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Oliver JAW, Kelbrick M, Ramkissoon NK, Dugdale A, Stephens BP, Kucukkilic-Stephens E, Fox-Powell MG, Schwenzer SP, Antunes A, Macey MC. Sulfur Cycling as a Viable Metabolism under Simulated Noachian/Hesperian Chemistries. Life (Basel) 2022; 12:life12040523. [PMID: 35455014 PMCID: PMC9024814 DOI: 10.3390/life12040523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/24/2022] [Accepted: 03/30/2022] [Indexed: 12/17/2022] Open
Abstract
Water present on the surface of early Mars (>3.0 Ga) may have been habitable. Characterising analogue environments and investigating the aspects of their microbiome best suited for growth under simulated martian chemical conditions is key to understanding potential habitability. Experiments were conducted to investigate the viability of microbes from a Mars analogue environment, Colour Peak Springs (Axel Heiberg Island, Canadian High Arctic), under simulated martian chemistries. The fluid was designed to emulate waters thought to be typical of the late Noachian, in combination with regolith simulant material based on two distinct martian geologies. These experiments were performed with a microbial community from Colour Peak Springs sediment. The impact on the microbes was assessed by cell counting and 16S rRNA gene amplicon sequencing. Changes in fluid chemistries were tested using ICP-OES. Both chemistries were shown to be habitable, with growth in both chemistries. Microbial communities exhibited distinct growth dynamics and taxonomic composition, comprised of sulfur-cycling bacteria, represented by either sulfate-reducing or sulfur-oxidising bacteria, and additional heterotrophic halophiles. Our data support the identification of Colour Peak Springs as an analogue for former martian environments, with a specific subsection of the biota able to survive under more accurate proxies for martian chemistries.
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Affiliation(s)
- James A. W. Oliver
- Biology Department, Edge Hill University, Ormskirk L39 4QP, UK; (J.A.W.O.); (M.K.)
| | - Matthew Kelbrick
- Biology Department, Edge Hill University, Ormskirk L39 4QP, UK; (J.A.W.O.); (M.K.)
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 3GJ, UK
| | - Nisha K. Ramkissoon
- AstrobiologyOU, School of Environment, Earth and Ecosystem Sciences, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK; (N.K.R.); (B.P.S.); (E.K.-S.); (M.G.F.-P.); (S.P.S.)
| | - Amy Dugdale
- AstrobiologyOU, School of Physical Sciences, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK;
- Biology Department, Maynooth University, Maynooth, W23 F2H6 Kildare, Ireland
| | - Ben P. Stephens
- AstrobiologyOU, School of Environment, Earth and Ecosystem Sciences, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK; (N.K.R.); (B.P.S.); (E.K.-S.); (M.G.F.-P.); (S.P.S.)
| | - Ezgi Kucukkilic-Stephens
- AstrobiologyOU, School of Environment, Earth and Ecosystem Sciences, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK; (N.K.R.); (B.P.S.); (E.K.-S.); (M.G.F.-P.); (S.P.S.)
| | - Mark G. Fox-Powell
- AstrobiologyOU, School of Environment, Earth and Ecosystem Sciences, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK; (N.K.R.); (B.P.S.); (E.K.-S.); (M.G.F.-P.); (S.P.S.)
- School of Earth & Environmental Sciences, University of St Andrews, Fife KY16 9AJ, UK
| | - Susanne P. Schwenzer
- AstrobiologyOU, School of Environment, Earth and Ecosystem Sciences, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK; (N.K.R.); (B.P.S.); (E.K.-S.); (M.G.F.-P.); (S.P.S.)
| | - André Antunes
- State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology (MUST), Macau, China;
- China National Space Administration (CNSA), Macau Center for Space Exploration and Science, Macau, China
| | - Michael C. Macey
- AstrobiologyOU, School of Environment, Earth and Ecosystem Sciences, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK; (N.K.R.); (B.P.S.); (E.K.-S.); (M.G.F.-P.); (S.P.S.)
- Correspondence:
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Bajpai A, Mahawar H, Dubey G, Atoliya N, Parmar R, Devi MH, Kollah B, Mohanty SR. Prospect of pink pigmented facultative methylotrophs in mitigating abiotic stress and climate change. J Basic Microbiol 2022; 62:889-899. [DOI: 10.1002/jobm.202200087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/03/2022] [Accepted: 03/13/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Apekcha Bajpai
- Indian Institute of Soil Science Indian Council of Agricultural Research Bhopal India
- Department of Microbiology Barkatullah University Bhopal India
| | - Himanshu Mahawar
- Indian Institute of Soil Science Indian Council of Agricultural Research Bhopal India
- ICAR‐Directorate of Weed Research Jabalpur India
| | - Garima Dubey
- Indian Institute of Soil Science Indian Council of Agricultural Research Bhopal India
| | - Nagvanti Atoliya
- Indian Institute of Soil Science Indian Council of Agricultural Research Bhopal India
| | - Rakesh Parmar
- Indian Institute of Soil Science Indian Council of Agricultural Research Bhopal India
| | - Mayanglambam H. Devi
- Indian Institute of Soil Science Indian Council of Agricultural Research Bhopal India
| | - Bharati Kollah
- Indian Institute of Soil Science Indian Council of Agricultural Research Bhopal India
| | - Santosh R. Mohanty
- Indian Institute of Soil Science Indian Council of Agricultural Research Bhopal India
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Tsola SL, Zhu Y, Ghurnee O, Economou CK, Trimmer M, Eyice Ö. Diversity of dimethylsulfide-degrading methanogens and sulfate-reducing bacteria in anoxic sediments along the Medway Estuary, UK. Environ Microbiol 2021; 23:4434-4449. [PMID: 34110089 DOI: 10.1111/1462-2920.15637] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 06/02/2021] [Accepted: 06/08/2021] [Indexed: 11/28/2022]
Abstract
Methane is a powerful greenhouse gas but the microbial diversity mediating methylotrophic methanogenesis is not well-characterized. One overlooked route to methane is via the degradation of dimethylsulfide (DMS), an abundant organosulfur compound in the environment. Methanogens and sulfate-reducing bacteria (SRB) can degrade DMS in anoxic sediments depending on sulfate availability. However, we know little about the underlying microbial community and how sulfate availability affects DMS degradation in anoxic sediments. We studied DMS-dependent methane production along the salinity gradient of the Medway Estuary (UK) and characterized, for the first time, the DMS-degrading methanogens and SRB using cultivation-independent tools. DMS metabolism resulted in high methane yield (39%-42% of the theoretical methane yield) in anoxic sediments regardless of their sulfate content. Methanomethylovorans, Methanolobus and Methanococcoides were dominant methanogens in freshwater, brackish and marine incubations respectively, suggesting niche-partitioning of the methanogens likely driven by DMS amendment and sulfate concentrations. Adding DMS also led to significant changes in SRB composition and abundance in the sediments. Increases in the abundance of Sulfurimonas and SRB suggest cryptic sulfur cycling coupled to DMS degradation. Our study highlights a potentially important pathway to methane production in sediments with contrasting sulfate content and sheds light on the diversity of DMS degraders.
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Affiliation(s)
- Stephania L Tsola
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Yizhu Zhu
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Oshin Ghurnee
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Chloe K Economou
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Mark Trimmer
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Özge Eyice
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
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Sulfur metabolites that facilitate oceanic phytoplankton-bacteria carbon flux. ISME JOURNAL 2019; 13:2536-2550. [PMID: 31227817 DOI: 10.1038/s41396-019-0455-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 04/08/2019] [Accepted: 05/03/2019] [Indexed: 11/09/2022]
Abstract
Unlike biologically available nitrogen and phosphorus, which are often at limiting concentrations in surface seawater, sulfur in the form of sulfate is plentiful and not considered to constrain marine microbial activity. Nonetheless, in a model system in which a marine bacterium obtains all of its carbon from co-cultured phytoplankton, bacterial gene expression suggests that at least seven dissolved organic sulfur (DOS) metabolites support bacterial heterotrophy. These labile exometabolites of marine dinoflagellates and diatoms include taurine, N-acetyltaurine, isethionate, choline-O-sulfate, cysteate, 2,3-dihydroxypropane-1-sulfonate (DHPS), and dimethylsulfoniopropionate (DMSP). Leveraging from the compounds identified in this model system, we assessed the role of sulfur metabolites in the ocean carbon cycle by mining the Tara Oceans dataset for diagnostic genes. In the 1.4 million bacterial genome equivalents surveyed, estimates of the frequency of genomes harboring the capability for DOS metabolite utilization ranged broadly, from only 1 out of every 190 genomes (for the C2 sulfonate isethionate) to 1 out of every 5 (for the sulfonium compound DMSP). Bacteria able to participate in DOS transformations are dominated by Alphaproteobacteria in the surface ocean, but by SAR324, Acidimicrobiia, and Gammaproteobacteria at mesopelagic depths, where the capability for utilization occurs in higher frequency than in surface bacteria for more than half the sulfur metabolites. The discovery of an abundant and diverse suite of marine bacteria with the genetic capacity for DOS transformation argues for an important role for sulfur metabolites in the pelagic ocean carbon cycle.
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O’Brien FJM, Dumont MG, Webb JS, Poppy GM. Rhizosphere Bacterial Communities Differ According to Fertilizer Regimes and Cabbage ( Brassica oleracea var. capitata L.) Harvest Time, but Not Aphid Herbivory. Front Microbiol 2018; 9:1620. [PMID: 30083141 PMCID: PMC6064718 DOI: 10.3389/fmicb.2018.01620] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 06/28/2018] [Indexed: 11/16/2022] Open
Abstract
Rhizosphere microbial communities are known to be highly diverse and strongly dependent on various attributes of the host plant, such as species, nutritional status, and growth stage. High-throughput 16S rRNA gene amplicon sequencing has been used to characterize the rhizosphere bacterial community of many important crop species, but this is the first study to date to characterize the bacterial and archaeal community of Brassica oleracea var. capitata. The study also tested the response of the bacterial community to fertilizer type (organic or synthetic) and N dosage (high or low), in addition to plant age (9 or 12 weeks) and aphid (Myzus persicae) herbivory (present/absent). The impact of aboveground herbivory on belowground microbial communities has received little attention in the literature, and since the type (organic or mineral) and amount of fertilizer applications are known to affect M. percicae populations, these treatments were applied at agricultural rates to test for synergistic effects on the soil bacterial community. Fertilizer type and plant growth were found to result in significantly different rhizosphere bacterial communities, while there was no effect of aphid herbivory. Several operational taxonomic units were identified as varying significantly in abundance between the treatment groups and age cohorts. These included members of the S-oxidizing genus Thiobacillus, which was significantly more abundant in organically fertilized 12-week-old cabbages, and the N-fixing cyanobacteria Phormidium, which appeared to decline in synthetically fertilized soils relative to controls. These responses may be an effect of accumulating root-derived glucosinolates in the B. oleracea rhizosphere and increased N-availability, respectively.
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Affiliation(s)
- Flora J. M. O’Brien
- Biological Sciences, University of Southampton, Southampton, United Kingdom
- NIAB EMR, East Malling, United Kingdom
| | - Marc G. Dumont
- Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Jeremy S. Webb
- Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Guy M. Poppy
- Biological Sciences, University of Southampton, Southampton, United Kingdom
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Eyice Ö, Myronova N, Pol A, Carrión O, Todd JD, Smith TJ, Gurman SJ, Cuthbertson A, Mazard S, Mennink-Kersten MA, Bugg TD, Andersson KK, Johnston AW, Op den Camp HJ, Schäfer H. Bacterial SBP56 identified as a Cu-dependent methanethiol oxidase widely distributed in the biosphere. ISME JOURNAL 2017; 12:145-160. [PMID: 29064480 PMCID: PMC5739008 DOI: 10.1038/ismej.2017.148] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Revised: 06/07/2017] [Accepted: 07/27/2017] [Indexed: 12/05/2022]
Abstract
Oxidation of methanethiol (MT) is a significant step in the sulfur cycle. MT is an intermediate of metabolism of globally significant organosulfur compounds including dimethylsulfoniopropionate (DMSP) and dimethylsulfide (DMS), which have key roles in marine carbon and sulfur cycling. In aerobic bacteria, MT is degraded by a MT oxidase (MTO). The enzymatic and genetic basis of MT oxidation have remained poorly characterized. Here, we identify for the first time the MTO enzyme and its encoding gene (mtoX) in the DMS-degrading bacterium Hyphomicrobium sp. VS. We show that MTO is a homotetrameric metalloenzyme that requires Cu for enzyme activity. MTO is predicted to be a soluble periplasmic enzyme and a member of a distinct clade of the Selenium-binding protein (SBP56) family for which no function has been reported. Genes orthologous to mtoX exist in many bacteria able to degrade DMS, other one-carbon compounds or DMSP, notably in the marine model organism Ruegeria pomeroyi DSS-3, a member of the Rhodobacteraceae family that is abundant in marine environments. Marker exchange mutagenesis of mtoX disrupted the ability of R. pomeroyi to metabolize MT confirming its function in this DMSP-degrading bacterium. In R. pomeroyi, transcription of mtoX was enhanced by DMSP, methylmercaptopropionate and MT. Rates of MT degradation increased after pre-incubation of the wild-type strain with MT. The detection of mtoX orthologs in diverse bacteria, environmental samples and its abundance in a range of metagenomic data sets point to this enzyme being widely distributed in the environment and having a key role in global sulfur cycling.
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Affiliation(s)
- Özge Eyice
- School of Life Sciences, University of Warwick, Coventry, UK.,School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | | | - Arjan Pol
- Department of Microbiology, Institute for Water and Wetland Research, Faculty of Science, Radboud University, Nijmegen, The Netherlands
| | - Ornella Carrión
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Tom J Smith
- Department of Biosciences and Chemistry, Sheffield Hallam University, Sheffield, UK
| | - Stephen J Gurman
- Department of Physics and Astronomy, University of Leicester, Leicester, UK
| | | | - Sophie Mazard
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Monique Ash Mennink-Kersten
- Department of Microbiology, Institute for Water and Wetland Research, Faculty of Science, Radboud University, Nijmegen, The Netherlands
| | - Timothy Dh Bugg
- Department of Chemistry, University of Warwick, Coventry, UK
| | | | | | - Huub Jm Op den Camp
- Department of Microbiology, Institute for Water and Wetland Research, Faculty of Science, Radboud University, Nijmegen, The Netherlands
| | - Hendrik Schäfer
- School of Life Sciences, University of Warwick, Coventry, UK
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Janahiraman V, Anandham R, Kwon SW, Sundaram S, Karthik Pandi V, Krishnamoorthy R, Kim K, Samaddar S, Sa T. Control of Wilt and Rot Pathogens of Tomato by Antagonistic Pink Pigmented Facultative Methylotrophic Delftia lacustris and Bacillus spp. FRONTIERS IN PLANT SCIENCE 2016; 7:1626. [PMID: 27872630 PMCID: PMC5097904 DOI: 10.3389/fpls.2016.01626] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 10/14/2016] [Indexed: 05/13/2023]
Abstract
The studies on the biocontrol potential of pink pigmented facultative methylotrophic (PPFM) bacteria other than the genus Methylobacterium are scarce. In the present study, we report three facultative methylotrophic isolates; PPO-1, PPT-1, and PPB-1, respectively, identified as Delftia lacustris, Bacillus subtilis, and Bacillus cereus by 16S rRNA gene sequence analysis. Hemolytic activity was tested to investigate the potential pathogenicity of isolates to plants and humans, the results indicates that the isolates PPO-1, PPT-1, and PPB-1 are not pathogenic strains. Under in vitro conditions, D. lacustris PPO-1, B. subtilis PPT-1, and B. cereus PPB-1 showed direct antagonistic effect by inhibiting the mycelial growth of fungal pathogens; Fusarium oxysporum f. sp. lycopersici (2.15, 2.05, and 1.95 cm), Sclerotium rolfsii (2.14, 2.04, and 1.94 cm), Pythium ultimum (2.12, 2.02, and 1.92 cm), and Rhizoctonia solani (2.18, 2.08, and 1.98 cm) and also produced volatile inhibitory compounds. Under plant growth chamber condition methylotrophic bacterial isolates; D. lacustris PPO-1, B. subtilis PPT-1, and B. cereus PPB-1 significantly reduced the disease incidence of tomato. Under greenhouse condition, D. lacustris PPO-1, B. subtilis PPT-1, and B. cereus PPB-1 inoculated tomato plants, when challenged with F. oxysporum f. sp. lycopersici, S. rolfsii, P. ultimum, and R. solani, increased the pathogenesis related proteins (β-1,3-glucanase and chitinase) and defense enzymes (phenylalanine ammonia lyase, peroxidase, polyphenol oxidase, and catalase) on day 5 after inoculation. In the current study, we first report the facultative methylotrophy in pink pigmented D. lacustris, B. subtilis, and B. cereus and their antagonistic potential against fungal pathogens. Direct antagonistic and ISR effects of these isolates against fungal pathogens of tomato evidenced their possible use as a biocontrol agent.
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Affiliation(s)
- Veeranan Janahiraman
- Department of Agricultural Microbiology, Agricultural College and Research Institute, Tamil Nadu Agricultural UniversityMadurai, India
| | - Rangasamy Anandham
- Department of Agricultural Microbiology, Agricultural College and Research Institute, Tamil Nadu Agricultural UniversityMadurai, India
- *Correspondence: Rangasamy Anandham
| | - Soon W. Kwon
- Korean Agricultural Culture Collection, National Academy of Agricultural Science, Rural Development AdministrationJeonju, South Korea
| | - Subbiah Sundaram
- Department of Agricultural Microbiology, Agricultural College and Research Institute, Tamil Nadu Agricultural UniversityMadurai, India
- Department of Environmental and Biological Chemistry, Chungbuk National UniversityCheongju, South Korea
| | - Veeranan Karthik Pandi
- Department of Plant Pathology, Agricultural College and Research Institute, Tamil Nadu Agricultural UniversityCoimbatore, India
| | - Ramasamy Krishnamoorthy
- Department of Agricultural Microbiology, Agricultural College and Research Institute, Tamil Nadu Agricultural UniversityMadurai, India
| | - Kiyoon Kim
- Department of Environmental and Biological Chemistry, Chungbuk National UniversityCheongju, South Korea
| | - Sandipan Samaddar
- Department of Environmental and Biological Chemistry, Chungbuk National UniversityCheongju, South Korea
| | - Tongmin Sa
- Department of Environmental and Biological Chemistry, Chungbuk National UniversityCheongju, South Korea
- Tongmin Sa
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