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Cisneros de la Cueva S, Jaimes Zuñiga SC, Pérez Vega SB, Mendoza Chacon J, Salmerón Ochoa I, Quintero Ramos A. Effect of the addition of an inorganic carbon source on the degradation of sotol vinasse by Rhodopseudomonastelluris. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 355:120350. [PMID: 38422846 DOI: 10.1016/j.jenvman.2024.120350] [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: 09/30/2023] [Revised: 01/13/2024] [Accepted: 02/08/2024] [Indexed: 03/02/2024]
Abstract
The difficulty of the microbial conversion process for the degradation of sotol vinasse due to its high acidity and organic load makes it an effluent with high potential for environmental contamination, therefore its treatment is of special interest. Calcium carbonate is found in great abundance and has the ability to act as a neutralizing agent, maintaining the alkalinity of the fermentation medium as well as, through its dissociation, releasing CO2 molecules that can be used by phototrophic CO2-fixing bacteria. This study evaluated the use of Rhodopseudomonas telluris (OR069658) for the degradation of vinasse in different concentrations of calcium carbonate (0, 2, 4, 6, 8 and 10% m/v). The results showed that calcium carbonate concentration influenced volatile fatty acids (VFA), alkalinity and pH, which in turn influenced changes in the degradation of chemical oxygen demand (COD), phenol and sulfate. Maximum COD and phenol degradation values of 83.16 ± 0.15% and 90.16 ± 0.30%, respectively, were obtained at a calcium carbonate concentration of 4%. At the same time, the lowest COD and phenol degradation values of 52.01 ± 0.38% and 68.21 ± 0.81%, respectively, were obtained at a calcium carbonate concentration of 0%. The data obtained also revealed to us that at high calcium carbonate concentrations of 6-10%, sotol vinasse can be biosynthesized by Rhodopseudomonas telluris (OR069658) to VFA, facilitating the degradation of sulfates. The findings of this study confirmed the potential for using Rhodopseudomonas telluris (OR069658) at a calcium carbonate concentration of 4% as an appropriate alternative treatment for sotol vinasse degradation.
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Affiliation(s)
- Sergio Cisneros de la Cueva
- Faculty of Chemical Sciences, Autonomous University of Chihuahua, Address: Circuit 1, New University Campus, 31125, Chihuahua, Chih., Mexico.
| | - Sara Citlaly Jaimes Zuñiga
- Faculty of Chemical Sciences, Autonomous University of Chihuahua, Address: Circuit 1, New University Campus, 31125, Chihuahua, Chih., Mexico
| | - Samuel Bernardo Pérez Vega
- Faculty of Chemical Sciences, Autonomous University of Chihuahua, Address: Circuit 1, New University Campus, 31125, Chihuahua, Chih., Mexico
| | - Johan Mendoza Chacon
- Faculty of Chemical Sciences, Autonomous University of Chihuahua, Address: Circuit 1, New University Campus, 31125, Chihuahua, Chih., Mexico
| | - Iván Salmerón Ochoa
- Faculty of Chemical Sciences, Autonomous University of Chihuahua, Address: Circuit 1, New University Campus, 31125, Chihuahua, Chih., Mexico
| | - Armando Quintero Ramos
- Faculty of Chemical Sciences, Autonomous University of Chihuahua, Address: Circuit 1, New University Campus, 31125, Chihuahua, Chih., Mexico
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Zehnle H, Otersen C, Benito Merino D, Wegener G. Potential for the anaerobic oxidation of benzene and naphthalene in thermophilic microorganisms from the Guaymas Basin. Front Microbiol 2023; 14:1279865. [PMID: 37840718 PMCID: PMC10570749 DOI: 10.3389/fmicb.2023.1279865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 09/13/2023] [Indexed: 10/17/2023] Open
Abstract
Unsubstituted aromatic hydrocarbons (UAHs) are recalcitrant molecules abundant in crude oil, which is accumulated in subsurface reservoirs and occasionally enters the marine environment through natural seepage or human-caused spillage. The challenging anaerobic degradation of UAHs by microorganisms, in particular under thermophilic conditions, is poorly understood. Here, we established benzene- and naphthalene-degrading cultures under sulfate-reducing conditions at 50°C and 70°C from Guaymas Basin sediments. We investigated the microorganisms in the enrichment cultures and their potential for UAH oxidation through short-read metagenome sequencing and analysis. Dependent on the combination of UAH and temperature, different microorganisms became enriched. A Thermoplasmatota archaeon was abundant in the benzene-degrading culture at 50°C, but catabolic pathways remained elusive, because the archaeon lacked most known genes for benzene degradation. Two novel species of Desulfatiglandales bacteria were strongly enriched in the benzene-degrading culture at 70°C and in the naphthalene-degrading culture at 50°C. Both bacteria encode almost complete pathways for UAH degradation and for downstream degradation. They likely activate benzene via methylation, and naphthalene via direct carboxylation, respectively. The two species constitute the first thermophilic UAH degraders of the Desulfatiglandales. In the naphthalene-degrading culture incubated at 70°C, a Dehalococcoidia bacterium became enriched, which encoded a partial pathway for UAH degradation. Comparison of enriched bacteria with related genomes from environmental samples indicated that pathways for benzene degradation are widely distributed, while thermophily and capacity for naphthalene activation are rare. Our study highlights the capacities of uncultured thermophilic microbes for UAH degradation in petroleum reservoirs and in contaminated environments.
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Affiliation(s)
- Hanna Zehnle
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Carolin Otersen
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - David Benito Merino
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Gunter Wegener
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
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Yang K, Zhao Y, Ji M, Li Z, Zhai S, Zhou X, Wang Q, Wang C, Liang B. Challenges and opportunities for the biodegradation of chlorophenols: Aerobic, anaerobic and bioelectrochemical processes. WATER RESEARCH 2021; 193:116862. [PMID: 33550168 DOI: 10.1016/j.watres.2021.116862] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 01/17/2021] [Accepted: 01/20/2021] [Indexed: 06/12/2023]
Abstract
Chlorophenols (CPs) are highly toxic and refractory contaminants which widely exist in various environments and cause serious harm to human and environment health and safety. This review provides comprehensive information on typical CPs biodegradation technologies, the most green and benign ones for CPs removal. The known aerobic and anaerobic degradative bacteria, functional enzymes, and metabolic pathways of CPs as well as several improving methods and critical parameters affecting the overall degradation efficiency are systematically summarized and clarified. The challenges for CPs mineralization are also discussed, mainly including the dechlorination of polychlorophenols (poly-CPs) under aerobic condition and the ring-cleavage of monochlorophenols (MCPs) under anaerobic condition. The coupling of functional materials and degraders as well as the operation of sequential anaerobic-aerobic bioreactors and bioelectrochemical system (BES) are promising strategies to overcome some current limitations. Future perspective and research gaps in this field are also proposed, including the further understanding of microbial information and the specific role of materials in CPs biodegradation, the potential application of innovative biotechnologies and new operating modes to optimize and maximize the function of the system, and the scale-up of bioreactors towards the efficient biodegradation of CPs.
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Affiliation(s)
- Kaichao Yang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Yingxin Zhao
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China.
| | - Min Ji
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Zhiling Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Siyuan Zhai
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Xu Zhou
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Qian Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Can Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Bin Liang
- School of Civil & Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China; State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China.
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Chen Q, Jia R, Li L, Qu D. Effects of high concentrations of sulfate on dissolved organic matter in paddy soils revealed by excitation-emission matrix analyzing. CHEMOSPHERE 2020; 249:126207. [PMID: 32088458 DOI: 10.1016/j.chemosphere.2020.126207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 02/10/2020] [Accepted: 02/12/2020] [Indexed: 06/10/2023]
Abstract
The problem of sulfate pollution is becoming increasingly serious in freshwater and wetlands. Since paddy fields are the largest constructed wetland in Earth's surface, the increased sulfate input may have great effect on dissolved organic matter (DOM) in paddy soils. To understand these effects, a 24-day anaerobic incubation experiment was conducted with four Chinese paddy soils amended with high concentrations (0, 10, 25, 50, and 100 mmol L-1) of Na2SO4. Dissolved organic carbon (DOC) and chlorophyll a (Chl a) concentrations were determined after incubation. Parallel factor analysis (PARAFAC) of the excitation-emission matrix (EEM) spectra was used to analyze the DOM composition. In all four soils, DOC concentrations generally increased with increasing sulfate concentration, while the Chl a concentrations decreased. The EEM spectra of DOM were resolved into four components by PARAFAC. With increasing sulfate concentration, the proportion of the ultraviolet C humic acid-like compound decreased and the tyrosine-like compound increased in two algae-rich soils (Sichuan and Tianjin). No obvious variation was observed in the humification index (HIX) or the ratio of peak β to peak α (β:α) in any soils with added sulfate. Specific ultra-violet absorbance at 254 nm (SUVA254) decreased with increasing sulfate concentration in Jilin, Tianjin, and Ningxia soils, and the fluorescence index (FI) decreased in two algae-rich soils. In conclusion, although sulfate addition increased the DOC concentration, the DOM composition depended more strongly on soil type and physicochemical properties than sulfate. Sulfate addition only affected soil DOM origin and composition by inhibiting algal growth in algae-rich paddy soils.
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Affiliation(s)
- Qin Chen
- Northwest Land and Resources Research Center, Shaanxi Normal University, Xi'an, 710119, People's Republic of China
| | - Rong Jia
- College of Natural Resources and Environment, Northwest A & F University, Yangling, 712100, People's Republic of China; Key Laboratory of Land Resources Evaluation and Monitoring in Southwest, Ministry of Education, Sichuan Normal University, Chengdu, 610066, People's Republic of China
| | - Lina Li
- College of Natural Resources and Environment, Northwest A & F University, Yangling, 712100, People's Republic of China; College of Resources and Environment, Shanxi Agricultural University, Taigu, 030801, People's Republic of China
| | - Dong Qu
- College of Natural Resources and Environment, Northwest A & F University, Yangling, 712100, People's Republic of China.
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Čanković M, Žučko J, Radić ID, Janeković I, Petrić I, Ciglenečki I, Collins G. Microbial diversity and long-term geochemical trends in the euxinic zone of a marine, meromictic lake. Syst Appl Microbiol 2019; 42:126016. [PMID: 31635887 DOI: 10.1016/j.syapm.2019.126016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 08/30/2019] [Accepted: 09/07/2019] [Indexed: 01/04/2023]
Abstract
Hypoxic and anoxic niches of meromictic lakes are important sites for studying the microbial ecology of conditions resembling ancient Earth. The expansion and increasing global distribution of such environments also means that information about them serves to understand future phenomena. In this study, a long-term chemical dataset (1996-2015) was explored together with seasonal (in 2015) information on the diversity and abundance of bacterial and archaeal communities residing in the chemocline, monimolimnion and surface sediment of the marine meromictic Rogoznica Lake. The results of quantitative PCR assays, and high-throughput sequencing, targeting 16S rRNA genes and transcripts, revealed a clear vertical structure of the microbial community with Gammaproteobacteria (Halochromatium) and cyanobacteria (Synechococcus spp.) dominating the chemocline, Deltaproteobacteria and Bacteroidetes dominating the monimolimnion, and significantly more abundant archaeal populations in the surface sediment, most of which affiliated to Nanoarchaeota. Seasonal changes in the community structure and abundance were not pronounced. Diversity in Rogoznica Lake was found to be high, presumably as a consequence of stable environmental conditions accompanied by high dissolved carbon and nutrient concentrations. Long-term data indicated that Rogoznica Lake exhibited climate changes that could alter its physico-chemical features and, consequently, induce structural and physiological changes within its microbial community.
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Affiliation(s)
- Milan Čanković
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia.
| | - Jurica Žučko
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10 000 Zagreb, Croatia
| | - Iris Dupčić Radić
- Institute for Marine and Coastal Research, University of Dubrovnik, Ul. kneza Damjana Jude 12, 20 000, Dubrovnik, Croatia
| | - Ivica Janeković
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia
| | - Ines Petrić
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia
| | - Irena Ciglenečki
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia
| | - Gavin Collins
- Microbial Communities Laboratory, Microbiology, School of Natural Sciences, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
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Zhuang L, Tang Z, Ma J, Yu Z, Wang Y, Tang J. Enhanced Anaerobic Biodegradation of Benzoate Under Sulfate-Reducing Conditions With Conductive Iron-Oxides in Sediment of Pearl River Estuary. Front Microbiol 2019; 10:374. [PMID: 30881355 PMCID: PMC6406033 DOI: 10.3389/fmicb.2019.00374] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 02/13/2019] [Indexed: 12/12/2022] Open
Abstract
Anaerobic biodegradation of aromatic compounds under sulfate-reducing conditions is important to marine sediments. Sulfate respiration by a single bacterial strain and syntrophic metabolism by a syntrophic bacterial consortium are primary strategies for sulfate-dependent biodegradation of aromatic compounds. The objective of this study was to investigate the potential of conductive iron oxides to facilitate the degradation of aromatic compounds under sulfate-reducing conditions in marine sediments, using benzoate as a model aromatic compound. Here, in anaerobic incubations of sediments from the Pearl River Estuary, the addition of hematite or magnetite (20 mM as Fe atom) enhanced the rates of sulfate-dependent benzoate degradation by 81.8 and 91.5%, respectively, compared with control incubations without iron oxides. Further experiments demonstrated that the rate of sulfate-dependent benzoate degradation accelerated with increased magnetite concentration (5, 10, and 20 mM). The detection of acetate as an intermediate product implied syntrophic benzoate degradation pathway, which was also supported by the abundance of putative acetate- or/and H2-utilizing sulfate reducers from microbial community analysis. Microbial reduction of iron oxides under sulfate-reducing conditions only accounted for 2–11% of electrons produced by benzoate oxidation, thus the stimulatory effect of conductive iron oxides on sulfate-dependent benzoate degradation was not mainly due to an increased pool of terminal electron acceptors. The enhanced rates of syntrophic benzoate degradation by the presence of conductive iron oxides probably resulted from the establishment of a direct interspecies electron transfer (DIET) between syntrophic partners. In the presence of magnetite, Bacteroidetes and Desulfobulbaceae with potential function of extracellular electron transfer might be involved in syntrophic benzoate degradation. Results from this study will contribute to the development of new strategies for in situ bioremediation of anaerobic sediments contaminated with aromatic compounds, and provide a new perspective for the natural attenuation of aromatic compounds in iron-rich marine sediments.
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Affiliation(s)
- Li Zhuang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, China
| | - Ziyang Tang
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-environmental Science and Technology, Guangzhou, China
| | - Jinlian Ma
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-environmental Science and Technology, Guangzhou, China
| | - Zhen Yu
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-environmental Science and Technology, Guangzhou, China
| | - Yueqiang Wang
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-environmental Science and Technology, Guangzhou, China
| | - Jia Tang
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-environmental Science and Technology, Guangzhou, China
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Shin B, Kim M, Zengler K, Chin KJ, Overholt WA, Gieg LM, Konstantinidis KT, Kostka JE. Anaerobic degradation of hexadecane and phenanthrene coupled to sulfate reduction by enriched consortia from northern Gulf of Mexico seafloor sediment. Sci Rep 2019; 9:1239. [PMID: 30718896 PMCID: PMC6361983 DOI: 10.1038/s41598-018-36567-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 11/12/2018] [Indexed: 11/16/2022] Open
Abstract
To advance understanding of the fate of hydrocarbons released from the Deepwater Horizon oil spill and deposited in marine sediments, this study characterized the microbial populations capable of anaerobic hydrocarbon degradation coupled with sulfate reduction in non-seep sediments of the northern Gulf of Mexico. Anaerobic, sediment-free enrichment cultures were obtained with either hexadecane or phenanthrene as sole carbon source and sulfate as a terminal electron acceptor. Phylogenetic analysis revealed that enriched microbial populations differed by hydrocarbon substrate, with abundant SSU rRNA gene amplicon sequences from hexadecane cultures showing high sequence identity (up to 98%) to Desulfatibacillum alkenivorans (family Desulfobacteraceae), while phenanthrene-enriched populations were most closely related to Desulfatiglans spp. (up to 95% sequence identity; family Desulfarculaceae). Assuming complete oxidation to CO2, observed stoichiometric ratios closely resembled the theoretical ratios of 12.25:1 for hexadecane and 8.25:1 for phenanthrene degradation coupled to sulfate reduction. Phenanthrene carboxylic acid was detected in the phenanthrene-degrading enrichment cultures, providing evidence to indicate carboxylation as an activation mechanism for phenanthrene degradation. Metagenome-assembled genomes (MAGs) revealed that phenanthrene degradation is likely mediated by novel genera or families of sulfate-reducing bacteria along with their fermentative syntrophic partners, and candidate genes linked to the degradation of aromatic hydrocarbons were detected for future study.
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Affiliation(s)
- Boryoung Shin
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, 30332, USA
| | - Minjae Kim
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, 30332, USA
| | - Karsten Zengler
- Department of Pediatrics, University of California, San Diego, 92093, USA
- Center for Microbiome Innovation, University of California, San Diego, 92093, USA
| | - Kuk-Jeong Chin
- Department of Biology, Georgia State University, Atlanta, 30302, USA
| | - Will A Overholt
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, 30332, USA
| | - Lisa M Gieg
- Department of Biological Sciences, University of Calgary, Calgary, T2N 1N4, Canada
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, 30332, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, 30332, USA
| | - Joel E Kostka
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, 30332, USA.
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, 30332, USA.
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Jochum LM, Schreiber L, Marshall IPG, Jørgensen BB, Schramm A, Kjeldsen KU. Single-Cell Genomics Reveals a Diverse Metabolic Potential of Uncultivated Desulfatiglans-Related Deltaproteobacteria Widely Distributed in Marine Sediment. Front Microbiol 2018; 9:2038. [PMID: 30233524 PMCID: PMC6129605 DOI: 10.3389/fmicb.2018.02038] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 08/13/2018] [Indexed: 11/13/2022] Open
Abstract
Desulfatiglans-related organisms comprise one of the most abundant deltaproteobacterial lineages in marine sediments where they occur throughout the sediment column in a gradient of increasing sulfate and organic carbon limitation with depth. Characterized Desulfatiglans isolates are dissimilatory sulfate reducers able to grow by degrading aromatic hydrocarbons. The ecophysiology of environmental Desulfatiglans-populations is poorly understood, however, possibly utilization of aromatic compounds may explain their predominance in marine subsurface sediments. We sequenced and analyzed seven Desulfatiglans-related single-cell genomes (SAGs) from Aarhus Bay sediments to characterize their metabolic potential with regard to aromatic compound degradation and energy metabolism. The average genome assembly size was 1.3 Mbp and completeness estimates ranged between 20 and 50%. Five of the SAGs (group 1) originated from the sulfate-rich surface part of the sediment while two (group 2) originated from sulfate-depleted subsurface sediment. Based on 16S rRNA gene amplicon sequencing group 2 SAGs represent the more frequent types of Desulfatiglans-populations in Aarhus Bay sediments. Genes indicative of aromatic compound degradation could be identified in both groups, but the two groups were metabolically distinct with regard to energy conservation. Group 1 SAGs carry a full set of genes for dissimilatory sulfate reduction, whereas the group 2 SAGs lacked any genetic evidence for sulfate reduction. The latter may be due to incompleteness of the SAGs, but as alternative energy metabolisms group 2 SAGs carry the genetic potential for growth by acetogenesis and fermentation. Group 1 SAGs encoded reductive dehalogenase genes, allowing them to access organohalides and possibly conserve energy by their reduction. Both groups possess sulfatases unlike their cultured relatives allowing them to utilize sulfate esters as source of organic carbon and sulfate. In conclusion, the uncultivated marine Desulfatiglans populations are metabolically diverse, likely reflecting different strategies for coping with energy and sulfate limitation in the subsurface seabed.
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Affiliation(s)
- Lara M Jochum
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Lars Schreiber
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Ian P G Marshall
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Bo B Jørgensen
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Andreas Schramm
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Kasper U Kjeldsen
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
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Enzymes involved in the anaerobic degradation of phenol by the sulfate-reducing bacterium Desulfatiglans anilini. BMC Microbiol 2018; 18:93. [PMID: 30157755 PMCID: PMC6114531 DOI: 10.1186/s12866-018-1238-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 08/17/2018] [Indexed: 11/11/2022] Open
Abstract
Background The sulfate-reducing bacterium Desulfatiglans anilini can grow with phenol as sole source of carbon and energy under strictly anaerobic, sulfate-reducing conditions. In the nitrate-reducing bacterium Thauera aromatica, the enzymes involved in phenol degradation have been well elucidated, whereas the anaerobic phenol degradation pathway by D. anilini was not studied in detail yet. Results The pathway of anaerobic phenol degradation by the sulfate-reducing bacterium Desulfatiglans anilini was studied by identification of genes coding for phenylphosphate synthase (encoded by pps genes) and phenylphosphate carboxylase (encoded by ppc genes) in the genome of D. anilini, by analysis of the transcription and translation of pps-ppc genes, and by measurement of phenylphosphate synthase activity in cell-free extracts of phenol-grown cells. The majority of genes involved in phenol degradation were found to be organized in one gene cluster. The gene cluster contained genes ppsα (phenylphosphate synthase alpha subunit), ppsβ (phenylphosphate synthase beta subunit), ppcβ (phenylphosphate carboxylase beta subunit), as well as 4-hydroxybenzoyl-CoA ligase and 4-hydroxylbenzoyl-CoA reductase-encoding genes. The genes ppsγ (phenylphosphate synthase gamma subunit), ppcα (phenylphosphate carboxylase alpha subunit) and ppcδ (phenylphosphate carboxylase delta subunit) were located elsewhere in the genome of D. anilini, and no obvious homologue of ppcγ (phenylphosphate carboxylase gamma subunit) was found in the genome. Induction of genes pps and ppc during growth on phenol was confirmed by reverse transcription polymerase chain reaction. Total proteome analysis revealed that the abundance of enzymes encoded by the gene cluster under study was much higher in phenol-grown cells than that in benzoate-grown cells. In in-vitro enzyme assays with cell-free extracts of phenol-grown cells, phenylphosphate was formed from phenol in the presence of ATP, Mg2+, Mn2+, K+ as co-factors. Conclusions The genes coding for enzymes involved in the anaerobic phenol degradation pathway were identified in the sulfate-reducing bacterium D. anilini. The results indicate that the first steps of anaerobic phenol degradation in D. anilini are phosphorylation of phenol to phenylphosphate by phenylphosphate synthase and carboxylation of phenylphosphate by phenylphosphate carboxylase. Electronic supplementary material The online version of this article (10.1186/s12866-018-1238-0) contains supplementary material, which is available to authorized users.
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Ju F, Wang Y, Zhang T. Bioreactor microbial ecosystems with differentiated methanogenic phenol biodegradation and competitive metabolic pathways unraveled with genome-resolved metagenomics. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:135. [PMID: 29774049 PMCID: PMC5946492 DOI: 10.1186/s13068-018-1136-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 04/29/2018] [Indexed: 05/07/2023]
Abstract
BACKGROUND Methanogenic biodegradation of aromatic compounds depends on syntrophic metabolism. However, metabolic enzymes and pathways of uncultured microorganisms and their ecological interactions with methanogenic consortia are unknown because of their resistance to isolation and limited genomic information. RESULTS Genome-resolved metagenomics approaches were used to reconstruct and dissect 23 prokaryotic genomes from 37 and 20 °C methanogenic phenol-degrading reactors. Comparative genomic evidence suggests that temperature difference leads to the colonization of two distinct cooperative sub-communities that can respire sulfate/sulfite/sulfur or nitrate/nitrite compounds and compete for uptake of methanogenic substrates (e.g., acetate and hydrogen). This competition may differentiate methanogenesis. The uncultured ε-Proteobacterium G1, whose close relatives have broad ecological niches including the deep-sea vents, aquifers, sediment, limestone caves, spring, and anaerobic digesters, is implicated as a Sulfurovum-like facultative anaerobic diazotroph with metabolic versatility and remarkable environmental adaptability. We provide first genomic evidence for butyrate, alcohol, and carbohydrate utilization by a Chloroflexi T78 clade bacterium, and phenol carboxylation and assimilatory sulfite reduction in a Cryptanaerobacter bacterium. CONCLUSION Genome-resolved metagenomics enriches our view on the differentiation of microbial community composition, metabolic pathways, and ecological interactions in temperature-differentiated methanogenic phenol-degrading bioreactors. These findings suggest optimization strategies for methanogenesis on phenol, such as temperature control, protection from light, feed desulfurization, and hydrogen sulfide removal from bioreactors. Moreover, decoding genome-borne properties (e.g., antibiotic, arsenic, and heavy metal resistance) of uncultured bacteria help to bring up alternative schemes to isolate them.
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Affiliation(s)
- Feng Ju
- Environmental Biotechnology Lab, The University of Hong Kong SAR, Pokfulam Road, Hong Kong, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Westlake University, Hangzhou, 310064 People’s Republic of China
| | - Yubo Wang
- Environmental Biotechnology Lab, The University of Hong Kong SAR, Pokfulam Road, Hong Kong, China
| | - Tong Zhang
- Environmental Biotechnology Lab, The University of Hong Kong SAR, Pokfulam Road, Hong Kong, China
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Kynadi AS, Suchithra TV. Bacterial Degradation of Phenol to Control Environmental Pollution. Microb Biotechnol 2017. [DOI: 10.1007/978-981-10-6847-8_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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12
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Zhou W, Guo W, Zhou H, Chen X. Phenol degradation by Sulfobacillus acidophilus TPY via the meta -pathway. Microbiol Res 2016; 190:37-45. [DOI: 10.1016/j.micres.2016.05.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 05/11/2016] [Accepted: 05/13/2016] [Indexed: 11/30/2022]
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13
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Meckenstock RU, Boll M, Mouttaki H, Koelschbach JS, Cunha Tarouco P, Weyrauch P, Dong X, Himmelberg AM. Anaerobic Degradation of Benzene and Polycyclic Aromatic Hydrocarbons. J Mol Microbiol Biotechnol 2016; 26:92-118. [DOI: 10.1159/000441358] [Citation(s) in RCA: 180] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Aromatic hydrocarbons such as benzene and polycyclic aromatic hydrocarbons (PAHs) are very slowly degraded without molecular oxygen. Here, we review the recent advances in the elucidation of the first known degradation pathways of these environmental hazards. Anaerobic degradation of benzene and PAHs has been successfully documented in the environment by metabolite analysis, compound-specific isotope analysis and microcosm studies. Subsequently, also enrichments and pure cultures were obtained that anaerobically degrade benzene, naphthalene or methylnaphthalene, and even phenanthrene, the largest PAH currently known to be degradable under anoxic conditions. Although such cultures grow very slowly, with doubling times of around 2 weeks, and produce only very little biomass in batch cultures, successful proteogenomic, transcriptomic and biochemical studies revealed novel degradation pathways with exciting biochemical reactions such as for example the carboxylation of naphthalene or the ATP-independent reduction of naphthoyl-coenzyme A. The elucidation of the first anaerobic degradation pathways of naphthalene and methylnaphthalene at the genetic and biochemical level now opens the door to studying the anaerobic metabolism and ecology of anaerobic PAH degraders. This will contribute to assessing the fate of one of the most important contaminant classes in anoxic sediments and aquifers.
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Wei X, Gilevska T, Wetzig F, Dorer C, Richnow HH, Vogt C. Characterization of phenol and cresol biodegradation by compound-specific stable isotope analysis. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2016; 210:166-73. [PMID: 26716730 DOI: 10.1016/j.envpol.2015.11.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 10/21/2015] [Accepted: 11/02/2015] [Indexed: 05/06/2023]
Abstract
Microbial degradation of phenol and cresols can occur under oxic and anoxic conditions by different degradation pathways. One recent technique to take insight into reaction mechanisms is compound-specific isotope analysis (CSIA). While enzymes and reaction mechanisms of several degradation pathways have been characterized in (bio)chemical studies, associated isotope fractionation patterns have been rarely reported, possibly due to constraints in current analytical methods. In this study, carbon enrichment factors and apparent kinetic isotope effects (AKIEc) of the initial steps of different aerobic and anaerobic phenol and cresols degradation pathways were analyzed by isotope ratio mass spectrometry connected with liquid chromatography (LC-IRMS). Significant isotope fractionation was detected for aerobic ring hydroxylation, anoxic side chain hydroxylation, and anoxic fumarate addition, while anoxic carboxylation reactions produced small and inconsistent fractionation. The results suggest that several microbial degradation pathways of phenol and cresols are detectable in the environment by CSIA.
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Affiliation(s)
- Xi Wei
- Helmholtz Centre for Environmental Research - UFZ, Department of Isotope Biogeochemistry, Leipzig, Germany; Friedrich Schiller University Jena, Institute for Microbiology, Department of Applied and Ecological Microbiology, Jena, Germany
| | - Tetyana Gilevska
- Helmholtz Centre for Environmental Research - UFZ, Department of Isotope Biogeochemistry, Leipzig, Germany
| | - Felix Wetzig
- Helmholtz Centre for Environmental Research - UFZ, Department of Isotope Biogeochemistry, Leipzig, Germany; Friedrich Schiller University Jena, Faculty of Chemistry and Earth Science, Jena, Germany
| | - Conrad Dorer
- Helmholtz Centre for Environmental Research - UFZ, Department of Isotope Biogeochemistry, Leipzig, Germany; University of Freiburg, Faculty of Biology, Schänzlestrasse 1, Freiburg, Germany
| | - Hans-Hermann Richnow
- Helmholtz Centre for Environmental Research - UFZ, Department of Isotope Biogeochemistry, Leipzig, Germany
| | - Carsten Vogt
- Helmholtz Centre for Environmental Research - UFZ, Department of Isotope Biogeochemistry, Leipzig, Germany.
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15
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Steen IH, Dahle H, Stokke R, Roalkvam I, Daae FL, Rapp HT, Pedersen RB, Thorseth IH. Novel Barite Chimneys at the Loki's Castle Vent Field Shed Light on Key Factors Shaping Microbial Communities and Functions in Hydrothermal Systems. Front Microbiol 2016; 6:1510. [PMID: 26779165 PMCID: PMC4703759 DOI: 10.3389/fmicb.2015.01510] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/14/2015] [Indexed: 01/23/2023] Open
Abstract
In order to fully understand the cycling of elements in hydrothermal systems it is critical to understand intra-field variations in geochemical and microbiological processes in both focused, high-temperature and diffuse, low-temperature areas. To reveal important causes and effects of this variation, we performed an extensive chemical and microbiological characterization of a low-temperature venting area in the Loki's Castle Vent Field (LCVF). This area, located at the flank of the large sulfide mound, is characterized by numerous chimney-like barite (BaSO4) structures (≤ 1 m high) covered with white cotton-like microbial mats. Results from geochemical analyses, microscopy (FISH, SEM), 16S rRNA gene amplicon-sequencing and metatranscriptomics were compared to results from previous analyses of biofilms growing on black smoker chimneys at LCVF. Based on our results, we constructed a conceptual model involving the geochemistry and microbiology in the LCVF. The model suggests that CH4 and H2S are important electron donors for microorganisms in both high-temperature and low-temperature areas, whereas the utilization of H2 seems restricted to high-temperature areas. This further implies that sub-seafloor processes can affect energy-landscapes, elemental cycling, and the metabolic activity of primary producers on the seafloor. In the cotton-like microbial mats on top of the active barite chimneys, a unique network of single cells of Epsilonproteobacteria interconnected by threads of extracellular polymeric substances (EPS) was seen, differing significantly from the long filamentous Sulfurovum filaments observed in biofilms on the black smokers. This network also induced nucleation of barite crystals and is suggested to play an essential role in the formation of the microbial mats and the chimneys. Furthermore, it illustrates variations in how different genera of Epsilonproteobacteria colonize and position cells in different vent fluid mixing zones within a vent field. This may be related to niche-specific physical characteristics. Altogether, the model provides a reference for future studies and illustrates the importance of systematic comparative studies of spatially closely connected niches in order to fully understand the geomicrobiology of hydrothermal systems.
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Affiliation(s)
- Ida H Steen
- Centre for Geobiology, University of BergenBergen, Norway; Department of Biology, University of BergenBergen, Norway
| | - Håkon Dahle
- Centre for Geobiology, University of BergenBergen, Norway; Department of Biology, University of BergenBergen, Norway
| | - Runar Stokke
- Centre for Geobiology, University of BergenBergen, Norway; Department of Biology, University of BergenBergen, Norway
| | - Irene Roalkvam
- Centre for Geobiology, University of BergenBergen, Norway; Department of Biology, University of BergenBergen, Norway
| | - Frida-Lise Daae
- Centre for Geobiology, University of BergenBergen, Norway; Department of Biology, University of BergenBergen, Norway
| | - Hans Tore Rapp
- Centre for Geobiology, University of BergenBergen, Norway; Department of Biology, University of BergenBergen, Norway
| | - Rolf B Pedersen
- Centre for Geobiology, University of BergenBergen, Norway; Department of Earth Science, University of BergenBergen, Norway
| | - Ingunn H Thorseth
- Centre for Geobiology, University of BergenBergen, Norway; Department of Earth Science, University of BergenBergen, Norway
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16
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Guan Y, Hikmawan T, Antunes A, Ngugi D, Stingl U. Diversity of methanogens and sulfate-reducing bacteria in the interfaces of five deep-sea anoxic brines of the Red Sea. Res Microbiol 2015; 166:688-99. [PMID: 26192212 DOI: 10.1016/j.resmic.2015.07.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 07/02/2015] [Accepted: 07/02/2015] [Indexed: 11/24/2022]
Abstract
Oceanic deep hypersaline anoxic basins (DHABs) are characterized by drastic changes in physico-chemical conditions in the transition from overlaying seawater to brine body. Brine-seawater interfaces (BSIs) of several DHABs across the Mediterranean Sea have been shown to possess methanogenic and sulfate-reducing activities, yet no systematic studies have been conducted to address the potential functional diversity of methanogenic and sulfate-reducing communities in the Red Sea DHABs. Here, we evaluated the relative abundance of Bacteria and Archaea using quantitative PCR and conducted phylogenetic analyses of nearly full-length 16S rRNA genes as well as functional marker genes encoding the alpha subunits of methyl-coenzyme M reductase (mcrA) and dissimilatory sulfite reductase (dsrA). Bacteria predominated over Archaea in most locations, the majority of which were affiliated with Deltaproteobacteria, while Thaumarchaeota were the most prevalent Archaea in all sampled locations. The upper convective layers of Atlantis II Deep, which bear increasingly harsh environmental conditions, were dominated by members of the class Thermoplasmata (Marine Benthic Group E and Mediterranean Sea Brine Lakes Group 1). Our study revealed unique microbial compositions, the presence of niche-specific groups, and collectively, a higher diversity of sulfate-reducing communities compared to methanogenic communities in all five studied locations.
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Affiliation(s)
- Yue Guan
- Red Sea Research Center, King Abdullah University of Science and Technology, 23955-6900, Thuwal, Saudi Arabia
| | - Tyas Hikmawan
- Red Sea Research Center, King Abdullah University of Science and Technology, 23955-6900, Thuwal, Saudi Arabia
| | - André Antunes
- Computational Bioscience Research Centre, King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia
| | - David Ngugi
- Red Sea Research Center, King Abdullah University of Science and Technology, 23955-6900, Thuwal, Saudi Arabia
| | - Ulrich Stingl
- Red Sea Research Center, King Abdullah University of Science and Technology, 23955-6900, Thuwal, Saudi Arabia.
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A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes. Adv Microb Physiol 2015. [PMID: 26210106 DOI: 10.1016/bs.ampbs.2015.05.002] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Dissimilatory sulphate reduction is the unifying and defining trait of sulphate-reducing prokaryotes (SRP). In their predominant habitats, sulphate-rich marine sediments, SRP have long been recognized to be major players in the carbon and sulphur cycles. Other, more recently appreciated, ecophysiological roles include activity in the deep biosphere, symbiotic relations, syntrophic associations, human microbiome/health and long-distance electron transfer. SRP include a high diversity of organisms, with large nutritional versatility and broad metabolic capacities, including anaerobic degradation of aromatic compounds and hydrocarbons. Elucidation of novel catabolic capacities as well as progress in the understanding of metabolic and regulatory networks, energy metabolism, evolutionary processes and adaptation to changing environmental conditions has greatly benefited from genomics, functional OMICS approaches and advances in genetic accessibility and biochemical studies. Important biotechnological roles of SRP range from (i) wastewater and off gas treatment, (ii) bioremediation of metals and hydrocarbons and (iii) bioelectrochemistry, to undesired impacts such as (iv) souring in oil reservoirs and other environments, and (v) corrosion of iron and concrete. Here we review recent advances in our understanding of SRPs focusing mainly on works published after 2000. The wealth of publications in this period, covering many diverse areas, is a testimony to the large environmental, biogeochemical and technological relevance of these organisms and how much the field has progressed in these years, although many important questions and applications remain to be explored.
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Effects of Redox Mediators on Anaerobic Degradation of Phenol by Shewanella sp. XB. Appl Biochem Biotechnol 2015; 175:3162-72. [DOI: 10.1007/s12010-015-1490-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 01/12/2015] [Indexed: 01/05/2023]
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García-Solares SM, Ordaz A, Monroy-Hermosillo O, Jan-Roblero J, Guerrero-Barajas C. High sulfate reduction efficiency in a UASB using an alternative source of sulfidogenic sludge derived from hydrothermal vent sediments. Appl Biochem Biotechnol 2014; 174:2919-40. [PMID: 25234397 DOI: 10.1007/s12010-014-1237-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 09/10/2014] [Indexed: 10/24/2022]
Abstract
Sulfidogenesis in reactors is mostly achieved through adaptation of predominantly methanogenic granular sludge to sulfidogenesis. In this work, an upflow anaerobic sludge blanket (UASB) reactor operated under sulfate-reducing conditions was inoculated with hydrothermal vent sediments to carry out sulfate reduction using volatile fatty acids (VFAs) as substrate and chemical oxygen demand (COD)/SO4 (-2) ratios between 0.49 and 0.64. After a short period of adaptation, a robust non-granular sludge was capable of achieving high sulfate reduction efficiencies while avoiding competence with methanogens and toxicity to the microorganisms due to high sulfide concentration. The highest sulfide concentration (2,552 mg/L) was obtained with acetate/butyrate, and sulfate reduction efficiencies were up to 98 %. A mixture of acetate/butyrate, which produced a higher yielding of HS(-), was preferred over acetate/propionate/butyrate since the consumption of COD was minimized during the process. Sludge was analyzed, and some of the microorganisms identified in the sludge belong to the genera Desulfobacterium, Marinobacter, and Clostridium. The tolerance of the sludge to sulfide may be attributed to the syntrophy among these microorganisms, some of which have been reported to tolerate high concentrations of sulfide. To the best of our knowledge, this is the first report on the analysis of the direct utilization of hydrothermal vent sediments as an alternate source of sludge for sulfate reduction under high sulfide concentrations.
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Affiliation(s)
- Selene Montserrat García-Solares
- Departamento de Bioprocesos, Laboratorio de Biotecnología Ambiental, Unidad Profesional Interdisciplinaria de Biotecnología (UPIBI), Instituto Politécnico Nacional, Mexico City, 07340, Mexico
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Suzuki D, Li Z, Cui X, Zhang C, Katayama A. Reclassification of Desulfobacterium anilini as Desulfatiglans anilini comb. nov. within Desulfatiglans gen. nov., and description of a 4-chlorophenol-degrading sulfate-reducing bacterium, Desulfatiglans parachlorophenolica sp. nov. Int J Syst Evol Microbiol 2014; 64:3081-3086. [PMID: 24944334 DOI: 10.1099/ijs.0.064360-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A strictly anaerobic, mesophilic, sulfate-reducing bacterial strain (DS(T)), isolated from river sediment contaminated with volatile organic compounds, was characterized phenotypically and phylogenetically. Cells were Gram-reaction-negative, non-motile short rods. For growth, optimum NaCl concentration was 0.9 g l(-1), optimum temperature was 30 °C and optimum pH was 7.2. Strain DS(T) utilized phenol, benzoate, 4-hydroxybenzoate, 4-methylphenol, 4-chlorophenol, acetate, butyrate and pyruvate as electron donors for sulfate reduction. Electron donors were completely oxidized. Strain DS(T) did not utilize sulfite, thiosulfate or nitrate as electron acceptors. The genomic DNA G+C content of strain DS(T) was 58.9 mol%. Major cellular fatty acids were iso-C14 : 0, anteiso-C15 : 0 and C18 : 1ω7c. Phylogenetic analyses based on the 16S rRNA gene indicated its closest relatives were strains of Desulfobacterium anilini (about 98-99 % sequence similarity) but the DNA-DNA hybridization value with Desulfobacterium anilini Ani1(T) was around 40 %. Although strain DS(T) and its relatives shared most phenotypic and chemotaxonomic characteristics, the utilization of 4-chlorophenol, the range of electron acceptors and the optimum growth conditions differed. Strain DS(T) is closely related to strains of Desulfobacterium anilini, but constitutes a different species within the genus. Based on phylogeny, phenotypic characteristics and chemotaxonomic characteristics, strain DS(T) and Desulfobacterium anilini were clearly different from strains of other species of the genus Desulfobacterium. We thus propose the reclassification of Desulfobacterium anilini within a new genus, Desulfatiglans gen. nov., as Desulfatiglans anilini comb. nov. We also propose Desulfatiglans parachlorophenolica sp. nov. to accommodate strain DS(T). The type strain is DS(T) ( = JCM 19179(T) = DSM 27197(T)).
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Affiliation(s)
- Daisuke Suzuki
- EcoTopia Science Institute, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8603, Japan
| | - Zhiling Li
- School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090, PR China
| | - Xinxin Cui
- School of Engineering, Department of Civil Engineering and Architecture, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8603, Japan
| | - Chunfung Zhang
- Institute of Marine Biology, Ocean College, Zhejiang University, Hangzhou 310058, China.,EcoTopia Science Institute, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8603, Japan
| | - Arata Katayama
- EcoTopia Science Institute, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8603, Japan
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Philipp B, Schink B. Different strategies in anaerobic biodegradation of aromatic compounds: nitrate reducers versus strict anaerobes. ENVIRONMENTAL MICROBIOLOGY REPORTS 2012; 4:469-478. [PMID: 23760891 DOI: 10.1111/j.1758-2229.2011.00304.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Mononuclear aromatic compounds are degraded anaerobically through pathways that are basically different from those used in the presence of oxygen. Whereas aerobic degradation destabilizes the aromatic π-electron system by oxidative steps through oxygenase reactions, anaerobic degradation is most often initiated by a reductive attack. The benzoyl-CoA pathway is the most important metabolic route in this context, and a broad variety of mononuclear aromatics, including phenol, cresols, toluene, xylenes and ethylbenzene, are channelled into this pathway through various modification reactions. Multifunctional phenolic compounds are metabolized via the reductive resorcinol pathway, the oxidative resorcinol pathway with hydroxyhydroquinone as key intermediate, and the phloroglucinol pathway. Comparison of the various pathways used for modification and degradation of aromatics in the absence of oxygen indicates that the strategies of breakdown of these compounds are largely determined by the redox potentials of the electron acceptors used, and by the overall reaction energetics. Consequently, nitrate reducers quite often use strategies for primary attack on aromatic compounds that differ from those used by sulfate-reducing, iron-reducing or fermenting bacteria.
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Affiliation(s)
- Bodo Philipp
- Department of Biology, University of Konstanz, Universitätsstr. 10, D-78457 Konstanz, Germany
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Huang J, Wen Y, Ding N, Xu Y, Zhou Q. Fast start-up and stable performance coupled to sulfate reduction in the nitrobenzene bio-reduction system and its microbial community. BIORESOURCE TECHNOLOGY 2012; 114:201-206. [PMID: 22487131 DOI: 10.1016/j.biortech.2012.03.050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Revised: 03/14/2012] [Accepted: 03/16/2012] [Indexed: 05/31/2023]
Abstract
Three laboratory-scale sequence batch reactors were set up in this study. It was found that a successfully established sulfate-reducing system - operating at COD/SO42- ratio of 5.0 - could speed up the start-up process, leading to a high performance. It took about 100 and 60 days, respectively, for a non-sulfate-reducing system and a sulfate-reducing control system to achieve stable and high removal of NB. However, it maintained a complete NB removal in sulfate-reducing system throughout the study. Rapid and stable NB reduction was coupled to the on-going sulfate reducing process. Denaturing gradient gel electrophoresis profile demonstrated that the predominant bacterial groups in the non-sulfate-reducing system and the sulfate-reducing control system were affiliated to Deltaproteobacterium and Acinetobacter, while in the sulfate-reducing system were sulfate-reducing and sulfur-oxidizing bacteria.
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Affiliation(s)
- Jingang Huang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
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Key players and team play: anaerobic microbial communities in hydrocarbon-contaminated aquifers. Appl Microbiol Biotechnol 2012; 94:851-73. [PMID: 22476263 DOI: 10.1007/s00253-012-4025-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2012] [Revised: 03/13/2012] [Accepted: 03/14/2012] [Indexed: 02/06/2023]
Abstract
Biodegradation of anthropogenic pollutants in shallow aquifers is an important microbial ecosystem service which is mainly brought about by indigenous anaerobic microorganisms. For the management of contaminated sites, risk assessment and control of natural attenuation, the assessment of in situ biodegradation and the underlying microbial processes is essential. The development of novel molecular methods, "omics" approaches, and high-throughput techniques has revealed new insight into complex microbial communities and their functions in anoxic environmental systems. This review summarizes recent advances in the application of molecular methods to study anaerobic microbial communities in contaminated terrestrial subsurface ecosystems. We focus on current approaches to analyze composition, dynamics, and functional diversity of subsurface communities, to link identity to activity and metabolic function, and to identify the ecophysiological role of not yet cultured microbes and syntrophic consortia. We discuss recent molecular surveys of contaminated sites from an ecological viewpoint regarding degrader ecotypes, abiotic factors shaping anaerobic communities, and biotic interactions underpinning the importance of microbial cooperation for microbial ecosystem services such as contaminant degradation.
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