternwartestraße 15, Innsbruck, Austria
| | - Heribert Insam
- Department of Microbiology, University of Innsbruck, Technikerstraße 25, Innsbruck, Austria
| | - Georg Wohlfahrt
- Department of Ecology, University of Innsbruck, Sternwartestraße 15, Innsbruck, Austria
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8
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Meredith LK, Ogée J, Boye K, Singer E, Wingate L, von Sperber C, Sengupta A, Whelan M, Pang E, Keiluweit M, Brüggemann N, Berry JA, Welander PV. Soil exchange rates of COS and CO 18O differ with the diversity of microbial communities and their carbonic anhydrase enzymes. ISME JOURNAL 2018; 13:290-300. [PMID: 30214028 PMCID: PMC6330096 DOI: 10.1038/s41396-018-0270-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 04/30/2018] [Accepted: 08/04/2018] [Indexed: 12/29/2022]
Abstract
Differentiating the contributions of photosynthesis and respiration to the global carbon cycle is critical for improving predictive climate models. Carbonic anhydrase (CA) activity in leaves is responsible for the largest biosphere-atmosphere trace gas fluxes of carbonyl sulfide (COS) and the oxygen-18 isotopologue of carbon dioxide (CO18O) that both reflect gross photosynthetic rates. However, CA activity also occurs in soils and will be a source of uncertainty in the use of COS and CO18O as carbon cycle tracers until process-based constraints are improved. In this study, we measured COS and CO18O exchange rates and estimated the corresponding CA activity in soils from a range of biomes and land use types. Soil CA activity was not uniform for COS and CO2, and patterns of divergence were related to microbial community composition and CA gene expression patterns. In some cases, the same microbial taxa and CA classes catalyzed both COS and CO2 reactions in soil, but in other cases the specificity towards the two substrates differed markedly. CA activity for COS was related to fungal taxa and β-D-CA expression, whereas CA activity for CO2 was related to algal and bacterial taxa and α-CA expression. This study integrates gas exchange measurements, enzyme activity models, and characterization of soil taxonomic and genetic diversity to build connections between CA activity and the soil microbiome. Importantly, our results identify kinetic parameters to represent soil CA activity during application of COS and CO18O as carbon cycle tracers.
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Affiliation(s)
- Laura K Meredith
- Department of Earth System Science, Stanford University, Stanford, CA, 94305, USA. .,School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, 85721, USA.
| | - Jérôme Ogée
- INRA/Bordeaux Science Agro, UMR 1391 ISPA, Bordeaux Science Agro, Villenave d'Ornon, Bordeaux, 33140, France
| | - Kristin Boye
- SLAC National Laboratory, Stanford Synchrotron Radiation Lightsource, Menlo Park, CA, 94025, USA
| | - Esther Singer
- Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Lisa Wingate
- INRA/Bordeaux Science Agro, UMR 1391 ISPA, Bordeaux Science Agro, Villenave d'Ornon, Bordeaux, 33140, France
| | - Christian von Sperber
- Institute for Crop Science and Resource Conservation (INRES), Soil Science and Soil Ecology, University of Bonn, Bonn, 53115, Germany.,Department of Geography, McGill University, 805 Sherbrooke St. W., Montreal, QC, H3A 0B9, Canada
| | - Aditi Sengupta
- University of Arizona, Biosphere 2, Tucson, AZ, 85721, USA
| | - Mary Whelan
- Department of Global Change Ecology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Erin Pang
- Department of Earth System Science, Stanford University, Stanford, CA, 94305, USA
| | - Marco Keiluweit
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA, 01003, USA
| | - Nicolas Brüggemann
- Forschungszentrum Jülich, Institute of Bio- and Geosciences, Agrosphere (IBG-3), Wilhelm-Johnen-Strasse, Jülich, 52428, Germany
| | - Joe A Berry
- Department of Global Change Ecology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Paula V Welander
- Department of Earth System Science, Stanford University, Stanford, CA, 94305, USA
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9
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Coupled Biological and Abiotic Mechanisms Driving Carbonyl Sulfide Production in Soils. SOIL SYSTEMS 2018. [DOI: 10.3390/soilsystems2030037] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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10
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Ogawa T, Hattori S, Kamezaki K, Kato H, Yoshida N, Katayama Y. Isotopic Fractionation of Sulfur in Carbonyl Sulfide by Carbonyl Sulfide Hydrolase of Thiobacillus thioparus THI115. Microbes Environ 2017; 32:367-375. [PMID: 29199215 PMCID: PMC5745022 DOI: 10.1264/jsme2.me17130] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 09/24/2017] [Indexed: 11/25/2022] Open
Abstract
Carbonyl sulfide (COS) is one of the major sources of stratospheric sulfate aerosols, which affect the global radiation balance and ozone depletion. COS-degrading microorganisms are ubiquitous in soil and important for the global flux of COS. We examined the sulfur isotopic fractionation during the enzymatic degradation of COS by carbonyl sulfide hydrolase (COSase) from Thiobacillus thioparus THI115. The isotopic fractionation constant (34ɛ value) was -2.2±0.2‰. Under experimental conditions performed at parts per million by volume level of COS, the 34ɛ value for intact cells of T. thioparus THI115 was -3.6±0.7‰, suggesting that, based on Rees' model, the 34ɛ value mainly depended on COS transport into the cytoplasm. The 34ɛ value for intact cells of T. thioparus THI115 was similar to those for Mycobacterium spp. and Williamsia sp., which are known to involve the conserved region of nucleotide sequences encoding the clade D of β-class carbonic anhydrase (β-CA) including COSase. On the other hand, the 34ɛ value was distinct from those for bacteria in the genus Cupriavidus. These results provide an insight into biological COS degradation, which is indispensable for estimating the COS global budget based on the isotope because of the significant contribution of COS degradation by microorganisms harboring β-CA family enzymes.
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Affiliation(s)
- Takahiro Ogawa
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology3–5–8 Saiwai-cho, Fuchu, Tokyo 183–8509Japan
| | - Shohei Hattori
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226–8502Japan
| | - Kazuki Kamezaki
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226–8502Japan
| | - Hiromi Kato
- Graduate School of Life Sciences, Tohoku University2–1–1 Katahira, Aoba-Ku, Sendai, Miyagi 980–8577Japan
| | - Naohiro Yoshida
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226–8502Japan
- Earth-Life Science Institute, Tokyo Institute of Technology2–12–1–IE–1 Ookayama, Meguro-ku, Tokyo 152–8550Japan
| | - Yoko Katayama
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology3–5–8 Saiwai-cho, Fuchu, Tokyo 183–8509Japan
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11
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Ogawa T, Kato H, Higashide M, Nishimiya M, Katayama Y. Degradation of carbonyl sulfide by Actinomycetes and detection of clade D of β-class carbonic anhydrase. FEMS Microbiol Lett 2016; 363:fnw223. [PMID: 27671711 DOI: 10.1093/femsle/fnw223] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/14/2016] [Accepted: 09/23/2016] [Indexed: 11/14/2022] Open
Abstract
Carbonyl sulfide (COS) is an atmospheric trace gas and one of the sources of stratospheric aerosol contributing to climate change. Although one of the major sinks of COS is soil, the distribution of COS degradation ability among bacteria remains unclear. Seventeen out of 20 named bacteria belonging to Actinomycetales had COS degradation activity at mole fractions of 30 parts per million by volume (ppmv) COS. Dietzia maris NBRC 15801T and Mycobacterium sp. THI405 had the activity comparable to a chemolithoautotroph Thiobacillus thioparus THI115 that degrade COS by COS hydrolase for energy production. Among 12 bacteria manifesting rapid degradation at 30 ppmv COS, D. maris NBRC 15801T and Streptomyces ambofaciens NBRC 12836T degraded ambient COS (∼500 parts per trillion by volume). Geodermatophilus obscurus NBRC 13315T and Amycolatopsis orientalis NBRC 12806T increased COS concentrations. Moreover, six of eight COS-degrading bacteria isolated from soils had partial nucleotide sequences similar to that of the gene encoding clade D of β-class carbonic anhydrase, which included COS hydrolase. These results indicate the potential importance of Actinomycetes in the role of soils as sinks of atmospheric COS.
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Affiliation(s)
- Takahiro Ogawa
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Hiromi Kato
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai, Miyagi 980-8577, Japan
| | - Mitsuru Higashide
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Mami Nishimiya
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Yoko Katayama
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
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12
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Masaki Y, Ozawa R, Kageyama K, Katayama Y. Degradation and emission of carbonyl sulfide, an atmospheric trace gas, by fungi isolated from forest soil. FEMS Microbiol Lett 2016; 363:fnw197. [PMID: 27559044 DOI: 10.1093/femsle/fnw197] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/13/2016] [Indexed: 11/13/2022] Open
Abstract
Soil is thought to be important both as a source and a sink of carbonyl sulfide (COS) in the troposphere, but the mechanism affecting COS uptake, especially for fungi, remains uncertain. Fungal isolates that were collected randomly from forest soil showed COS-degrading ability at high frequencies: 38 out of 43 isolates grown on potato dextrose agar showed degradation of 30 ppmv COS within 24 h. Of these isolates, eight degraded 30 ppmv of COS to below the detection limit within 2 h. These isolates also showed an ability to degrade COS included in ambient air (around 500 pptv) and highly concentrated (12 500 ppmv) level, even though the latter is higher than the lethal level for mammals. COS-degrading activity was estimated by using ergosterol as a biomass index for fungi. Trichoderma sp. THIF08 had the highest COS-degrading activity of all the isolates. Interestingly, Umbelopsis/Mortierella spp. THIF09 and THIF13 were unable to degrade 30 ppmv COS within 24 h, and actually emitted COS during the cultivation in ambient air. These results indicate a fungal contribution to the flux of COS between the terrestrial and atmospheric environments.
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Affiliation(s)
- Yoshihito Masaki
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Rie Ozawa
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Kei Kageyama
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Yoko Katayama
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
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Kamezaki K, Hattori S, Ogawa T, Toyoda S, Kato H, Katayama Y, Yoshida N. Sulfur Isotopic Fractionation of Carbonyl Sulfide during Degradation by Soil Bacteria. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:3537-3544. [PMID: 26967120 DOI: 10.1021/acs.est.5b05325] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We performed laboratory incubation experiments on the degradation of gaseous phase carbonyl sulfide (OCS) by soil bacteria to determine its sulfur isotopic fractionation constants ((34)ε). Incubation experiments were conducted using strains belonging to the genera Mycobacterium, Williamsia, and Cupriavidus isolated from natural soil environments. The (34)ε values determined were -3.67 ± 0.33‰, -3.99 ± 0.19‰, -3.57 ± 0.22‰, and -3.56 ± 0.23‰ for Mycobacterium spp. strains THI401, THI402, THI404, and THI405; -3.74 ± 0.29‰ for Williamsia sp. strain THI410; and -2.09 ± 0.07‰ and -2.38 ± 0.35‰ for Cupriavidus spp. strains THI414 and THI415. Although OCS degradation rates divided by cell numbers (cell-specific activity) were different among strains of the same genus, the (34)ε values for same genus showed no significant differences. Even though the numbers of bacterial species examined were limited, our results suggest that (34)ε values for OCS bacterial degradation depend not on cell-specific activities, but on genus-level biological differences, suggesting that (34)ε values are dependent on enzymatic and/or membrane properties. Taking our (34)ε values as representative for bacterial OCS degradation, the expected atmospheric changes in δ(34)S values of OCS range from 0.5‰ to 0.9‰, based on previously reported decreases in OCS concentrations at Mt. Fuji, Japan. Consequently, tropospheric observation of δ(34)S values for OCS coupled with (34)ε values for OCS bacterial degradation can potentially be used to investigate soil as an OCS sink.
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Affiliation(s)
| | | | - Takahiro Ogawa
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology , 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | | | - Hiromi Kato
- Graduate School of Life Sciences, Tohoku University , 2-1-1 Katahira, Aoba-Ku, Sendai 980-8577, Japan
| | - Yoko Katayama
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology , 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Naohiro Yoshida
- Earth-Life Science Institute, Tokyo Institute of Technology , 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
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14
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Horn H, Keller A, Hildebrandt U, Kämpfer P, Riederer M, Hentschel U. Draft genome of the Arabidopsis thaliana phyllosphere bacterium, Williamsia sp. ARP1. Stand Genomic Sci 2016; 11:8. [PMID: 26779305 PMCID: PMC4715301 DOI: 10.1186/s40793-015-0122-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 12/21/2015] [Indexed: 11/25/2022] Open
Abstract
The Gram-positive actinomycete Williamsia sp. ARP1 was originally isolated from the Arabidopsis thaliana phyllosphere. Here we describe the general physiological features of this microorganism together with the draft genome sequence and annotation. The 4,745,080 bp long genome contains 4434 protein-coding genes and 70 RNA genes. To our knowledge, this is only the second reported genome from the genus Williamsia and the first sequenced strain from the phyllosphere. The presented genomic information is interpreted in the context of an adaptation to the phyllosphere habitat.
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Affiliation(s)
- Hannes Horn
- Department of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of Würzburg, Julius-von-Sachs-Platz 3, D-97082 Würzburg, Germany ; GEOMAR Helmholtz Centre for Ocean Research, RD3 Marine Microbiology and Christian-Albrechts University of Kiel, Düsternbrooker Weg 20, D-24105 Kiel, Germany
| | - Alexander Keller
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Am Hubland, D-97074 Germany
| | - Ulrich Hildebrandt
- Department of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of Würzburg, Julius-von-Sachs-Platz 3, D-97082 Würzburg, Germany
| | - Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 26, D-35392 Giessen, Germany
| | - Markus Riederer
- Department of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of Würzburg, Julius-von-Sachs-Platz 3, D-97082 Würzburg, Germany
| | - Ute Hentschel
- Department of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of Würzburg, Julius-von-Sachs-Platz 3, D-97082 Würzburg, Germany ; GEOMAR Helmholtz Centre for Ocean Research, RD3 Marine Microbiology and Christian-Albrechts University of Kiel, Düsternbrooker Weg 20, D-24105 Kiel, Germany
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15
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Sources and sinks of carbonyl sulfide in an agricultural field in the Southern Great Plains. Proc Natl Acad Sci U S A 2014; 111:9064-9. [PMID: 24927594 DOI: 10.1073/pnas.1319132111] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Net photosynthesis is the largest single flux in the global carbon cycle, but controls over its variability are poorly understood because there is no direct way of measuring it at the ecosystem scale. We report observations of ecosystem carbonyl sulfide (COS) and CO2 fluxes that resolve key gaps in an emerging framework for using concurrent COS and CO2 measurements to quantify terrestrial gross primary productivity. At a wheat field in Oklahoma we found that in the peak growing season the flux-weighted leaf relative uptake of COS and CO2 during photosynthesis was 1.3, at the lower end of values from laboratory studies, and varied systematically with light. Due to nocturnal stomatal conductance, COS uptake by vegetation continued at night, contributing a large fraction (29%) of daily net ecosystem COS fluxes. In comparison, the contribution of soil fluxes was small (1-6%) during the peak growing season. Upland soils are usually considered sinks of COS. In contrast, the well-aerated soil at the site switched from COS uptake to emissions at a soil temperature of around 15 °C. We observed COS production from the roots of wheat and other species and COS uptake by root-free soil up to a soil temperature of around 25 °C. Our dataset demonstrates that vegetation uptake is the dominant ecosystem COS flux in the peak growing season, providing support of COS as an independent tracer of terrestrial photosynthesis. However, the observation that ecosystems may become a COS source at high temperature needs to be considered in global modeling studies.
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Bacterial CS2 hydrolases from Acidithiobacillus thiooxidans strains are homologous to the archaeal catenane CS2 hydrolase. J Bacteriol 2013; 195:4046-56. [PMID: 23836868 DOI: 10.1128/jb.00627-13] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Carbon disulfide (CS(2)) and carbonyl sulfide (COS) are important in the global sulfur cycle, and CS(2) is used as a solvent in the viscose industry. These compounds can be converted by sulfur-oxidizing bacteria, such as Acidithiobacillus thiooxidans species, to carbon dioxide (CO(2)) and hydrogen sulfide (H2S), a property used in industrial biofiltration of CS(2)-polluted airstreams. We report on the mechanism of bacterial CS(2) conversion in the extremely acidophilic A. thiooxidans strains S1p and G8. The bacterial CS(2) hydrolases were highly abundant. They were purified and found to be homologous to the only other described (archaeal) CS(2) hydrolase from Acidianus strain A1-3, which forms a catenane of two interlocked rings. The enzymes cluster in a group of β-carbonic anhydrase (β-CA) homologues that may comprise a subclass of CS(2) hydrolases within the β-CA family. Unlike CAs, the CS(2) hydrolases did not hydrate CO(2) but converted CS(2) and COS with H(2)O to H(2)S and CO(2). The CS(2) hydrolases of A. thiooxidans strains G8, 2Bp, Sts 4-3, and BBW1, like the CS(2) hydrolase of Acidianus strain A1-3, exist as both octamers and hexadecamers in solution. The CS(2) hydrolase of A. thiooxidans strain S1p forms only octamers. Structure models of the A. thiooxidans CS(2) hydrolases based on the structure of Acidianus strain A1-3 CS(2) hydrolase suggest that the A. thiooxidans strain G8 CS(2) hydrolase may also form a catenane. In the A. thiooxidans strain S1p enzyme, two insertions (positions 26 and 27 [PD] and positions 56 to 61 [TPAGGG]) and a nine-amino-acid-longer C-terminal tail may prevent catenane formation.
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Ogawa T, Noguchi K, Saito M, Nagahata Y, Kato H, Ohtaki A, Nakayama H, Dohmae N, Matsushita Y, Odaka M, Yohda M, Nyunoya H, Katayama Y. Carbonyl Sulfide Hydrolase from Thiobacillus thioparus Strain THI115 Is One of the β-Carbonic Anhydrase Family Enzymes. J Am Chem Soc 2013; 135:3818-25. [DOI: 10.1021/ja307735e] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | | | | | | | - Hiroshi Nakayama
- Biomolecular Characterization
Team, Advanced Technology Support Division, Advanced Science Institute, RIKEN, Wako, Saitama 351-0198, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization
Team, Advanced Technology Support Division, Advanced Science Institute, RIKEN, Wako, Saitama 351-0198, Japan
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18
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Kusumi A, Li XS, Katayama Y. Mycobacteria isolated from angkor monument sandstones grow chemolithoautotrophically by oxidizing elemental sulfur. Front Microbiol 2011; 2:104. [PMID: 21747806 PMCID: PMC3128992 DOI: 10.3389/fmicb.2011.00104] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Accepted: 04/27/2011] [Indexed: 11/30/2022] Open
Abstract
To characterize sulfate-producing microorganisms from the deteriorated sandstones of Angkor monuments in Cambodia, strains of Mycobacterium spp. were isolated from most probable number-positive cultures. All five strains isolated were able to use both elemental sulfur (S0) for chemolithoautotrophic growth and organic substances for chemoorganoheterotrophic growth. Results of phylogenetic and phenotypic analyses indicated that all five isolates were rapid growers of the genus Mycobacterium and were most similar to Mycobacterium cosmeticum and Mycobacterium pallens. Chemolithoautotrophic growth was further examined in the representative strain THI503. When grown in mineral salts medium, strain THI503 oxidized S0 to thiosulfate and sulfate; oxidation was accompanied by a decrease in the pH of the medium from 4.7 to 3.6. The link between sulfur oxidation and energy metabolism was confirmed by an increase in ATP. Fluorescence microscopy of DAPI-stained cells revealed that strain THI503 adheres to and proliferates on the surface of sulfur particles. The flexible metabolic ability of facultative chemolithoautotrophs enables their survival in nutrient-limited sandstone environments.
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Affiliation(s)
- Asako Kusumi
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology Tokyo, Japan
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Li XS, Sato T, Ooiwa Y, Kusumi A, Gu JD, Katayama Y. Oxidation of elemental sulfur by Fusarium solani strain THIF01 harboring endobacterium Bradyrhizobium sp. MICROBIAL ECOLOGY 2010; 60:96-104. [PMID: 20571793 DOI: 10.1007/s00248-010-9699-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Accepted: 06/02/2010] [Indexed: 05/29/2023]
Abstract
Nineteen fungal strains having an ability to oxidize elemental sulfur in mineral salts medium were isolated from deteriorated sandstones of Angkor monuments. These fungi formed clearing zone on agar medium supplemented with powder sulfur due to the dissolution of sulfur. Representative of the isolates, strain THIF01, was identified as Fusarium solani on the basis of morphological characteristics and phylogenetic analyses. PCR amplification targeting 16S rRNA gene and analyses of full 16S rRNA gene sequence indicated strain THIF01 harbors an endobacterium Bradyrhizobium sp.; however, involvement of the bacterium in the sulfur oxidation is still unclear. Strain THIF01 oxidized elemental sulfur to thiosulfate and then sulfate. Germination of the spores of strain THIF01 was observed in a liquid medium containing mineral salts supplemented with elemental sulfur (rate of germinated spores against total spores was 60.2%), and the culture pH decreased from pH 4.8 to 4.0. On the contrary, neither germination (rate of germinated spores against total spores was 1.0%) nor pH decrease was observed without the supplement of elemental sulfur. Strain THIF01 could also degrade 30 ppmv and ambient level (approximate 500 pptv) of carbonyl sulfide.
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Affiliation(s)
- Xian Shu Li
- Department of Material Science and Engineering, Nagoya Institute of Technology, Showa-ku, Nagoya, Japan
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