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Liu X, Wang XR, Zhou F, Xue YR, Yu XY, Liu CH. Novel insights into dimethylsulfoniopropionate cleavage by deep subseafloor fungi. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 933:173057. [PMID: 38729372 DOI: 10.1016/j.scitotenv.2024.173057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/07/2024] [Accepted: 05/06/2024] [Indexed: 05/12/2024]
Abstract
Dimethylsulfoniopropionate (DMSP), a key organic sulfur compound in marine and subseafloor sediments, is degraded by phytoplankton and bacteria, resulting in the release of the climate-active volatile gas dimethylsulfide (DMS). However, it remains unclear if dominant eukaryotic fungi in subseafloor sediments possess specific abilities and metabolic mechanisms for DMSP degradation and DMS formation. Our study provides the first evidence that fungi from coal-bearing sediments ∼2 km below the seafloor, such as Aspergillus spp., Chaetomium globosum, Cladosporium sphaerospermum, and Penicillium funiculosum, can degrade DMSP and produce DMS. In Aspergillus sydowii 29R-4-F02, which exhibited the highest DMSP-dependent DMS production rate (16.95 pmol/μg protein/min), two DMSP lyase genes, dddP and dddW, were identified. Remarkably, the dddW gene, previously observed only in bacteria, was found to be crucial for fungal DMSP cleavage. These findings not only extend the list of fungi capable of degrading DMSP, but also enhance our understanding of DMSP lyase diversity and the role of fungi in DMSP decomposition in subseafloor sedimentary ecosystems.
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Affiliation(s)
- Xuan Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Xin-Ran Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Fan Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Ya-Rong Xue
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Xiang-Yang Yu
- Jiangsu Key Laboratory for Food Quality, Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
| | - Chang-Hong Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China.
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Perkins AK, Rose AL, Grossart HP, Schulz KG, Neubauer D, Tonge MP, Rosentreter JA, Eyre BD, Rojas-Jimenez K, Deschaseaux E, Oakes JM. Fungi increases kelp (Ecklonia radiata) remineralisation and dissolved organic carbon, alkalinity, and dimethylsulfoniopropionate (DMSP) production. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:166957. [PMID: 37704140 DOI: 10.1016/j.scitotenv.2023.166957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 09/15/2023]
Abstract
Fungi are key players in terrestrial organic matter (OM) degradation, but little is known about their role in marine environments. Here we compared the degradation of kelp (Ecklonia radiata) in mesocosms with and without fungicides over 45 days. The aim was to improve our understanding of the vital role of fungal OM degradation and remineralisation and its relevance to marine biogeochemical cycles (e.g., carbon, nitrogen, sulfur, or volatile sulfur). In the presence of fungi, 68 % of the kelp detritus degraded over 45 days, resulting in the production of 0.6 mol of dissolved organic carbon (DOC), 0.16 mol of dissolved inorganic carbon (DIC), 0.23 mol of total alkalinity (TA), and 0.076 mol of CO2, which was subsequently emitted to the atmosphere. Conversely, when fungi were inhibited, the bacterial community diversity was reduced, and only 25 % of the kelp detritus degraded over 45 days. The application of fungicides resulted in the generation of an excess amount of 1.5 mol of DOC, but we observed only 0.02 mol of DIC, and 0.04 mol of TA per one mole of kelp detritus, accompanied by a CO2 emission of 0.081 mol. In contrast, without fungi, remineralisation of kelp detritus to DIC, TA, dimethyl sulfide (DMS), dimethylsulfoniopropionate (DMSP) and methanethiol (MeSH) was significantly reduced. Fungal kelp remineralisation led to a remarkable 100,000 % increase in DMSP production. The observed substantial changes in sediment chemistry when fungi are inhibited highlight the important biogeochemical role of fungal remineralisation, which likely plays a crucial role in defining coastal biogeochemical cycling, blue carbon sequestration, and thus climate regulation.
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Affiliation(s)
- Anita K Perkins
- Centre for Coastal Biogeochemistry, Faculty of Science and Engineering, Southern Cross University, Lismore, 2480, NSW, Australia; Southern Cross Geoscience, Faculty of Science and Engineering, Southern Cross University, Lismore, 2480, NSW, Australia.
| | - Andrew L Rose
- Centre for Coastal Biogeochemistry, Faculty of Science and Engineering, Southern Cross University, Lismore, 2480, NSW, Australia; Southern Cross Geoscience, Faculty of Science and Engineering, Southern Cross University, Lismore, 2480, NSW, Australia
| | - Hans-Peter Grossart
- Leibniz Institute for Freshwater Ecology and Inland Fisheries (IGB), Experimental Limnology, 16775 Neuglobsow, Germany; University of Potsdam, Institute of Biochemistry and Biology, Maulbeerallee 2, 14469 Potsdam, Germany
| | - Kai G Schulz
- Centre for Coastal Biogeochemistry, Faculty of Science and Engineering, Southern Cross University, Lismore, 2480, NSW, Australia
| | - Darshan Neubauer
- Leibniz Institute for Freshwater Ecology and Inland Fisheries (IGB), Experimental Limnology, 16775 Neuglobsow, Germany; University of Potsdam, Institute of Biochemistry and Biology, Maulbeerallee 2, 14469 Potsdam, Germany
| | - Matthew P Tonge
- Southern Cross Geoscience, Faculty of Science and Engineering, Southern Cross University, Lismore, 2480, NSW, Australia
| | - Judith A Rosentreter
- Centre for Coastal Biogeochemistry, Faculty of Science and Engineering, Southern Cross University, Lismore, 2480, NSW, Australia
| | - Bradley D Eyre
- Centre for Coastal Biogeochemistry, Faculty of Science and Engineering, Southern Cross University, Lismore, 2480, NSW, Australia
| | | | - Elisabeth Deschaseaux
- Centre for Coastal Biogeochemistry, Faculty of Science and Engineering, Southern Cross University, Lismore, 2480, NSW, Australia
| | - Joanne M Oakes
- Centre for Coastal Biogeochemistry, Faculty of Science and Engineering, Southern Cross University, Lismore, 2480, NSW, Australia
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Roik A, Reverter M, Pogoreutz C. A roadmap to understanding diversity and function of coral reef-associated fungi. FEMS Microbiol Rev 2022; 46:fuac028. [PMID: 35746877 PMCID: PMC9629503 DOI: 10.1093/femsre/fuac028] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/01/2022] [Accepted: 06/14/2022] [Indexed: 01/09/2023] Open
Abstract
Tropical coral reefs are hotspots of marine productivity, owing to the association of reef-building corals with endosymbiotic algae and metabolically diverse bacterial communities. However, the functional importance of fungi, well-known for their contribution to shaping terrestrial ecosystems and global nutrient cycles, remains underexplored on coral reefs. We here conceptualize how fungal functional traits may have facilitated the spread, diversification, and ecological adaptation of marine fungi on coral reefs. We propose that functions of reef-associated fungi may be diverse and go beyond their hitherto described roles of pathogens and bioeroders, including but not limited to reef-scale biogeochemical cycles and the structuring of coral-associated and environmental microbiomes via chemical mediation. Recent technological and conceptual advances will allow the elucidation of the physiological, ecological, and chemical contributions of understudied marine fungi to coral holobiont and reef ecosystem functioning and health and may help provide an outlook for reef management actions.
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Affiliation(s)
- Anna Roik
- Helmholtz Institute for Functional Marine Biodiversity, University of Oldenburg, Ammerländer Heerstraße 231, 26129 Oldenburg, Germany
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Wilhelmshaven, 26046, Germany
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research (AWI), Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Miriam Reverter
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Wilhelmshaven, 26046, Germany
- School of Biological and Marine Sciences, University of Plymouth, Plymouth PL4 8AA, United Kingdom
| | - Claudia Pogoreutz
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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Sun JY, Song Y, Ma ZP, Zhang HJ, Yang ZD, Cai ZH, Zhou J. Fungal community dynamics during a marine dinoflagellate (Noctiluca scintillans) bloom. MARINE ENVIRONMENTAL RESEARCH 2017; 131:183-194. [PMID: 29017729 DOI: 10.1016/j.marenvres.2017.10.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 09/27/2017] [Accepted: 10/02/2017] [Indexed: 06/07/2023]
Abstract
Contamination and eutrophication have caused serious ecological events (such as algal bloom) in coastal area. During this ecological process, microbial community structure is critical for algal bloom succession. The diversity and composition of bacteria and archaea communities in algal blooms have been widely investigated; however, those of fungi are poorly understood. To fill this gap, we used pyrosequencing and correlation approaches to assess fungal patterns and associations during a dinoflagellate (Noctiluca scintillans) bloom. Phylum level fungal types were predominated by Ascomycota, Chytridiomycota, Mucoromycotina, and Basidiomycota. At the genus level drastic changes were observed with Hysteropatella, Malassezia and Saitoella dominating during the initial bloom stage, while Malassezia was most abundant (>50%) during onset and peak-bloom stages. Saitoella and Lipomyces gradually became more abundant and, in the decline stage, contributed almost 70% of sequences. In the terminal stage of the bloom, Rozella increased rapidly to a maximum of 50-60%. Fungal population structure was significantly influenced by temperature and substrate (N and P) availability (P < 0.05). Inter-specific network analyses demonstrated that Rozella and Saitoella fungi strongly impacted the ecological trajectory of N. scintillans. The functional prediction show that symbiotrophic fungi was dominated in the onset stage; saprotroph type was the primary member present during the exponential growth period; whereas pathogentroph type fungi enriched in decline phase. Overall, fungal communities and functions correlated significantly with N. scintillans processes, suggesting that they may regulate dinoflagellate bloom fates. Our results will facilitate deeper understanding of the ecological importance of marine fungi and their roles in algal bloom formation and collapse.
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Affiliation(s)
- Jing-Yun Sun
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, Guangdong Province, PR China; School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou 730050, Gansu Province, PR China
| | - Yu Song
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, Guangdong Province, PR China
| | - Zhi-Ping Ma
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, Guangdong Province, PR China
| | - Huai-Jing Zhang
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, Guangdong Province, PR China
| | - Zhong-Duo Yang
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou 730050, Gansu Province, PR China; The Provincial Education Key Laboratory of Screening, Evaluation and Advanced Processing of Traditional Chinese Medicine and Tibetan Medicine, School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, 730050, Gansu Province, PR China
| | - Zhong-Hua Cai
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, Guangdong Province, PR China.
| | - Jin Zhou
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, Guangdong Province, PR China.
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Elmer WH, Useman S, Schneider RW, Marra RE, LaMondia JA, Mendelssohn IA, Jiménez-Gasco MM, Caruso FL. Sudden Vegetation Dieback in Atlantic and Gulf Coast Salt Marshes. PLANT DISEASE 2013; 97:436-445. [PMID: 30722244 DOI: 10.1094/pdis-09-12-0871-fe] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Salt marshes rank as the most productive ecosystems on the planet. Biomass production can be greater than 3 kg dry matter/m2/year, which is 40% more biomass than tropical rainforests produce. Salt marshes provide multiple benefits to mankind. For example, coastal communities receive protection from storm surges and wave erosion. Salt marshes absorb excess nitrogen and phosphorus from sewage and fertilizer run-off into rivers, which, in turn, prevents algal blooms and hypoxia in coastal waters. In addition, these unique ecosystems provide habitat and shelter for many hundreds of species of shellfish, finfish, migratory and sedentary birds, and other marine animals. Despite the richness in animal species, the intertidal marshes of the salt marsh ecosystem are dominated by only a few plant species. Of these, the most prevalent plant species in a marsh are the tall and short forms of smooth cordgrass (Spartina alterniflora). The first recorded account of a dieback in a U.S. salt marsh was in the early 1990s in the Florida panhandle where patches of Sp. alterniflora as large as 1 ha died. This article explores possible causes of Sudden Vegetation Dieback.
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Affiliation(s)
- W H Elmer
- The Connecticut Agricultural Experiment Station, New Haven
| | - S Useman
- Louisiana State University, Baton Rouge
| | - R W Schneider
- Department of Plant Pathology & Crop Physiology, Louisiana State University Agricultural Center
| | - R E Marra
- The Connecticut Agricultural Experiment Station, New Haven
| | - J A LaMondia
- The Valley Laboratory, The Connecticut Agricultural Experiment Station, Windsor
| | | | | | - F L Caruso
- Cranberry Research Station, University of Massachusetts, East Wareham
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Lyons JI, Alber M, Hollibaugh JT. Ascomycete fungal communities associated with early decaying leaves of Spartina spp. from central California estuaries. Oecologia 2009; 162:435-42. [DOI: 10.1007/s00442-009-1460-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2008] [Accepted: 08/31/2009] [Indexed: 11/27/2022]
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Todd JD, Curson ARJ, Dupont CL, Nicholson P, Johnston AWB. The dddP gene, encoding a novel enzyme that converts dimethylsulfoniopropionate into dimethyl sulfide, is widespread in ocean metagenomes and marine bacteria and also occurs in some Ascomycete fungi. Environ Microbiol 2009; 11:1376-85. [PMID: 19220400 DOI: 10.1111/j.1462-2920.2009.01864.x] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The marine alphaproteobacterium Roseovarius nubinhibens ISM can produce the gas dimethyl sulfide (DMS) from dimethylsulfoniopropionate (DMSP), a widespread secondary metabolite that occurs in many phytoplankton. Roseovarius possesses a novel gene, termed dddP, which when cloned, confers on Escherichia coli the ability to produce DMS. The DddP polypeptide is in the large family of M24 metallopeptidases and is wholly different from two other enzymes, DddD and DddL, which were previously shown to generate DMS from dimethylsulfoniopropionate. Close homologues of DddP occur in other alphaproteobacteria and more surprisingly, in some Ascomycete fungi. These were the biotechnologically important Aspergillus oryzae and the plant pathogen, Fusarium graminearum. The dddP gene is abundant in the bacterial metagenomic sequences in the Global Ocean Sampling Expedition. Thus, dddP has several novel features and is widely dispersed, both taxonomically and geographically.
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Affiliation(s)
- J D Todd
- School of Biological Sciences, University of East Anglia, Norwich, UK
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Trotsenko YA, Doronina NV, Li TD, Reshetnikov AS. Moderately haloalkaliphilic aerobic methylobacteria. Microbiology (Reading) 2007. [DOI: 10.1134/s0026261707030010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Yoch DC. Dimethylsulfoniopropionate: its sources, role in the marine food web, and biological degradation to dimethylsulfide. Appl Environ Microbiol 2002; 68:5804-15. [PMID: 12450799 PMCID: PMC134419 DOI: 10.1128/aem.68.12.5804-5815.2002] [Citation(s) in RCA: 183] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Duane C Yoch
- Department of Biological Sciences, University of South Carolina, Columbia 29208, USA.
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Ansede JH, Pellechia PJ, Yoch DC. Metabolism of acrylate to beta-hydroxypropionate and its role in dimethylsulfoniopropionate lyase induction by a salt marsh sediment bacterium, Alcaligenes faecalis M3A. Appl Environ Microbiol 1999; 65:5075-81. [PMID: 10543825 PMCID: PMC91683 DOI: 10.1128/aem.65.11.5075-5081.1999] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/1999] [Accepted: 08/31/1999] [Indexed: 11/20/2022] Open
Abstract
Dimethylsulfoniopropionate (DMSP) is degraded to dimethylsulfide (DMS) and acrylate by the enzyme DMSP lyase. DMS or acrylate can serve as a carbon source for both free-living and endophytic bacteria in the marine environment. In this study, we report on the mechanism of DMSP-acrylate metabolism by Alcaligenes faecalis M3A. Suspensions of citrate-grown cells expressed a low level of DMSP lyase activity that could be induced to much higher levels in the presence of DMSP, acrylate, and its metabolic product, beta-hydroxypropionate. DMSP was degraded outside the cell, resulting in an extracellular accumulation of acrylate, which in suspensions of citrate-grown cells was then metabolized at a low endogenous rate. The inducible nature of acrylate metabolism was evidenced by both an increase in the rate of its degradation over time and the ability of acrylate-grown cells to metabolize this molecule at about an eight times higher rate than citrate-grown cells. Therefore, acrylate induces both its production (from DMSP) and its degradation by an acrylase enzyme. (1)H and (13)C nuclear magnetic resonance analyses were used to identify the products resulting from [1-(13)C]acrylate metabolism. The results indicated that A. faecalis first metabolized acrylate to beta-hydroxypropionate outside the cell, which was followed by its intracellular accumulation and subsequent induction of DMSP lyase activity. In summary, the mechanism of DMSP degradation to acrylate and the subsequent degradation of acrylate to beta-hydroxypropionate in the aerobic beta-Proteobacterium A. faecalis has been described.
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Affiliation(s)
- J H Ansede
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208, USA
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