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Qiu S, Zhang X, Xia W, Li Z, Wang L, Chen Z, Ge S. Effect of extreme pH conditions on methanogenesis: Methanogen metabolism and community structure. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 877:162702. [PMID: 36898547 DOI: 10.1016/j.scitotenv.2023.162702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 03/03/2023] [Accepted: 03/03/2023] [Indexed: 05/06/2023]
Abstract
The control of pH is effective for inhibiting methanogenesis in the chain elongation fermentation (CEF) system. However, obscure conclusions exist especially with regard to the underlying mechanism. This study comprehensively explored the responses of methanogenesis in granular sludge at various pH levels, ranging from 4.0 to 10.0, from multiple aspects including methane production, methanogenesis pathway, microbial community structure, energy metabolism and electron transport. Results demonstrated that compared with that at pH 7.0, pH at 4.0, 5.5, 8.5 and 10.0 triggered a 100%, 71.7%, 23.8% and 92.1% suppression on methanogenesis by the end of 3 cycles lasting 21 days. This might be explained by the remarkably inhibited metabolic pathways and intracellular regulations. To be more specific, extreme pH conditions decreased the abundance of the acetoclastic methanogens. However, obligate hydrogenotrophic and facultative acetolactic/hydrogenotrophic methanogens were significantly enriched by 16.9%-19.5 fold. pH stress reduced the gene abundance and/or activity of most enzymes involved in methanogenesis such as acetate kinase (by 81.1%-93.1%), formylmethanofuran dehydrogenase (by 10.9%-54.0%) and tetrahydromethanopterin S-methyltransferase (by 9.3%-41.5%). Additionally, pH stress suppressed electron transport via improper electron carriers and decreased electron amount as evidenced by 46.3%-70.4% reduced coenzyme F420 content and diminished abundance of CO dehydrogenase (by 15.5%-70.5%) and NADH:ubiquinone reductase (by 20.2%-94.5%). pH stress also regulated energy metabolism with inhibited ATP synthesis (e.g., ATP citrate synthase level reduced by 20.1%-95.3%). Interestingly, the protein and carbohydrate content secreted in EPS failed to show consistent responses to acidic and alkaline conditions. Specifically, when compared with pH 7.0, the acidic condition remarkably reduced the levels of total EPS and EPS protein while both levels were enhanced in the alkaline condition. However, the EPS carbohydrate content at pH 4.0 and 10.0 both decreased. This study is expected to promote the understanding of the pH control-induced methanogenesis inhibition in the CEF system.
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Affiliation(s)
- Shuang Qiu
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Xiao Ling Wei 200, Nanjing 210094, Jiangsu, China
| | - Xingchen Zhang
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Xiao Ling Wei 200, Nanjing 210094, Jiangsu, China
| | - Wenhao Xia
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Xiao Ling Wei 200, Nanjing 210094, Jiangsu, China
| | - Zimu Li
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Xiao Ling Wei 200, Nanjing 210094, Jiangsu, China
| | - Lingfeng Wang
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Xiao Ling Wei 200, Nanjing 210094, Jiangsu, China
| | - Zhipeng Chen
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Xiao Ling Wei 200, Nanjing 210094, Jiangsu, China
| | - Shijian Ge
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Xiao Ling Wei 200, Nanjing 210094, Jiangsu, China.
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Qiu S, Xia W, Xu J, Li Z, Ge S. Impacts of 2-bromoethanesulfonic sodium on methanogenesis: Methanogen metabolism and community structure. WATER RESEARCH 2023; 230:119527. [PMID: 36580800 DOI: 10.1016/j.watres.2022.119527] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 12/14/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
Production of medium-chain carboxylic acids (MCCAs) by chain elongation (CE) presents a competitive alternative to conventional products of methane in anaerobic digestion treating organic waste streams, considering energy recovery, economic, and environmental profits. However, the system stability and performance largely rely on the selective suppression of methanogens while stimulation of CE bacteria. Commercial inhibitors such as 2-bromoethanesulfonic sodium (BES) was shown to be effective, but controversial conclusions exist on its inhibition characteristics and the inhibition mechanism remains unclear. Therefore, this study systematically investigated the responses of methanogenesis in granular sludge to various BES levels, focusing on methane production, methanogenic pathway, dynamic populations, electron transport and energy metabolism. Results showed that compared with the control, 3.0 g/L BES was sufficient to induce a 72.9% reduced level on accumulative methane production by the end of 4 cycles (28 days), which was likely to be attributed to the significantly suppressed metabolic pathways and intracellular regulations. Specifically, BES suppressed the electron transport via unproper electron carriers and reduced electron amount as indicated by the decreased level of enzymes and genes involved such as coenzyme F420, CO dehydrogenase and NADH:ubiquinone reductase (H+-translocating). Moreover, BES regulated the intracellular energy metabolism, leading to the impeded ATP synthesis but enhanced ATP consumption as evidenced by the variations on the activity or abundance of acetate kinase, A1Ao-ATP synthase, nitrogenase and ATP citrate synthase. Additionally, BES enriched hydrogenotrophic methanogenesis over acetoclastic one as supported by variations on the archaeal community structures and regulations of differentially expressed genes involved. Moreover, BES also reduced the contents of both protein and carbohydrate in extracellular polymeric substances (EPS). This study is expected to enhance understanding of BES contribution to methanogenesis inhibition but MCCAs production in CE bioreactors.
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Affiliation(s)
- Shuang Qiu
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Xiao Ling Wei 200, Nanjing 210094, Jiangsu, China
| | - Wenhao Xia
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Xiao Ling Wei 200, Nanjing 210094, Jiangsu, China
| | - Jiajie Xu
- School of Marine Science, Ningbo University, Ningbo 315211, China
| | - Zimu Li
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Xiao Ling Wei 200, Nanjing 210094, Jiangsu, China
| | - Shijian Ge
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Xiao Ling Wei 200, Nanjing 210094, Jiangsu, China.
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Su R, Zhou L, Ding L, Fu B, Fu H, Shuang Y, Ye L, Hu H, Ma H, Ren H. How anaerobic sludge microbiome respond to different concentrations of nitrite, nitrate, and ammonium ions: a comparative analysis. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:49026-49037. [PMID: 36763271 DOI: 10.1007/s11356-023-25704-3] [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: 09/15/2022] [Accepted: 01/30/2023] [Indexed: 02/11/2023]
Abstract
High concentrations of ammonium, nitrite, and nitrate always induce inhibition in anaerobic wastewater treatment. Due to the complexity and vulnerability of the microbial community (especially methanogens) in anaerobic sludge, little is understood about its underlying microbial mechanism under such inhibition. In this study, the shifts of microbial communities in anaerobic sludge under increasing levels of nitrite, nitrate, and ammonium ions were compared. Results show that although half maximal inhibitory concentrations (methanogenesis) were different for nitrite, nitrate, and ammonium ions with EC50 values of 12, 30, and 3000 mg N/L, respectively, bacteria genera Kosmotoga and Brooklawnia dominated in all of the three high-stress inhibitory systems. Network analysis and redundancy analysis (RDA) of the microbial community showed the treatments with nitrate and nitrite ions decreased the modularity of anaerobic microorganisms. RDA showed that specific methanogenic activity was positively related to coenzyme F420 under nitrite inhibition (rp = 0.833, p < 0.05) and closely correlated with viability under nitrate inhibition. Gram-positive and nonmotile Brooklawnia genus showed a negative correlation with physiological characteristics in the ammonia treatments, suggesting its high resistance to ammonia.
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Affiliation(s)
- Runhua Su
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing, 210023, China
| | - Lina Zhou
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing, 210023, China
| | - Lili Ding
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing, 210023, China.
| | - Bo Fu
- School of Environmental and Civil Engineering, Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Jiangnan University, Wuxi, 214122, China
| | - Huimin Fu
- National Research Base of Intelligent Manufacturing Service, Chongqing Technology and Business University, Chongqing, 400067, China
| | - Yanan Shuang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing, 210023, China
| | - Lin Ye
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing, 210023, China
| | - Haidong Hu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing, 210023, China
| | - Haijun Ma
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing, 210023, China
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing, 210023, China
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The pathway for coenzyme M biosynthesis in bacteria. Proc Natl Acad Sci U S A 2022; 119:e2207190119. [PMID: 36037354 PMCID: PMC9457059 DOI: 10.1073/pnas.2207190119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mercaptoethane sulfonate or coenzyme M (CoM) is the smallest known organic cofactor and is most commonly associated with the methane-forming step in all methanogenic archaea but is also associated with the anaerobic oxidation of methane to CO2 in anaerobic methanotrophic archaea and the oxidation of short-chain alkanes in Syntrophoarchaeum species. It has also been found in a small number of bacteria capable of the metabolism of small organics. Although many of the steps for CoM biosynthesis in methanogenic archaea have been elucidated, a complete pathway for the biosynthesis of CoM in archaea or bacteria has not been reported. Here, we present the complete CoM biosynthesis pathway in bacteria, revealing distinct chemical steps relative to CoM biosynthesis in methanogenic archaea. The existence of different pathways represents a profound instance of convergent evolution. The five-step pathway involves the addition of sulfite, the elimination of phosphate, decarboxylation, thiolation, and the reduction to affect the sequential conversion of phosphoenolpyruvate to CoM. The salient features of the pathway demonstrate reactivities for members of large aspartase/fumarase and pyridoxal 5'-phosphate-dependent enzyme families.
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Rajbongshi A, Gogoi SB. A review on anaerobic microorganisms isolated from oil reservoirs. World J Microbiol Biotechnol 2021; 37:111. [PMID: 34076736 DOI: 10.1007/s11274-021-03080-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 05/26/2021] [Indexed: 11/25/2022]
Abstract
The Role of microorganisms in the petroleum industry is wide-ranging. To understand the role of microorganisms in hydrocarbon transformation, identification of such microorganisms is vital, especially the ones capable of in situ degradation. Microorganisms play a pivotal role in the degradation of hydrocarbons and remediation of heavy metals. Anaerobic microorganisms such as Sulphate Reducing Bacteria (SRB), responsible for the production of hydrogen sulphide (H2S) within the reservoir, reduces the oil quality by causing reservoir souring and reduction in oil viscosity. This paper reviews the diversity of SRB, methanogens, Nitrogen Reducing Bacteria (NRB), and fermentative bacteria present in oil reservoirs. It also reviews the extensive diversity of these microorganisms, their applications in petroleum industries, characteristics and adaptability to survive in different conditions, the potential to alter the petroleum hydrocarbons properties, the propensity to petroleum hydrocarbon degradation, and remediation of metals.
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Affiliation(s)
- Amarjit Rajbongshi
- Brahmaputra Valley Fertilizer Corporation Limited, Namrup, Assam, India.
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Valente IM, Oliveira HM, Vaz CD, Ramos RM, Fonseca AJ, Cabrita AR, Rodrigues JA. Determination of ammonia nitrogen in solid and liquid high-complex matrices using one-step gas-diffusion microextraction and fluorimetric detection. Talanta 2017; 167:747-753. [DOI: 10.1016/j.talanta.2017.01.091] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 01/25/2017] [Accepted: 01/30/2017] [Indexed: 12/14/2022]
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van de Pol JAA, van Best N, Mbakwa CA, Thijs C, Savelkoul PH, Arts ICW, Hornef MW, Mommers M, Penders J. Gut Colonization by Methanogenic Archaea Is Associated with Organic Dairy Consumption in Children. Front Microbiol 2017; 8:355. [PMID: 28344572 PMCID: PMC5344914 DOI: 10.3389/fmicb.2017.00355] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 02/21/2017] [Indexed: 11/16/2022] Open
Abstract
The gut microbiota represents a complex and diverse ecosystem with a profound impact on human health, promoting immune maturation, and host metabolism as well as colonization resistance. Important members that have often been disregarded are the methanogenic archaea. Methanogenic archaea reduce hydrogen levels via the production of methane, thereby stimulating food fermentation by saccharolytic bacteria. On the other hand, colonization by archaea has been suggested to promote a number of gastrointestinal and metabolic diseases such as colorectal cancer, inflammatory bowel disease, and obesity. Archaea have been shown to be absent during infancy while omnipresent in school-aged children, suggesting that colonization may result from environmental exposure during childhood. The factors that determine the acquisition of methanogenic archaea, however, have remained undefined. Therefore, we aimed to explore determinants associated with the acquisition of the two main gastrointestinal archaeal species, Methanobrevibacter smithii and Methanosphaera stadtmanae, in children. Within the context of the KOALA Birth Cohort Study, fecal samples from 472 children aged 6–10 years were analyzed for the abundance of M. smithii and M. stadtmanae using qPCR. Environmental factors such as diet, lifestyle, hygiene, child rearing, and medication were recorded by repeated questionnaires. The relationship between these determinants and the presence and abundance of archaea was analyzed by logistic and linear regression respectively. Three hundred and sixty-nine out of the 472 children (78.2%) were colonized by M. smithii, and 39 out of the 472 children (8.3%) by M. stadtmanae. The consumption of organic yogurt (odds ratio: 4.25, CI95: 1.51; 11.95) and the consumption of organic milk (odds ratio: 5.58, CI95: 1.83; 17.01) were positively associated with the presence of M. smithii. We subsequently screened raw milk, processed milk, and yogurt samples for methanogens. We identified milk products as possible source for M. smithii, but not M. stadtmanae. In conclusion, M. smithii seems present in milk products and their consumption may determine archaeal gut colonization in children. For the first time, a large variety of determinants have been explored in association with gut colonization by methanogenic archaea. Although more information is needed to confirm and unravel the mechanisms in detail, it provides new insights on microbial colonization processes in early life.
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Affiliation(s)
- Jeroen A A van de Pol
- Department of Epidemiology, Care and Public Health Research Institute, Maastricht UniversityMaastricht, Netherlands; Department of Epidemiology, Grow - School for Oncology and Developmental Biology, Maastricht UniversityMaastricht, Netherlands
| | - Niels van Best
- Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism, Maastricht University Medical CentreMaastricht, Netherlands; Institute of Medical Microbiology, RWTH Aachen University HospitalAachen, Germany
| | - Catherine A Mbakwa
- Department of Epidemiology, Care and Public Health Research Institute, Maastricht University Maastricht, Netherlands
| | - Carel Thijs
- Department of Epidemiology, Care and Public Health Research Institute, Maastricht University Maastricht, Netherlands
| | - Paul H Savelkoul
- Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism, Maastricht University Medical CentreMaastricht, Netherlands; Department of Medical Microbiology, Care and Public Health Research Institute, Maastricht University Medical CentreMaastricht, Netherlands
| | - Ilja C W Arts
- Maastricht Centre for Systems Biology and Department of Epidemiology, School for Cardiovascular Diseases (CARIM), Maastricht University Maastricht, Netherlands
| | - Mathias W Hornef
- Institute of Medical Microbiology, RWTH Aachen University Hospital Aachen, Germany
| | - Monique Mommers
- Department of Epidemiology, Care and Public Health Research Institute, Maastricht University Maastricht, Netherlands
| | - John Penders
- Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism, Maastricht University Medical CentreMaastricht, Netherlands; Department of Medical Microbiology, Care and Public Health Research Institute, Maastricht University Medical CentreMaastricht, Netherlands
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Waghmode TR, Haque MM, Kim SY, Kim PJ. Effective Suppression of Methane Emission by 2-Bromoethanesulfonate during Rice Cultivation. PLoS One 2015; 10:e0142569. [PMID: 26562416 PMCID: PMC4642961 DOI: 10.1371/journal.pone.0142569] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 10/24/2015] [Indexed: 11/25/2022] Open
Abstract
2-bromoethanesulfonate (BES) is a structural analogue of coenzyme M (Co-M) and potent inhibitor of methanogenesis. Several studies confirmed, BES can inhibit CH4 prodcution in rice soil, but the suppressing effectiveness of BES application on CH4 emission under rice cultivation has not been studied. In this pot experiment, different levels of BES (0, 20, 40 and 80 mg kg-1) were applied to study its effect on CH4 emission and plant growth during rice cultivation. Application of BES effectively suppressed CH4 emission when compared with control soil during rice cultivation. The CH4 emission rates were significantly (P<0.001) decreased by BES application possibly due to significant (P<0.001) reduction of methnaogenic biomarkers like Co-M concentration and mcrA gene copy number (i.e. methanogenic abunadance). BES significantly (P<0.001) reduced methanogen activity, while it did not affect soil dehydrogenase activity during rice cultivation. A rice plant growth and yield parameters were not affected by BES application. The maximum CH4 reduction (49% reduction over control) was found at 80 mg kg-1 BES application during rice cultivation. It is, therefore, concluded that BES could be a suitable soil amendment for reducing CH4 emission without affecting rice plant growth and productivity during rice cultivation.
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Affiliation(s)
- Tatoba R. Waghmode
- Division of Applied Life Sciences (BK 21 PLUS program), Gyeongsang National University, Jinju 660–701, South Korea
| | - Md. Mozammel Haque
- Division of Applied Life Sciences (BK 21 PLUS program), Gyeongsang National University, Jinju 660–701, South Korea
| | - Sang Yoon Kim
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Wageningen, The Netherlands
| | - Pil Joo Kim
- Division of Applied Life Sciences (BK 21 PLUS program), Gyeongsang National University, Jinju 660–701, South Korea
- Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju 660–701, South Korea
- * E-mail:
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9
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Hori T, Haruta S, Sasaki D, Hanajima D, Ueno Y, Ogata A, Ishii M, Igarashi Y. Reorganization of the bacterial and archaeal populations associated with organic loading conditions in a thermophilic anaerobic digester. J Biosci Bioeng 2015; 119:337-44. [DOI: 10.1016/j.jbiosc.2014.09.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Revised: 07/28/2014] [Accepted: 09/02/2014] [Indexed: 10/24/2022]
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Ziegler S, Dolch K, Geiger K, Krause S, Asskamp M, Eusterhues K, Kriews M, Wilhelms-Dick D, Goettlicher J, Majzlan J, Gescher J. Oxygen-dependent niche formation of a pyrite-dependent acidophilic consortium built by archaea and bacteria. THE ISME JOURNAL 2013; 7:1725-37. [PMID: 23619304 PMCID: PMC3749503 DOI: 10.1038/ismej.2013.64] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 03/01/2013] [Accepted: 03/11/2013] [Indexed: 11/09/2022]
Abstract
Biofilms can provide a number of different ecological niches for microorganisms. Here, a multispecies biofilm was studied in which pyrite-oxidizing microbes are the primary producers. Its stability allowed not only detailed fluorescence in situ hybridization (FISH)-based characterization of the microbial population in different areas of the biofilm but also to integrate these results with oxygen and pH microsensor measurements conducted before. The O2 concentration declined rapidly from the outside to the inside of the biofilm. Hence, part of the population lives under microoxic or anoxic conditions. Leptospirillum ferrooxidans strains dominate the microbial population but are only located in the oxic periphery of the snottite structure. Interestingly, archaea were identified only in the anoxic parts of the biofilm. The archaeal community consists mainly of so far uncultured Thermoplasmatales as well as novel ARMAN (Archaeal Richmond Mine Acidophilic Nanoorganism) species. Inductively coupled plasma analysis and X-ray absorption near edge structure spectra provide further insight in the biofilm characteristics but revealed no other major factors than oxygen affecting the distribution of bacteria and archaea. In addition to catalyzed reporter deposition FISH and oxygen microsensor measurements, microautoradiographic FISH was used to identify areas in which active CO2 fixation takes place. Leptospirilla as well as acidithiobacilli were identified as primary producers. Fixation of gaseous CO2 seems to proceed only in the outer rim of the snottite. Archaea inhabiting the snottite core do not seem to contribute to the primary production. This work gives insight in the ecological niches of acidophilic microorganisms and their role in a consortium. The data provided the basis for the enrichment of uncultured archaea.
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Affiliation(s)
- Sibylle Ziegler
- Department of Microbiology, Albert-Ludwigs University, Freiburg, Germany
- Department of Applied Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Kerstin Dolch
- Department of Applied Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Katharina Geiger
- Department of Applied Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Susanne Krause
- Department of Applied Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Maximilian Asskamp
- Department of Microbiology, Albert-Ludwigs University, Freiburg, Germany
| | - Karin Eusterhues
- Department of Mineralogy, Friedrich Schiller University, Jena, Germany
| | - Michael Kriews
- Department of Geosciences/Glaciology, Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
| | | | - Joerg Goettlicher
- Institute for Synchrotron Radiation, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Juraj Majzlan
- Department of Mineralogy, Friedrich Schiller University, Jena, Germany
| | - Johannes Gescher
- Department of Applied Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
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Hamilton TL, Peters JW, Skidmore ML, Boyd ES. Molecular evidence for an active endogenous microbiome beneath glacial ice. ISME JOURNAL 2013; 7:1402-12. [PMID: 23486249 PMCID: PMC3695297 DOI: 10.1038/ismej.2013.31] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Geologic, chemical and isotopic evidence indicate that Earth has experienced numerous intervals of widespread glaciation throughout its history, with roughly 11% of present day Earth's land surface covered in ice. Despite the pervasive nature of glacial ice both today and in Earth's past and the potential contribution of these systems to global biogeochemical cycles, the composition and phylogenetic structure of an active microbial community in subglacial systems has yet to be described. Here, using RNA-based approaches, we demonstrate the presence of active and endogenous archaeal, bacterial and eukaryal assemblages in cold (0–1 °C) subglacial sediments sampled from Robertson Glacier, Alberta, Canada. Patterns in the phylogenetic structure and composition of subglacial sediment small subunit (SSU) ribosomal RNA (rRNA) assemblages indicate greater diversity and evenness than in glacial surface environments, possibly due to facilitative or competitive interactions among populations in the subglacial environment. The combination of phylogenetically more even and more diverse assemblages in the subglacial environment suggests minimal niche overlap and optimization to capture a wider spectrum of the limited nutrients and chemical energy made available from weathering of bedrock minerals. The prevalence of SSU rRNA affiliated with lithoautotrophic bacteria, autotrophic methane producing archaea and heterotrophic eukarya in the subglacial environment is consistent with this hypothesis and suggests an active contribution to the global carbon cycle. Collectively, our findings demonstrate that subglacial environments harbor endogenous active ecosystems that have the potential to impact global biogeochemical cycles over extended periods of time.
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Affiliation(s)
- Trinity L Hamilton
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
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Kumar S, Dagar SS, Mohanty AK, Sirohi SK, Puniya M, Kuhad RC, Sangu KPS, Griffith GW, Puniya AK. Enumeration of methanogens with a focus on fluorescence in situ hybridization. Naturwissenschaften 2011; 98:457-72. [PMID: 21475941 DOI: 10.1007/s00114-011-0791-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Revised: 03/19/2011] [Accepted: 03/20/2011] [Indexed: 10/18/2022]
Abstract
Methanogens, the members of domain Archaea are potent contributors in global warming. Being confined to the strict anaerobic environment, their direct cultivation as pure culture is quite difficult. Therefore, a range of culture-independent methods have been developed to investigate their numbers, substrate uptake patterns, and identification in complex microbial communities. Unlike other approaches, fluorescence in situ hybridization (FISH) is not only used for faster quantification and accurate identification but also to reveal the physiological properties and spatiotemporal dynamics of methanogens in their natural environment. Aside from the methodological aspects and application of FISH, this review also focuses on culture-dependent and -independent techniques employed in enumerating methanogens along with associated problems. In addition, the combination of FISH with micro-autoradiography that could also be an important tool in investigating the activities of methanogens is also discussed.
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Affiliation(s)
- Sanjay Kumar
- Dairy Microbiology Division, National Dairy Research Institute, Karnal 132001, India
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13
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Boyd ES, Skidmore M, Mitchell AC, Bakermans C, Peters JW. Methanogenesis in subglacial sediments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2010; 2:685-692. [PMID: 23766256 DOI: 10.1111/j.1758-2229.2010.00162.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Methanogenic archaea have a unique role in Earth's global carbon cycle as producers of the greenhouse gas methane (CH4 ). However, despite the fact that ice covers 11% of Earth's continental landmass, evidence for methanogenic activity in subglacial environments has yet to be clearly demonstrated. Here we present genetic, biochemical and geochemical evidence indicative of an active population of methanogens associated with subglacial sediments from Robertson Glacier (RG), Canadian Rockies. Porewater CH4 was quantified in two subglacial sediment cores at concentrations of 16 and 29 ppmv. Coenzyme M (CoM), a metabolic biomarker for methanogens, was detected at a concentration of 1.3 nmol g sediment(-1) corresponding to ∼3 × 10(3) active cells g sediment(-1) . Genetic characterization of communities associated with subglacial sediments indicated the presence of several archaeal 16S rRNA and methyl CoM reductase subunit A (mcrA) gene phylotypes, all of which were affiliated with the euryarchaeal order Methanosarcinales. Further, CH4 was produced at 9-51 fmol g dry weight sediment(-1) h(-1) in enrichment cultures of RG sediments incubated at 4°C. Collectively, these findings have important implications for the global carbon cycle in light of recent estimates indicating that the Earth's subglacial biome ranges from 10(4) to 10(6) km(3) sediment.
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Affiliation(s)
- Eric S Boyd
- Department of Chemistry and Biochemistry, The Astrobiology Biogeocatalysis Research Center, Montana State University, Bozeman, MT 59717, USA. Department of Earth Sciences and Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717, USA
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Qing-Hao H, Xiu-Fen L, Jian C. Effect of nitrilotriacetic acid on batch methane fermentation of sulfate-containing wastewater. Process Biochem 2008. [DOI: 10.1016/j.procbio.2008.01.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Stabnikova O, Liu XY, Wang JY, Ivanov V. Quantification of methanogens by fluorescence in situ hybridization with oligonucleotide probe. Appl Microbiol Biotechnol 2006; 73:696-702. [PMID: 16767462 DOI: 10.1007/s00253-006-0490-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2006] [Revised: 04/26/2006] [Accepted: 05/02/2006] [Indexed: 11/27/2022]
Abstract
To monitor anaerobic environmental engineering system, new method of quantification for methanogens was tested. It is based on the measurement of specific binding (hybridization) of 16S rRNA-targeted oligonucleotide probe Arc915, performed by fluorescence in situ hybridization (FISH) and quantified by fluorescence spectrometry. Average specific binding of Arc915 probe was 13.4+/-0.5 amol/cell of autofluorescent methanogens. It was 14.3, 13.3, and 12.9 amol/cell at the log phase, at stationary phase and at the period of cell lysis of batch culture, respectively. Specific binding of Arc915 probe per 1 ml of microbial sludge suspension from anaerobic digester linearly correlated with concentration of autofluorescent cells of methanogens. Coefficient of correlation was 0.95. Specific binding of oligonucleotide probe Arc915 can be used for the comparative estimation of methanogens during anaerobic digestion of organic waste. Specific binding of Arc915 probe was linear function of anaerobic sludge concentration when it was between 1.4 and 14.0 mg/ml. Accuracy of the measurements in this region was from 5 to 12%.
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Affiliation(s)
- O Stabnikova
- School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore.
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Elias DA, Krumholz LR, Wong D, Long PE, Suflita JM. Characterization of microbial activities and U reduction in a shallow aquifer contaminated by uranium mill tailings. MICROBIAL ECOLOGY 2003; 46:83-91. [PMID: 12754659 DOI: 10.1007/s00248-002-1060-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2002] [Accepted: 02/04/2003] [Indexed: 05/24/2023]
Abstract
A characterization of the Shiprock, NM, uranium mill tailing site focused on the geochemical and microbiological factors governing in-situ uranium-redox reactions. Groundwater and aqueous extracts of sediment samples contained a wide concentration range of sulfate, nitrate, and U(VI) with median values of 21.2 mM, 16.1 micro M, and 2.7 micro M, respectively. Iron(III) was not detected in groundwater, but a median value of 0.3 mM in sediment extracts was measured. Bacterial diversity down gradient from the disposal pile reflected the predominant geochemistry with relatively high numbers of sulfate- and nitrate-reducing microorganisms, and smaller numbers of acetogenic, methanogenic, nitrate-dependent Fe(II)-oxidizing, Fe(III)-reducing, and sulfide-oxidizing bacteria. In aquifer slurry incubations, nitrate reduction was always preferred and had a negative impact on sulfate-, Fe(III)-, and U-reduction rates. We also found that sulfate-reduction rates decreased sharply in the presence of clay, while Fe(III)-reduction increased with no clear impact on U reduction. In the absence of clay, iron and sulfate reduction correlated with concentrations of Fe(III) and sulfate, respectively. Rates of U(VI) loss did not correlate with the concentration of any electron acceptor. With the exception of Fe(III), electron donor amendment was largely unsuccessful in stimulating electron acceptor loss over a 2-week incubation period, suggesting that endogenous forms of organic matter were sufficient to support microbial activity. Our findings suggest that efforts to accelerate biological U reduction should initially focus on stimulating nitrate removal.
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Affiliation(s)
- D A Elias
- Institute for Energy and the Environment and the Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
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Martín D, Piera C, Mazzi U, Rossin R, Solans X, Font-Bardia M, Suades J. Rhenium and technetium-99m complexes with coenzyme M (MESNA). Dalton Trans 2003. [DOI: 10.1039/b305042d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Abstract
Glutathione metabolism is associated with oxygenic cyanobacteria and the oxygen-utilizing purple bacteria, but is absent in many other prokaryotes. This review focuses on novel thiols found in those bacteria lacking glutathione. Included are glutathione amide and its perthiol, produced by phototrophic purple sulfur bacteria and apparently involved in their sulfide metabolism. Among archaebacteria, coenzyme M (2-mercaptoethanesulfonic acid) and coenzyme B (7-mercaptoheptanoylthreonine phosphate) play central roles in the anaerobic production of CH4 and associated energy conversion by methanogens, whereas the major thiol in the aerobic phototrophic halobacteria is gamma-glutamylcysteine. The highly aerobic actinomycetes produce mycothiol, a conjugate of N-acetylcysteine with a pseudodisaccharide of glucosamine and myo-inositol, AcCys-GlcNalpha(1 --> 1)Ins, which appears to play an antioxidant role similar to glutathione. Ergothioneine, also produced by actinomycetes, remains a mystery despite many years of study. Available data on the biosynthesis and metabolism of these and other novel thiols is summarized and key areas for additional study are identified.
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Affiliation(s)
- R C Fahey
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA.
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Abstract
In the past two decades, a number of biotechnologies for anaerobic (methanogenic) wastewater treatment have been created, and practical applications of these processes are now being extended to more recalcitrant wastewaters and to wastewaters at extreme temperatures. Our knowledge of methanogenic organic degradation associated with bioreactors is also accumulating at a rapid rate. The recent advancement of such fundamental understanding is attributed to modern molecular biology techniques applied to the study of microbial communities and to continuous challenges to the cultivation of many important but recalcitrant anaerobes in bioreactors.
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Affiliation(s)
- Y Sekiguchi
- Department of Environmental Systems Engineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, 940-2188, Niigata, Japan.
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Krum JG, Ensign SA. Heterologous expression of bacterial Epoxyalkane:Coenzyme M transferase and inducible coenzyme M biosynthesis in Xanthobacter strain Py2 and Rhodococcus rhodochrous B276. J Bacteriol 2000; 182:2629-34. [PMID: 10762269 PMCID: PMC111331 DOI: 10.1128/jb.182.9.2629-2634.2000] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/1999] [Accepted: 02/04/2000] [Indexed: 11/20/2022] Open
Abstract
Coenzyme M (CoM) (2-mercaptoethanesulfonic acid) biosynthesis is shown to be coordinately regulated with the expression of the enzymes of alkene and epoxide metabolism in the propylene-oxidizing bacteria Xanthobacter strain Py2 and Rhodococcus rhodochrous strain B276. These results provide the first evidence for the involvement of CoM in propylene metabolism by R. rhodochrous and demonstrate for the first time the inducible nature of eubacterial CoM biosynthesis.
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Affiliation(s)
- J G Krum
- Department of Chemistry, Utah State University, Logan, Utah 84322-0300, USA
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