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Bushra R, Ahmed I, Li JL, Lian Z, Li S, Ali A, Uzair B, Amin A, Ehsan M, Liu YH, Li WJ. Untapped rich microbiota of mangroves of Pakistan: diversity and community compositions. Folia Microbiol (Praha) 2024; 69:595-612. [PMID: 37843797 DOI: 10.1007/s12223-023-01095-3] [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: 04/24/2023] [Accepted: 09/11/2023] [Indexed: 10/17/2023]
Abstract
The mangrove ecosystem is the world's fourth most productive ecosystem in terms of service value and offering rich biological resources. Microorganisms play vital roles in these ecological processes, thus researching the mangroves-microbiota is crucial for a deeper comprehension of mangroves dynamics. Amplicon sequencing that targeted V4 region of 16S rRNA gene was employed to profile the microbial diversities and community compositions of 19 soil samples, which were collected from the rhizosphere of 3 plant species (i.e., Avicennia marina, Ceriops tagal, and Rhizophora mucronata) in the mangrove forests of Lasbela coast, Pakistan. A total of 67 bacterial phyla were observed from three mangroves species, and these taxa were classified into 188 classes, 453 orders, 759 families, and 1327 genera. We found that Proteobacteria (34.9-38.4%) and Desulfobacteria (7.6-10.0%) were the dominant phyla followed by Chloroflexi (6.6-7.3%), Gemmatimonadota (5.4-6.8%), Bacteroidota (4.3-5.5%), Planctomycetota (4.4-4.9%) and Acidobacteriota (2.7-3.4%), Actinobacteriota (2.5-3.3%), and Crenarchaeota (2.5-3.3%). After considering the distribution of taxonomic groups, we prescribe that the distinctions in bacterial community composition and diversity are ascribed to the changes in physicochemical attributes of the soil samples (i.e., electrical conductivity (ECe), pH, total organic matter (OM), total organic carbon (OC), available phosphorus (P), and extractable potassium (CaCO3). The findings of this study indicated a high-level species diversity in Pakistani mangroves. The outcomes may also aid in the development of effective conservation policies for mangrove ecosystems, which have been hotspots for anthropogenic impacts in Pakistan. To our knowledge, this is the first microbial research from a Pakistani mangrove forest.
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Affiliation(s)
- Rabia Bushra
- National Culture Collection of Pakistan (NCCP), Land Resources Research Institute (LRRI), National Agriculture Research Center (NARC), Islamabad 45500, Pakistan
- Department of Biological Sciences, International Islamic University, Islamabad 44000, Pakistan
| | - Iftikhar Ahmed
- National Culture Collection of Pakistan (NCCP), Land Resources Research Institute (LRRI), National Agriculture Research Center (NARC), Islamabad 45500, Pakistan.
| | - Jia-Ling Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Zhenghan Lian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Shuai Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Ahmad Ali
- National Culture Collection of Pakistan (NCCP), Land Resources Research Institute (LRRI), National Agriculture Research Center (NARC), Islamabad 45500, Pakistan
| | - Bushra Uzair
- Department of Biological Sciences, International Islamic University, Islamabad 44000, Pakistan
| | - Arshia Amin
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad 45500, Pakistan
| | | | - Yong-Hong Liu
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
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2
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Wang Y, Tang L, Chen J, Joseph A, Wu Y, Rene ER, Tang J, Zhu N, Wang P. Susceptibility of Cd availability in microplastics contaminated paddy soil: Influence of ferric minerals and sulfate reduction. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133343. [PMID: 38147753 DOI: 10.1016/j.jhazmat.2023.133343] [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: 09/14/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 12/28/2023]
Abstract
The combined contamination of cadmium (Cd) and microplastics (MPs) in paddy soil always occurred, while its influence on Cd availability remained unclear. This study investigated the Cd availability in Cd-MPs co-contaminated paddy soil in consideration of both ferric minerals and sulfate reduction under flooding conditions. The presence of MPs resulted in a higher Cd releasing risk, as represented by the increase in the available Cd and decrease in Fe-Mn oxide-bound Cd contents, especially on the 7th and 14th days based on the sequential extraction results. MPs facilitated the formation of Fe-organic ligands, which accelerated the reductive dissolution of iron minerals but decreased the amounts of amorphous iron minerals due to the release of dissolved organic substances into pore water. Furthermore, MPs promoted the relative abundance of sulfate-reducing bacteria (such as Streptomyces and Desulfovibrio genera), thus increasing the contents of reductive S species, which was advantageous to the co-precipitation of Fe, S, and Cd on the surface of MPs based on our experimental and statistical results. Taken together, both iron and sulfate reduction under anaerobic conditions played a critical role in Cd mobilization in Cd-MPs co-contaminated paddy fields.
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Affiliation(s)
- Yimin Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Li Tang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Juan Chen
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Akaninyene Joseph
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China; Department of Biosciences and Biotechnology, Faculty of Science, University of Medical Sciences, Ondo City 351101, Nigeria
| | - Yunjin Wu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
| | - Eldon R Rene
- Department of Water Supply, Sanitation and Environmental Engineering, IHE Delft Institute for Water Education, Westvest 7, 2611AX Delft, the Netherlands
| | - Jun Tang
- Institute of Soil Sciences, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China
| | - Ningyuan Zhu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China; Institute of Soil Sciences, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China.
| | - Peifang Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
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Tsola SL, Zhu Y, Chen Y, Sanders IA, Economou CK, Brüchert V, Eyice Ö. Methanolobus use unspecific methyltransferases to produce methane from dimethylsulphide in Baltic Sea sediments. MICROBIOME 2024; 12:3. [PMID: 38172958 PMCID: PMC10762971 DOI: 10.1186/s40168-023-01720-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 11/14/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND In anoxic coastal and marine sediments, degradation of methylated compounds is the major route to the production of methane, a powerful greenhouse gas. Dimethylsulphide (DMS) is the most abundant biogenic organic sulphur compound in the environment and an abundant methylated compound leading to methane production in anoxic sediments. However, understanding of the microbial diversity driving DMS-dependent methanogenesis is limited, and the metabolic pathways underlying this process in the environment remain unexplored. To address this, we used anoxic incubations, amplicon sequencing, genome-centric metagenomics and metatranscriptomics of brackish sediments collected along the depth profile of the Baltic Sea with varying sulphate concentrations. RESULTS We identified Methanolobus as the dominant methylotrophic methanogens in all our DMS-amended sediment incubations (61-99%) regardless of their sulphate concentrations. We also showed that the mtt and mta genes (trimethylamine- and methanol-methyltransferases) from Methanolobus were highly expressed when the sediment samples were incubated with DMS. Furthermore, we did not find mtsA and mtsB (methylsulphide-methyltransferases) in metatranscriptomes, metagenomes or in the Methanolobus MAGs, whilst mtsD and mtsF were found 2-3 orders of magnitude lower in selected samples. CONCLUSIONS Our study demonstrated that the Methanolobus genus is likely the key player in anaerobic DMS degradation in brackish Baltic Sea sediments. This is also the first study analysing the metabolic pathways of anaerobic DMS degradation in the environment and showing that methylotrophic methane production from DMS may not require a substrate-specific methyltransferase as was previously accepted. This highlights the versatility of the key enzymes in methane production in anoxic sediments, which would have significant implications for the global greenhouse gas budget and the methane cycle. Video Abstract.
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Affiliation(s)
- S L Tsola
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Y Zhu
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Y Chen
- School of Life Sciences, University of Warwick, Coventry, UK
| | - I A Sanders
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - C K Economou
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - V Brüchert
- Department of Geological Sciences, Stockholm University, Stockholm, Sweden
- Bolin Centre for Climate Research, Stockholm University, Stockholm, Sweden
| | - Ö Eyice
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK.
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Zhang J, Li X, Qian A, Xu X, Lv Y, Zhou X, Yang X, Zhu W, Zhang H, Ding Y. Effects of operating conditions on the in situ control of sulfur-containing odors by using a novel alternative landfill cover and its transformation mechanism. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:7959-7976. [PMID: 38175505 DOI: 10.1007/s11356-023-31721-z] [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: 08/14/2023] [Accepted: 12/21/2023] [Indexed: 01/05/2024]
Abstract
Sulfur-containing gases are main sources of landfill odors, which has become a big issue for pollution to environment and human health. Biocover is promising for treating landfill odors, with advantages of durability and environmental friendliness. In this study, charcoal sludge compost was utilized as the main effective component of a novel alternative landfill cover and the in situ control of sulfur-containing odors from municipal solid waste landfilling process was simulated under nine different operating conditions. Results showed that five sulfur-containing odors (hydrogen sulfide, H2S; methyl mercaptan, CH3SH; dimethyl sulfide, CH3SCH3; ethylmercaptan, CH3CH2SH; carbon disulfide, CS2) were monitored and removed by the biocover, with the highest removal efficiencies of 77.18% for H2S, 87.36% for CH3SH, and 92.19% for CH3SCH3 in reactor 8#, and 95.94% for CH3CH2SH and 94.44% for CS2 in reactor 3#. The orthogonal experiment showed that the factors influencing the removal efficiencies of sulfur-containing odors were ranked from high to low as follows: temperature > weight ratio > humidity content. The combination of parameters of 20% weight ratio, 25°C temperature, and 30% water content was more recommended based on the consideration of the removal efficiencies and economic benefits. The mechanisms of sulfur conversion inside biocover were analyzed. Most organic sulfur was firstly degraded to reduced sulfides or element sulfur, and then oxidized to sulfate which could be stable in the layer as the final state. In this process, sulfur-oxidizing bacteria play a great role, and the distribution of them in reactor 1#, 5#, and 8# was specifically monitored. Bradyrhizobiaceae and Rhodospirillaceae were the dominant species which can utilize sulfide as substance to produce sulfate and element sulfur, respectively. Based on the results of OUTs, the biodiversity of these sulfur-oxidizing bacteria, these microorganisms, was demonstrated to be affected by the different parameters. These results indicate that the novel alternative landfill cover modified with bamboo charcoal compost is effective in removing sulfur odors from landfills. Meanwhile, the findings have direct implications for addressing landfill odor problems through parameter adjustment.
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Affiliation(s)
- Jiayi Zhang
- Department of Environmental Science and Engineering, Hangzhou Normal University, Hangzhou, 310036, People's Republic of China
| | - Xiaowen Li
- Department of Environmental Science and Engineering, Hangzhou Normal University, Hangzhou, 310036, People's Republic of China
| | - Aiai Qian
- Department of Environmental Science and Engineering, Hangzhou Normal University, Hangzhou, 310036, People's Republic of China
| | - Xianwen Xu
- Department of Environmental Science and Engineering, Hangzhou Normal University, Hangzhou, 310036, People's Republic of China
| | - Ya Lv
- Department of Environmental Science and Engineering, Hangzhou Normal University, Hangzhou, 310036, People's Republic of China
| | - Xinrong Zhou
- Department of Environmental Science and Engineering, Hangzhou Normal University, Hangzhou, 310036, People's Republic of China
| | - Xinrui Yang
- Department of Environmental Science and Engineering, Hangzhou Normal University, Hangzhou, 310036, People's Republic of China
| | - Weiqin Zhu
- Department of Environmental Science and Engineering, Hangzhou Normal University, Hangzhou, 310036, People's Republic of China
| | - Hangjun Zhang
- Department of Environmental Science and Engineering, Hangzhou Normal University, Hangzhou, 310036, People's Republic of China
| | - Ying Ding
- Department of Environmental Science and Engineering, Hangzhou Normal University, Hangzhou, 310036, People's Republic of China.
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Tebbe DA, Gruender C, Dlugosch L, Lõhmus K, Rolfes S, Könneke M, Chen Y, Engelen B, Schäfer H. Microbial drivers of DMSO reduction and DMS-dependent methanogenesis in saltmarsh sediments. THE ISME JOURNAL 2023; 17:2340-2351. [PMID: 37880542 PMCID: PMC10689795 DOI: 10.1038/s41396-023-01539-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 10/27/2023]
Abstract
Saltmarshes are highly productive environments, exhibiting high abundances of organosulfur compounds. Dimethylsulfoniopropionate (DMSP) is produced in large quantities by algae, plants, and bacteria and is a potential precursor for dimethylsulfoxide (DMSO) and dimethylsulfide (DMS). DMSO serves as electron acceptor for anaerobic respiration leading to DMS formation, which is either emitted or can be degraded by methylotrophic prokaryotes. Major products of these reactions are trace gases with positive (CO2, CH4) or negative (DMS) radiative forcing with contrasting effects on the global climate. Here, we investigated organic sulfur cycling in saltmarsh sediments and followed DMSO reduction in anoxic batch experiments. Compared to previous measurements from marine waters, DMSO concentrations in the saltmarsh sediments were up to ~300 fold higher. In batch experiments, DMSO was reduced to DMS and subsequently consumed with concomitant CH4 production. Changes in prokaryotic communities and DMSO reductase gene counts indicated a dominance of organisms containing the Dms-type DMSO reductases (e.g., Desulfobulbales, Enterobacterales). In contrast, when sulfate reduction was inhibited by molybdate, Tor-type DMSO reductases (e.g., Rhodobacterales) increased. Vibrionales increased in relative abundance in both treatments, and metagenome assembled genomes (MAGs) affiliated to Vibrio had all genes encoding the subunits of DMSO reductases. Molar conversion ratios of <1.3 CH4 per added DMSO were accompanied by a predominance of the methylotrophic methanogens Methanosarcinales. Enrichment of mtsDH genes, encoding for DMS methyl transferases in metagenomes of batch incubations indicate their role in DMS-dependent methanogenesis. MAGs affiliated to Methanolobus carried the complete set of genes encoding for the enzymes in methylotrophic methanogenesis.
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Affiliation(s)
- Dennis Alexander Tebbe
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129, Oldenburg, Germany
| | | | - Leon Dlugosch
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129, Oldenburg, Germany
| | - Kertu Lõhmus
- Institute of Biology and Environmental Sciences, University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129, Oldenburg, Germany
| | - Sönke Rolfes
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129, Oldenburg, Germany
| | - Martin Könneke
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129, Oldenburg, Germany
| | - Yin Chen
- School of Life Sciences, University of Warwick, CV4 7AL, Coventry, UK
| | - Bert Engelen
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129, Oldenburg, Germany
| | - Hendrik Schäfer
- School of Life Sciences, University of Warwick, CV4 7AL, Coventry, UK.
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Sarat N, Salim A, Pal S, Subhash S, Prasad M, Nair BG, Madhavan A. Mitigation of biogenic methanethiol using bacteriophages in synthetic wastewater augmented with Pseudomonas putida. Sci Rep 2023; 13:19480. [PMID: 37945592 PMCID: PMC10636157 DOI: 10.1038/s41598-023-46938-8] [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: 08/27/2023] [Accepted: 11/07/2023] [Indexed: 11/12/2023] Open
Abstract
Wastewater malodour is the proverbial 'elephant in the room' notwithstanding its severe implications on sanitation, health, and hygiene. The predominant malodorous compounds associated with wastewater treatment plants and toilets are volatile organic compounds, such as hydrogen sulphide, ammonia, methanethiol, and organic acids. Among them, methanethiol warrants more attention owing to its relatively low olfactory threshold and associated cytotoxicity. This requires an efficient odour-abatement method since conventional techniques are either cost-prohibitive or leave recalcitrant byproducts. Bacteriophage-based methodology holds promise, and the described work explores the potential. In this study, a non-lysogenous Pseudomonas putida strain is used as a model organism that produces methanethiol in the presence of methionine. Two double-stranded DNA phages of genome sizes > 10 Kb were isolated from sewage. ɸPh_PP01 and ɸPh_PP02 were stable at suboptimal pH, temperature, and at 10% chloroform. Moreover, they showed adsorption efficiencies of 53% and 89% in 12 min and burst sizes of 507 ± 187 and 105 ± 7 virions per cell, respectively. In augmented synthetic wastewater, ɸPh_PP01 and ɸPh_PP02 reduced methanethiol production by 52% and 47%, respectively, with the concomitant reduction in P. putida by 3 logs in 6 h. On extension of the study in P. putida spiked-sewage sample, maximum reduction in methanethiol production was achieved in 3 h, with 49% and 48% for ɸPh_PP01 and ɸPh_PP02, respectively. But at 6 h, efficiency reduced to 36% with both the phages. The study clearly demonstrates the potential of phages as biocontrol agents in the reduction of malodour in wastewater.
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Affiliation(s)
- Niti Sarat
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, 690525, India
| | - Amrita Salim
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, 690525, India
| | - Sanjay Pal
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, 690525, India.
| | - Suja Subhash
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, 690525, India
| | - Megha Prasad
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, 690525, India
| | - Bipin G Nair
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, 690525, India
| | - Ajith Madhavan
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, 690525, India.
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Zhang C, Lu Q, Li Y. A review on sulfur transformation during anaerobic digestion of organic solid waste: Mechanisms, influencing factors and resource recovery. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 865:161193. [PMID: 36581268 DOI: 10.1016/j.scitotenv.2022.161193] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Anaerobic digestion (AD) is an economical and environment-friendly technology for treating organic solid wastes (OSWs). OSWs with high sulfur can lead to the accumulation of toxic and harmful hydrogen sulfide (H2S) during AD, so a considerable amount of studies have focused on removing H2S emissions. However, current studies have found that sulfide induces phosphate release from the sludge containing iron‑phosphorus compounds (FePs) and the feasibility of recovering elemental sulfur (S0) during AD. To tap the full potential of sulfur in OSWs resource recovery, deciphering the sulfur transformation pathway and its influencing factors is required. Therefore, in this review, the sulfur species and distributions in OSWs and the pathway of sulfur transformation during AD were systematically summarized. Then, the relationship between iron (ferric compounds and zero-valent iron), phosphorus (FePs) and sulfur were analyzed. It was found that the reaction of iron with sulfide during AD drove the conversion of sulfide to S0 and iron sulfide compounds (FeSx), and consequently iron was applied in sulfide abatement. In particular, ferric (hydr)oxide granules offer possibilities to improve the economic viability of hydrogen sulfide control by recovering S0. Sulfide is an interesting strategy to release phosphate from the sludge containing FePs for phosphorus recovery. Critical factors affecting sulfur transformation, including the carbon source, free ammonia and pretreatment methods, were summarized and discussed. Carbon source and free ammonia affected sulfur-related microbial diversity and enzyme activity and different sulfur transformation pathways in response to varying pretreatment methods. The study on S0 recovery, organic sulfur conversion, and phosphate release mechanism triggered by sulfur deserves further investigation. This review is expected to enrich our knowledge of the role of sulfur during AD and inspire new ideas for recovering phosphorus and sulfur resources from OSWs.
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Affiliation(s)
- Cong Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
| | - Qinyuan Lu
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
| | - Yongmei Li
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China.
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8
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Palit K, Rath S, Chatterjee S, Das S. Microbial diversity and ecological interactions of microorganisms in the mangrove ecosystem: Threats, vulnerability, and adaptations. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:32467-32512. [PMID: 35182344 DOI: 10.1007/s11356-022-19048-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
Mangroves are among the world's most productive ecosystems and a part of the "blue carbon" sink. They act as a connection between the terrestrial and marine ecosystems, providing habitat to countless organisms. Among these, microorganisms (e.g., bacteria, archaea, fungi, phytoplankton, and protozoa) play a crucial role in this ecosystem. Microbial cycling of major nutrients (carbon, nitrogen, phosphorus, and sulfur) helps maintain the high productivity of this ecosystem. However, mangrove ecosystems are being disturbed by the increasing concentration of greenhouse gases within the atmosphere. Both the anthropogenic and natural factors contribute to the upsurge of greenhouse gas concentration, resulting in global warming. Changing climate due to global warming and the increasing rate of human interferences such as pollution and deforestation are significant concerns for the mangrove ecosystem. Mangroves are susceptible to such environmental perturbations. Global warming, human interventions, and its consequences are destroying the ecosystem, and the dreadful impacts are experienced worldwide. Therefore, the conservation of mangrove ecosystems is necessary for protecting them from the changing environment-a step toward preserving the globe for better living. This review highlights the importance of mangroves and their microbial components on a global scale and the degree of vulnerability of the ecosystems toward anthropic and climate change factors. The future scenario of the mangrove ecosystem and the resilience of plants and microbes have also been discussed.
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Affiliation(s)
- Krishna Palit
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India
| | - Sonalin Rath
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India
| | - Shreosi Chatterjee
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India
| | - Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India.
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9
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Schmitz RA, Mohammadi SS, van Erven T, Berben T, Jetten MSM, Pol A, Op den Camp HJM. Methanethiol Consumption and Hydrogen Sulfide Production by the Thermoacidophilic Methanotroph Methylacidiphilum fumariolicum SolV. Front Microbiol 2022; 13:857442. [PMID: 35422776 PMCID: PMC9003020 DOI: 10.3389/fmicb.2022.857442] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 02/28/2022] [Indexed: 11/13/2022] Open
Abstract
Methanotrophs aerobically oxidize methane to carbon dioxide to make a living and are known to degrade various other short chain carbon compounds as well. Volatile organic sulfur compounds such as methanethiol (CH3SH) are important intermediates in the sulfur cycle. Although volatile organic sulfur compounds co-occur with methane in various environments, little is known about how these compounds affect methanotrophy. The enzyme methanethiol oxidase catalyzing the oxidation of methanethiol has been known for decades, but only recently the mtoX gene encoding this enzyme was identified in a methylotrophic bacterium. The presence of a homologous gene in verrucomicrobial methanotrophs prompted us to examine how methanotrophs cope with methanethiol. Here, we show that the verrucomicrobial methanotroph Methylacidiphilum fumariolicum SolV consumes methanethiol and produces H2S, which is concurrently oxidized. Consumption of methanethiol is required since methanethiol inhibits methane oxidation. Cells incubated with ∼15 μM methanethiol from the start clearly showed inhibition of growth. After depletion of methanethiol, growth resumed within 1 day. Genes encoding a putative methanethiol oxidase were found in a variety of methanotrophs. Therefore, we hypothesize that methanethiol degradation is a widespread detoxification mechanism in methanotrophs in a range of environments.
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Affiliation(s)
- Rob A Schmitz
- Department of Microbiology, Radboud Institute for Biological and Environmental Research, Radboud University, Nijmegen, Netherlands.,Environmental Chemistry, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, Zurich, Switzerland
| | - Sepehr S Mohammadi
- Department of Microbiology, Radboud Institute for Biological and Environmental Research, Radboud University, Nijmegen, Netherlands
| | - Timo van Erven
- Department of Microbiology, Radboud Institute for Biological and Environmental Research, Radboud University, Nijmegen, Netherlands
| | - Tom Berben
- Department of Microbiology, Radboud Institute for Biological and Environmental Research, Radboud University, Nijmegen, Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Radboud Institute for Biological and Environmental Research, Radboud University, Nijmegen, Netherlands
| | - Arjan Pol
- Department of Microbiology, Radboud Institute for Biological and Environmental Research, Radboud University, Nijmegen, Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, Radboud Institute for Biological and Environmental Research, Radboud University, Nijmegen, Netherlands
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10
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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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11
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Huang D, Zhang Z, Sun M, Feng Z, Ye M. Characterization and ecological function of bacterial communities in seabed sediments of the southwestern Yellow Sea and northwestern East China Sea, Western Pacific. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 761:143233. [PMID: 33158535 DOI: 10.1016/j.scitotenv.2020.143233] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/21/2020] [Accepted: 09/22/2020] [Indexed: 06/11/2023]
Abstract
The marine ecosystems of the marginal seas of the Western Pacific region are frequently disturbed by terrigenous materials. It is of great significance to investigate the ecological functioning of these marine areas, which can be well understood by exploring the microbial communities of sediments. However, the geographical distribution, composition, and genetic functions of sedimentary bacterial communities of the Yellow Sea and East China Sea (YEC Seas) are poorly understood. In this work, sediment samples were collected from YEC Sea areas to investigate bacterial communities by high-throughput sequencing. A total of 1960 genera were determined, with Proteobacteria being the dominant phylum (45.03%), followed by Planctomycetes, Bacteroidetes, Acidobacteria, and Chloroflexi. Correlation analysis indicates that the bacterial composition is influenced by environmental factors, including pressure, depth, seawater density, salinity, organic matter content, nutrient, and heavy metal. Approximately 178 metabolism pathways annotated in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database were detected in the bacterial communities, including ones for nutrient metabolism (C, 3.04%; S, 0.70%; N, 0.52%; and P, 0.22%) and exogenous pollutant metabolism (e.g., polycyclic aromatic hydrocarbons (PAHs), chlorobenzene, and benzoate; up to 4.97%). The results demonstrate that the abundant bacterial communities in the sediments of the YEC Seas are important for maintaining marine ecological functioning, especially for elemental biogeochemical cycling and exogenous pollutant transformation.
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Affiliation(s)
- Dan Huang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Zhongyun Zhang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Mingming Sun
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Jiangsu Key Laboratory for Solid Organic Waste Utilization, Nanjing, PR China
| | - Zhengyao Feng
- College of Mining Engineering, Taiyuan University of Technology, Taiyuan 030024, PR China
| | - Mao Ye
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China.
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12
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Zhang K, Zheng X, He Z, Yang T, Shu L, Xiao F, Wu Y, Wang B, Li Z, Chen P, Yan Q. Fish growth enhances microbial sulfur cycling in aquaculture pond sediments. Microb Biotechnol 2020; 13:1597-1610. [PMID: 32940416 PMCID: PMC7415356 DOI: 10.1111/1751-7915.13622] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 06/08/2020] [Accepted: 06/11/2020] [Indexed: 12/20/2022] Open
Abstract
Microbial sulfate reduction and sulfur oxidation are vital processes to enhance organic matter degradation in sediments. However, the diversity and composition of sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) and their environmental driving factors are still poorly understood in aquaculture ponds, which received mounting of organic matter. In this study, bacterial communities, SRB and SOB from sediments of aquaculture ponds with different sizes of grass carp (Ctenopharyngodon idellus) were analysed using high-throughput sequencing and quantitative real-time PCR (qPCR). The results indicated that microbial communities in aquaculture pond sediments of large juvenile fish showed the highest richness and abundance of SRB and SOB, potentially further enhancing microbial sulfur cycling. Specifically, SRB were dominated by Desulfobulbus and Desulfovibrio, whereas SOB were dominated by Dechloromonas and Leptothrix. Although large juvenile fish ponds had relatively lower concentrations of sulfur compounds (i.e. total sulfur, acid-volatile sulfide and elemental sulfur) than those of larval fish ponds, more abundant SRB and SOB were found in the large juvenile fish ponds. Further redundancy analysis (RDA) and linear regression indicated that sulfur compounds and sediment suspension are the major environmental factors shaping the abundance and community structure of SRB and SOB in aquaculture pond sediments. Findings of this study expand our current understanding of microbial driving sulfur cycling in aquaculture ecosystems and also provide novel insights for ecological and green aquaculture managements.
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Affiliation(s)
- Keke Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)School of Environmental Science and EngineeringEnvironmental Microbiomics Research CenterSun Yat‐sen UniversityGuangzhouGuangdong510006China
| | - Xiafei Zheng
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)School of Environmental Science and EngineeringEnvironmental Microbiomics Research CenterSun Yat‐sen UniversityGuangzhouGuangdong510006China
| | - Zhili He
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)School of Environmental Science and EngineeringEnvironmental Microbiomics Research CenterSun Yat‐sen UniversityGuangzhouGuangdong510006China
- College of AgronomyHunan Agricultural UniversityChangsha410128China
| | - Tony Yang
- Swift Current Research and Development CentreAgriculture & Agri‐Food CanadaSwift CurrentSKCanada
| | - Longfei Shu
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)School of Environmental Science and EngineeringEnvironmental Microbiomics Research CenterSun Yat‐sen UniversityGuangzhouGuangdong510006China
| | - Fanshu Xiao
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)School of Environmental Science and EngineeringEnvironmental Microbiomics Research CenterSun Yat‐sen UniversityGuangzhouGuangdong510006China
| | - Yongjie Wu
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)School of Environmental Science and EngineeringEnvironmental Microbiomics Research CenterSun Yat‐sen UniversityGuangzhouGuangdong510006China
| | - Binhao Wang
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)School of Environmental Science and EngineeringEnvironmental Microbiomics Research CenterSun Yat‐sen UniversityGuangzhouGuangdong510006China
| | - Zhou Li
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)School of Environmental Science and EngineeringEnvironmental Microbiomics Research CenterSun Yat‐sen UniversityGuangzhouGuangdong510006China
| | - Pubo Chen
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)School of Environmental Science and EngineeringEnvironmental Microbiomics Research CenterSun Yat‐sen UniversityGuangzhouGuangdong510006China
| | - Qingyun Yan
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)School of Environmental Science and EngineeringEnvironmental Microbiomics Research CenterSun Yat‐sen UniversityGuangzhouGuangdong510006China
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13
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Kurth JM, Op den Camp HJM, Welte CU. Several ways one goal-methanogenesis from unconventional substrates. Appl Microbiol Biotechnol 2020; 104:6839-6854. [PMID: 32542472 PMCID: PMC7374477 DOI: 10.1007/s00253-020-10724-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/27/2020] [Accepted: 06/04/2020] [Indexed: 12/15/2022]
Abstract
Abstract Methane is the second most important greenhouse gas on earth. It is produced by methanogenic archaea, which play an important role in the global carbon cycle. Three main methanogenesis pathways are known: in the hydrogenotrophic pathway H2 and carbon dioxide are used for methane production, whereas in the methylotrophic pathway small methylated carbon compounds like methanol and methylated amines are used. In the aceticlastic pathway, acetate is disproportionated to methane and carbon dioxide. However, next to these conventional substrates, further methanogenic substrates and pathways have been discovered. Several phylogenetically distinct methanogenic lineages (Methanosphaera, Methanimicrococcus, Methanomassiliicoccus, Methanonatronarchaeum) have evolved hydrogen-dependent methylotrophic methanogenesis without the ability to perform either hydrogenotrophic or methylotrophic methanogenesis. Genome analysis of the deep branching Methanonatronarchaeum revealed an interesting membrane-bound hydrogenase complex affiliated with the hardly described class 4 g of multisubunit hydrogenases possibly providing reducing equivalents for anabolism. Furthermore, methylated sulfur compounds such as methanethiol, dimethyl sulfide, and methylmercaptopropionate were described to be converted into adapted methylotrophic methanogenesis pathways of Methanosarcinales strains. Moreover, recently it has been shown that the methanogen Methermicoccus shengliensis can use methoxylated aromatic compounds in methanogenesis. Also, tertiary amines like choline (N,N,N-trimethylethanolamine) or betaine (N,N,N-trimethylglycine) have been described as substrates for methane production in Methanococcoides and Methanolobus strains. This review article will provide in-depth information on genome-guided metabolic reconstructions, physiology, and biochemistry of these unusual methanogenesis pathways. Key points • Newly discovered methanogenic substrates and pathways are reviewed for the first time. • The review provides an in-depth analysis of unusual methanogenesis pathways. • The hydrogenase complex of the deep branching Methanonatronarchaeum is analyzed.
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Affiliation(s)
- Julia M Kurth
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
| | - Cornelia U Welte
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands. .,Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
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14
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Microbial community structure of soils in Bamenwan mangrove wetland. Sci Rep 2019; 9:8406. [PMID: 31182804 PMCID: PMC6557889 DOI: 10.1038/s41598-019-44788-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 05/23/2019] [Indexed: 11/30/2022] Open
Abstract
Microbial community diversity and composition are important for the maintenance of mangrove ecosystem. Bacterial and archaeal community composition of the Bamenwan Mangrove Wetland soil in Hainan, China, was determined using pyrosequencing technique. Bacterial community composition presented differences among the five soil samples. Rhizobiales with higher abundance were observed in inner mangrove forest samples, while Desulfobacterales were in the seaward edge samples, and Frankiales, Gaiellales and Rhodospirillales in the landedge sample. For archaea, Crenarchaeota and Euryarchaeota dominated in five samples, but the proportion in each samples were different. Dominant archaeal community composition at the order level was similar in the seaward edge samples. The dominant archaeal clusters in the two inner mangrove forest samples were different, with Soil Crenarchaeotic Group (SCG) and Halobacteriales in sample inside of Bruguiera sexangula forest and SCG, Methanosarcinales and Marine Benthic Group B (MBGB) in sample inside of Xylocarpus mekongensis forest. The dominant archaeal clusters in land sample were unique, with Terrestrial Group and South African Gold Mine Group 1. The metabolic pathways including metabolism, genetic information processing, environmental information processing, cellular processes, organismal systems and human diseases were all detected for bacterial and archaeal functional profiles, but metabolic potentials among five samples were different.
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15
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Carrión O, Pratscher J, Richa K, Rostant WG, Farhan Ul Haque M, Murrell JC, Todd JD. Methanethiol and Dimethylsulfide Cycling in Stiffkey Saltmarsh. Front Microbiol 2019; 10:1040. [PMID: 31134039 PMCID: PMC6524544 DOI: 10.3389/fmicb.2019.01040] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 04/25/2019] [Indexed: 11/13/2022] Open
Abstract
Methanethiol (MeSH) and dimethylsulfide (DMS) are volatile organic sulfur compounds (VOSCs) with important roles in sulfur cycling, signaling and atmospheric chemistry. DMS can be produced from MeSH through a reaction mediated by the methyltransferase MddA. The mddA gene is present in terrestrial and marine metagenomes, being most abundant in soil environments. The substrate for MddA, MeSH, can also be oxidized by bacteria with the MeSH oxidase (MTO) enzyme, encoded by the mtoX gene, found in marine, freshwater and soil metagenomes. Methanethiol-dependent DMS production (Mdd) pathways have been shown to function in soil and marine sediments, but have not been characterized in detail in the latter environments. In addition, few molecular studies have been conducted on MeSH consumption in the environment. Here, we performed process measurements to confirm that Mdd-dependent and Mdd-independent MeSH consumption pathways are active in tested surface saltmarsh sediment when MeSH is available. We noted that appreciable natural Mdd-independent MeSH and DMS consumption processes masked Mdd activity. 16S rRNA gene amplicon sequencing and metagenomics data showed that Methylophaga, a bacterial genus known to catabolise DMS and MeSH, was enriched by the presence of MeSH. Moreover, some MeSH and/or DMS-degrading bacteria isolated from this marine environment lacked known DMS and/or MeSH cycling genes and can be used as model organisms to potentially identify novel genes in these pathways. Thus, we are likely vastly underestimating the abundance of MeSH and DMS degraders in these marine sediment environments. The future discovery and characterization of novel enzymes involved in MeSH and/or DMS cycling is essential to better assess the role and contribution of microbes to global organosulfur cycling.
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Affiliation(s)
- Ornella Carrión
- School of Environmental Sciences, University of East Anglia, Norwich, United Kingdom
| | | | - Kumari Richa
- School of the Environment, Florida Agricultural and Mechanical University, Tallahassee, FL, United States
| | - Wayne G Rostant
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | | | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich, United Kingdom
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
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16
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Carrión O, Pratscher J, Curson ARJ, Williams BT, Rostant WG, Murrell JC, Todd JD. Methanethiol-dependent dimethylsulfide production in soil environments. ISME JOURNAL 2017; 11:2379-2390. [PMID: 28763056 PMCID: PMC5607357 DOI: 10.1038/ismej.2017.105] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 05/04/2017] [Accepted: 05/12/2017] [Indexed: 11/17/2022]
Abstract
Dimethylsulfide (DMS) is an environmentally important trace gas with roles in sulfur cycling, signalling to higher organisms and in atmospheric chemistry. DMS is believed to be predominantly produced in marine environments via microbial degradation of the osmolyte dimethylsulfoniopropionate (DMSP). However, significant amounts of DMS are also generated from terrestrial environments, for example, peat bogs can emit ~6 μmol DMS m−2 per day, likely via the methylation of methanethiol (MeSH). A methyltransferase enzyme termed ‘MddA’, which catalyses the methylation of MeSH, generating DMS, in a wide range of bacteria and some cyanobacteria, may mediate this process, as the mddA gene is abundant in terrestrial metagenomes. This is the first study investigating the functionality of MeSH-dependent DMS production (Mdd) in a wide range of aerobic environments. All soils and marine sediment samples tested produced DMS when incubated with MeSH. Cultivation-dependent and cultivation-independent methods were used to assess microbial community changes in response to MeSH addition in a grassland soil where 35.9% of the bacteria were predicted to contain mddA. Bacteria of the genus Methylotenera were enriched in the presence of MeSH. Furthermore, many novel Mdd+ bacterial strains were isolated. Despite the abundance of mddA in the grassland soil, the Mdd pathway may not be a significant source of DMS in this environment as MeSH addition was required to detect DMS at only very low conversion rates.
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Affiliation(s)
- Ornella Carrión
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Jennifer Pratscher
- School of Environmental Sciences, University of East Anglia, Norwich, UK
| | - Andrew R J Curson
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Beth T Williams
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Wayne G Rostant
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich, UK
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich, UK
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17
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Sun Y, Qiu J, Chen D, Ye J, Chen J. Characterization of the novel dimethyl sulfide-degrading bacterium Alcaligenes sp. SY1 and its biochemical degradation pathway. JOURNAL OF HAZARDOUS MATERIALS 2016; 304:543-552. [PMID: 26623933 DOI: 10.1016/j.jhazmat.2015.11.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 11/03/2015] [Accepted: 11/05/2015] [Indexed: 06/05/2023]
Abstract
Recently, the biodegradation of volatile organic sulfur compounds (VOSCs) has become a burgeoning field, with a growing focus on the reduction of VOSCs. The reduction of VOSCs encompasses both organic emission control and odor control. Herein, Alcaligenes sp. SY1 was isolated from active sludge and found to utilize dimethyl sulfide (DMS) as a growth substrate in a mineral salt medium. Response surface methodology (RSM) analysis was applied to optimize the incubation conditions. The following conditions for optimal degradation were identified: temperature 27.03°C; pH 7.80; inoculum salinity 0.84%; and initial DMS concentration 1585.39 μM. Under these conditions, approximately 99% of the DMS was degraded within 30 h of incubation. Two metabolic compounds were detected and identified by gas chromatography-mass spectrometry (GC-MS): dimethyl disulfide (DMDS) and dimethyl trisulfide (DMTS). The DMS degradation kinetics for different concentrations were evaluated using the Haldane-Andrews model and the pseudo first-order model. The maximum specific growth rate and degradation rate of Alcaligenes sp. SY1 were 0.17 h(-1) and 0.63 gs gx(-1)h(-1). A possible degradation pathway is proposed, and the results suggest that Alcaligenes sp. SY1 has the potential to control odor emissions under aerobic conditions.
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Affiliation(s)
- Yiming Sun
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Biological and Environmental Engineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Jiguo Qiu
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Biological and Environmental Engineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Dongzhi Chen
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Biological and Environmental Engineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Jiexu Ye
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Biological and Environmental Engineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Jianmeng Chen
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Biological and Environmental Engineering, Zhejiang University of Technology, Hangzhou 310014, PR China.
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18
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Dominance of Oscillospira and Bacteroides in the bacterial community associated with the degradation of high-concentration dimethyl sulfide under iron-reducing condition. ANN MICROBIOL 2016. [DOI: 10.1007/s13213-016-1207-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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19
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Chen DZ, Sun YM, Han LM, Chen J, Ye JX, Chen JM. A newly isolated Pseudomonas putida S-1 strain for batch-mode-propanethiol degradation and continuous treatment of propanethiol-containing waste gas. JOURNAL OF HAZARDOUS MATERIALS 2016; 302:232-240. [PMID: 26476310 DOI: 10.1016/j.jhazmat.2015.09.063] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 09/27/2015] [Accepted: 09/28/2015] [Indexed: 06/05/2023]
Abstract
Pseudomonas putida S-1 was isolated from activated sludge. This novel strain was capable of degrading malodorous 1-propanethiol (PT). PT degradation commenced with no lag phase by cells pre-grown in nutrition-rich media, such as Luria-Bertani (LB), and PT-contained mineral medium at specific growth rates of 0.10-0.19 h(-1); this phenomenon indicated the operability of a large-scale cell culture. A possible PT degradation pathway was proposed on the basis of the detected metabolites, including dipropyl disulfide, 3-hexanone, 2-hexanone, 3-hexanol, 2-hexanol, S(0), SO4(2-), and CO2. P. putida S-1 could degrade mixed pollutants containing PT, diethyl disulfide, isopropyl alcohol, and acetaldehyde, and LB-pre-cultured cells underwent diauxic growth. Waste gas contaminated with 200-400 mg/m(3) PT was continuously treated by P. putida S-1 pre-cultured in LB medium in a completely stirred tank reactor. The removal efficiencies exceeded 88% when PT stream was mixed with 200 mg/m(3) isopropanol; by contrast, the removal efficiencies decreased to 60% as the empty bed residence time was shortened from 40 s to 20 s.
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Affiliation(s)
- Dong-Zhi Chen
- College of Biological and Environmental Engineering, Zhejiang University of Technology, Hangzhou 310032, China.
| | - Yi-Ming Sun
- College of Biological and Environmental Engineering, Zhejiang University of Technology, Hangzhou 310032, China
| | - Li-Mei Han
- College of Biological and Environmental Engineering, Zhejiang University of Technology, Hangzhou 310032, China
| | - Jing Chen
- College of Food and Pharmacy, Zhejiang Ocean University, Zhoushan 316004, China
| | - Jie-Xu Ye
- College of Biological and Environmental Engineering, Zhejiang University of Technology, Hangzhou 310032, China
| | - Jian-Meng Chen
- College of Biological and Environmental Engineering, Zhejiang University of Technology, Hangzhou 310032, China
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20
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Sun J, Hu S, Sharma KR, Ni BJ, Yuan Z. Degradation of methanethiol in anaerobic sewers and its correlation with methanogenic activities. WATER RESEARCH 2015; 69:80-89. [PMID: 25437340 DOI: 10.1016/j.watres.2014.11.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 11/04/2014] [Accepted: 11/05/2014] [Indexed: 05/07/2023]
Abstract
Methanethiol (MT) is considered one of the predominant odorants in sewer systems. Therefore, understanding MT transformation in sewers is essential to sewer odor assessment and abatement. In this study, we investigated the degradation of MT in laboratory anaerobic sewers. Experiments were carried out in seven anaerobic sewer reactors with biofilms at different stages of development. MT degradation was found to be strongly dependent on the methanogenic activity of sewer biofilms. The MT degradation rate accelerated with the increase of methanogenic activity of sewer biofilms, resulting in MT accumulation (i.e. net production) in sewer reactors with relatively low methanogenic activities, and MT removal in reactors with higher methanogenic activities. A Monod-type kinetic expression was developed to describe MT degradation kinetics in anaerobic sewers, in which the maximum degradation rate was modeled as a function of the maximum methane production rate through a power function. It was also found that MT concentration had a linear relationship with acetate concentration, which may be used for preliminary assessment of MT presence in anaerobic sewers.
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Affiliation(s)
- Jing Sun
- Advanced Water Management Centre, The University of Queensland, St. Lucia 4072, Queensland, Australia
| | - Shihu Hu
- Advanced Water Management Centre, The University of Queensland, St. Lucia 4072, Queensland, Australia
| | - Keshab Raj Sharma
- Advanced Water Management Centre, The University of Queensland, St. Lucia 4072, Queensland, Australia
| | - Bing-Jie Ni
- Advanced Water Management Centre, The University of Queensland, St. Lucia 4072, Queensland, Australia
| | - Zhiguo Yuan
- Advanced Water Management Centre, The University of Queensland, St. Lucia 4072, Queensland, Australia.
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21
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Varon-Lopez M, Dias ACF, Fasanella CC, Durrer A, Melo IS, Kuramae EE, Andreote FD. Sulphur-oxidizing and sulphate-reducing communities in Brazilian mangrove sediments. Environ Microbiol 2013; 16:845-55. [DOI: 10.1111/1462-2920.12237] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 07/20/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Maryeimy Varon-Lopez
- Department of Soil Science; ‘Luiz de Queiroz’ College of Agriculture; University of São Paulo; Piracicaba SP Brazil
- Department of Microbial Ecology; Netherlands Institute of Ecology (NIOO/KNAW); Wageningen The Netherlands
| | | | - Cristiane Cipolla Fasanella
- Department of Soil Science; ‘Luiz de Queiroz’ College of Agriculture; University of São Paulo; Piracicaba SP Brazil
| | - Ademir Durrer
- Department of Soil Science; ‘Luiz de Queiroz’ College of Agriculture; University of São Paulo; Piracicaba SP Brazil
| | - Itamar Soares Melo
- Laboratory of Environmental Microbiology; Embrapa Environment; Jaguariúna SP Brazil
| | - Eiko Eurya Kuramae
- Department of Microbial Ecology; Netherlands Institute of Ecology (NIOO/KNAW); Wageningen The Netherlands
| | - Fernando Dini Andreote
- Department of Soil Science; ‘Luiz de Queiroz’ College of Agriculture; University of São Paulo; Piracicaba SP Brazil
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Andrade LL, Leite DCA, Ferreira EM, Ferreira LQ, Paula GR, Maguire MJ, Hubert CRJ, Peixoto RS, Domingues RMCP, Rosado AS. Microbial diversity and anaerobic hydrocarbon degradation potential in an oil-contaminated mangrove sediment. BMC Microbiol 2012; 12:186. [PMID: 22935169 PMCID: PMC3579730 DOI: 10.1186/1471-2180-12-186] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2012] [Accepted: 08/23/2012] [Indexed: 12/04/2022] Open
Abstract
Background Mangrove forests are coastal wetlands that provide vital ecosystem services and serve as barriers against natural disasters like tsunamis, hurricanes and tropical storms. Mangroves harbour a large diversity of organisms, including microorganisms with important roles in nutrient cycling and availability. Due to tidal influence, mangroves are sites where crude oil from spills farther away can accumulate. The relationship between mangrove bacterial diversity and oil degradation in mangrove sediments remains poorly understood. Results Mangrove sediment was sampled from 0–5, 15–20 and 35–40 cm depth intervals from the Suruí River mangrove (Rio de Janeiro, Brazil), which has a history of oil contamination. DGGE fingerprinting for bamA, dsr and 16S rRNA encoding fragment genes, and qPCR analysis using dsr and 16S rRNA gene fragment revealed differences with sediment depth. Conclusions Analysis of bacterial 16S rRNA gene diversity revealed changes with depth. DGGE for bamA and dsr genes shows that the anaerobic hydrocarbon-degrading community profile also changed between 5 and 15 cm depth, and is similar in the two deeper sediments, indicating that below 15 cm the anaerobic hydrocarbon-degrading community appears to be well established and homogeneous in this mangrove sediment. qPCR analysis revealed differences with sediment depth, with general bacterial abundance in the top layer (0–5 cm) being greater than in both deeper sediment layers (15–20 and 35–40 cm), which were similar to each other.
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Affiliation(s)
- Luiza L Andrade
- Laboratório de Ecologia Molecular Microbiana, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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Abstract
Sulfur is central to the metabolisms of many organisms that inhabit extreme environments. While biotic and abiotic cycling of organic sulfur compounds has been well documented in low-temperature anaerobic environments, cycling of organic sulfur in hydrothermal environments has received less attention. Recently published thermodynamic data have been used to estimate aqueous alkyl thiol and sulfide activities in deep-sea hydrothermal systems. Here we use geochemical mixing models to predict fluid compositions that result from mixing end-member hydrothermal fluid from the East Pacific Rise with bottom seawater. These fluid compositions are combined with estimates of methanethiol and dimethylsulfide activities to evaluate energy yields for potential organic sulfur-based metabolisms under hydrothermal conditions. Aerobic respiration has the highest energy yields (over -240 kJ/mol e⁻) at lower temperature; however, oxygen is unlikely to persist at high temperatures, restricting aerobic respiration to mesophilic communities. Nitrite reduction to N₂ has the highest energy yields at higher temperatures (greater than ∼40 °C). Nitrate and nitrite reduction to ammonium also yield significant energy (up to -70 kJ/mol e⁻). Much lower, but still feasible energy yields are calculated for sulfate reduction, disproportionation, and reduction with H₂. Organic compound family and the activity of methanethiol and dimethylsulfide were less important than metabolic strategy in determining overall energy yields. All metabolic strategies considered were exergonic within some portion of the mixing regime suggesting that organic sulfur-based metabolisms may be prevalent within deep-sea hydrothermal vent microbial communities.
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Affiliation(s)
- Karyn L Rogers
- Department of Geological Sciences, University of Missouri, Columbia, MO 65203, USA.
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Magalhães C, Kiene RP, Buchan A, Machado A, Wiebe WJ, Bordalo AA. Methanethiol accumulation exacerbates release of N2 O during denitrification in estuarine sediments and bacterial cultures. ENVIRONMENTAL MICROBIOLOGY REPORTS 2011; 3:308-314. [PMID: 23761276 DOI: 10.1111/j.1758-2229.2010.00226.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Microbes play critical roles in the biogeochemical cycling of nitrogen and sulfur in aquatic environments. Here we investigated the interaction between the naturally occurring organic sulfur compound methanethiol (MeSH) and the final step of the denitrification pathway, the reduction of nitrous oxide (N2 O) to dinitrogen (N2 ) gas, in sediment slurries from the temperate Douro and Ave estuaries (NW Portugal) and in pure cultures of the marine bacterium Ruegeria pomeroyi. Sediment slurries and cell suspensions were amended with a range of concentrations of either MeSH (0-120 µM) or methionine (0-5 mM), a known precursor of MeSH. MeSH or methionine additions caused N2 O to accumulate and this accumulation was linearly related to MeSH concentrations in both coastal sediments (R(2) = 0.7-0.9, P < 0.05) and R. pomeroyi cell suspensions (R(2) = 0.9, P < 0.01). Our results suggest that MeSH inhibits the final step of denitrification resulting in N2 O accumulation.
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Affiliation(s)
- C Magalhães
- CIMAR/CIIMAR - Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas, n° 289, 4050-123 Porto, Portugal Department of Marine Sciences, University of South Alabama, LSCB 25 Mobile, AL 36688 USA Department of Microbiology, University of Tennessee, M409 Walters Life Sciences Knoxville, TN 37996-0845, USA Laboratory of Hydrobiology, Institute of Biomedical Sciences (ICBAS-UP), University of Porto, Largo Prof. Abel Salazar n° 2, 4099-003 Porto, Portugal Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA
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Gomes NCM, Cleary DFR, Pinto FN, Egas C, Almeida A, Cunha A, Mendonça-Hagler LCS, Smalla K. Taking root: enduring effect of rhizosphere bacterial colonization in mangroves. PLoS One 2010; 5:e14065. [PMID: 21124923 PMCID: PMC2989908 DOI: 10.1371/journal.pone.0014065] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Accepted: 10/26/2010] [Indexed: 11/18/2022] Open
Abstract
Background Mangrove forests are of global ecological and economic importance, but are also one of the world's most threatened ecosystems. Here we present a case study examining the influence of the rhizosphere on the structural composition and diversity of mangrove bacterial communities and the implications for mangrove reforestation approaches using nursery-raised plants. Methodology/Principal Findings A barcoded pyrosequencing approach was used to assess bacterial diversity in the rhizosphere of plants in a nursery setting, nursery-raised transplants and native (non-transplanted) plants in the same mangrove habitat. In addition to this, we also assessed bacterial composition in the bulk sediment in order to ascertain if the roots of mangrove plants affect sediment bacterial composition. We found that mangrove roots appear to influence bacterial abundance and composition in the rhizosphere. Due to the sheer abundance of roots in mangrove habitat, such an effect can have an important impact on the maintenance of bacterial guilds involved in nutrient cycling and other key ecosystem functions. Surprisingly, we also noted a marked impact of initial nursery conditions on the rhizosphere bacterial composition of replanted mangrove trees. This result is intriguing because mangroves are periodically inundated with seawater and represent a highly dynamic environment compared to the more controlled nursery environment. Conclusions/Significance In as far as microbial diversity and composition influences plant growth and health, this study indicates that nursery conditions and early microbial colonization patterns of the replants are key factors that should be considered during reforestation projects. In addition to this, our results provide information on the role of the mangrove rhizosphere as a habitat for bacteria from estuarine sediments.
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Affiliation(s)
- Newton C M Gomes
- CESAM and Department of Biology, University of Aveiro, Aveiro, Portugal.
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