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Zhao L, Wang P, Li Y, Yu M, Zheng Y, Ren L, Wang Y, Li J. Feasibility of anaerobic co-digestion of biodegradable plastics with food waste, investigation of microbial diversity and digestate phytotoxicity. BIORESOURCE TECHNOLOGY 2024; 393:130029. [PMID: 37977495 DOI: 10.1016/j.biortech.2023.130029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 11/10/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023]
Abstract
The effects of biodegradable plastics of different thicknesses (30 and 40 μm) and sizes (20 × 20, 2 × 2, and 1 × 1 mm) on anaerobic digestion of food waste and digestate phytotoxicity were investigated. Methane productions (38 days) for the groups with 20 × 20, 2 × 2, and 1 × 1 mm of 30 μm plastics were 92.46, 138.27, and 259.95 mL/gVSremoval, respectively which are nearly 58 % higher than the control group (58.86 mL/gVSremoval). Methane production in 40 μm plastics groups was lower than in 30 μm groups of equal size. All sizes of 30 µm plastics promoted substrate hydrolysis, acidification, and relative abundance of key hydrolytic bacteria and methanogens. Phytotoxicity tests results showed that seed root elongation was inhibited in groups with 40 μm plastics. In conclusion, 30 μm biodegradable plastics were more suitable for anaerobic digestion with food waste than 40 μm.
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Affiliation(s)
- Liya Zhao
- School of Ecology and Environment, State Environmental Protection Key Laboratory of Food Chain Pollution Control, Beijing Technology and Business University, Beijing 100048, China
| | - Pan Wang
- School of Ecology and Environment, State Environmental Protection Key Laboratory of Food Chain Pollution Control, Beijing Technology and Business University, Beijing 100048, China
| | - Yingnan Li
- School of Ecology and Environment, State Environmental Protection Key Laboratory of Food Chain Pollution Control, Beijing Technology and Business University, Beijing 100048, China
| | - Miao Yu
- School of Ecology and Environment, State Environmental Protection Key Laboratory of Food Chain Pollution Control, Beijing Technology and Business University, Beijing 100048, China
| | - Yi Zheng
- Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Suzhou 215128, China; College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing 100193, China
| | - Lianhai Ren
- School of Ecology and Environment, State Environmental Protection Key Laboratory of Food Chain Pollution Control, Beijing Technology and Business University, Beijing 100048, China
| | - Yongjing Wang
- School of Ecology and Environment, State Environmental Protection Key Laboratory of Food Chain Pollution Control, Beijing Technology and Business University, Beijing 100048, China.
| | - Ji Li
- Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Suzhou 215128, China; College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing 100193, China
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Tauber J, Möstl D, Vierheilig J, Saracevic E, Svardal K, Krampe J. Biological Methanation in an Anaerobic Biofilm Reactor—Trace Element and Mineral Requirements for Stable Operation. Processes (Basel) 2023. [DOI: 10.3390/pr11041013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023] Open
Abstract
Biological methanation of carbon dioxide using hydrogen makes it possible to improve the methane and energy content of biogas produced from sewage sludge and organic residuals and to reach the requirements for injection into the natural gas network. Biofilm reactors, so-called trickling bed reactors, offer a relatively simple, energy-efficient, and reliable technique for upgrading biogas via ex-situ methanation. A mesophilic lab-scale biofilm reactor was operated continuously for nine months to upgrade biogas from anaerobic sewage sludge digestion to a methane content >98%. To supply essential trace elements to the biomass, a stock solution was fed to the trickling liquid. Besides standard parameters and gas quality, concentrations of Na, K, Ca, Mg, Ni, and Fe were measured in the liquid and the biofilm using ICP-OES (inductively coupled plasma optical emission spectrometry) to examine the biofilms load-dependent uptake rate and to calculate quantities required for a stable operation. Additionally, microbial community dynamics were monitored by amplicon sequencing (16S rRNA gene). It was found that all investigated (trace) elements are taken up by the biomass. Some are absorbed depending on the load, others independently of it. For example, a biomass-specific uptake of 0.13 mg·g−1·d−1 for Ni and up to 50 mg·g−1·d−1 for Mg were measured.
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Liczbiński P, Borowski S, Nowak A. Isolation and Use of Coprothermobacter spp. to Improve Anaerobic Thermophilic Digestion of Grass. Molecules 2022; 27:molecules27144338. [PMID: 35889215 PMCID: PMC9319358 DOI: 10.3390/molecules27144338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/30/2022] [Accepted: 07/04/2022] [Indexed: 12/24/2022] Open
Abstract
The isolation of microorganisms was performed from digestate from the process of the anaerobic digestion (AD) of grass after hyperthermophilic pretreatment. The bacterium that was isolated and identified was Coprothermobacter sp. Using the isolated bacteria, an AD process on fresh grass (GB) and pretreated grass (PGB) was carried out with 10% of its addition. The highest methane yield of 219 NmlCH4/gVS was recorded for PGB at 55 °C. In contrast, fresh grass subjected to thermophilic digestion produced only 63 NmlCH4/gVS. Due to the addition of bacteria in the AD process, an increase in the efficiency of hydrogen and methane production was observed in both fresh grass and grass after pretreatment.
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Lv J, Yuan R, Wang S. Water diversion induces more changes in bacterial and archaeal communities of river sediments than seasonality. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 293:112876. [PMID: 34098351 DOI: 10.1016/j.jenvman.2021.112876] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 05/01/2021] [Accepted: 05/21/2021] [Indexed: 06/12/2023]
Abstract
Previous studies have demonstrated that seasonal variation is often the most important factor affecting aquatic bacterial assemblages. Whether anthropogenic activities can dominate community dynamics remains unknown. Based on 16S rRNA high-throughput sequencing technology, this study revealed and compared the relative influence of water diversions and seasonality on bacterial and archaeal communities in river sediments from a region with obvious seasonality. The results indicate that the influence of water diversion on bacteria and archaea in water-receiving river sediments exceeded the influence of seasonal variation. Water diversion affected microbes by increasing EC, salinity, water flow rate, and organic matter carbon and nitrogen contents. Seasonal variations affected microbes by altering water temperature. Diversion responders but no season responders were classified by statistical methods in the microbial community. Diversion responder numbers were related to nitrogen concentrations, complex organic carbon contents and EC values, which were mainly affected by water diversion. With the joint impact of water diversion and seasonality, the correlations of bacterial and archaeal numbers with environmental factors were obviously weakened due to the increases in the ecological niche breadths of microorganisms. Natural seasonal changes in bacterial and archaeal communities were totally altered by changes in salinity, nutrients, and hydrological conditions induced by anthropogenic water diversions. These results highlight that human activity may be a stronger driver than natural seasonality in the alteration of bacterial and archaeal communities.
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Affiliation(s)
- Jiali Lv
- College of Environmental and Resource Sciences, Shanxi University, Taiyuan, 030006, China; Shanxi Laboratory for Yellow River, Taiyuan, 030006, China; Key Laboratory of Agricultural Water Resources Research, Innovation Academy for Seed Design, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, China; Sino-Danish College of University of Chinese Academy of Sciences, Beijing, 101408, China; Sino-Danish Centre for Education and Research, Beijing, 101408, China
| | - Ruiqiang Yuan
- College of Environmental and Resource Sciences, Shanxi University, Taiyuan, 030006, China; Shanxi Laboratory for Yellow River, Taiyuan, 030006, China.
| | - Shiqin Wang
- Key Laboratory of Agricultural Water Resources Research, Innovation Academy for Seed Design, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, China
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Granatto CF, Grosseli GM, Sakamoto IK, Fadini PS, Varesche MBA. Influence of metabolic cosubstrates on methanogenic potential and degradation of triclosan and propranolol in sanitary sewage. ENVIRONMENTAL RESEARCH 2021; 199:111220. [PMID: 33992637 DOI: 10.1016/j.envres.2021.111220] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/27/2021] [Accepted: 04/22/2021] [Indexed: 06/12/2023]
Abstract
Triclosan (TCS) and propranolol (PRO) are emerging micropollutants that are difficult to remove in wastewater treatment plants. In this study, methanogenic potential (P) of anaerobic sludge submitted to TCS (3.6 ± 0.1 to 15.5 ± 0.1 mg L-1) and PRO (6.1 ± 0.1 to 55.9 ± 1.2 mg L-1) in sanitary sewage, was investigated in batch reactors. The use of cosubstrates (200 mg L-1 of organic matter) ethanol, methanol:ethanol and fumarate was evaluated for micropollutant degradation. Without cosubstrates, P values for 5.0 ± 0.1 mgTCS L-1, 15.5 ± 0.1 mgTCS L-1 and 55.0 ± 1.3 mgPRO L-1 were 50.53%, 98.24% and 17.66% lower in relation to Control assay (855 ± 5 μmolCH4) with sanitary sewage, without micropollutants and cosubstrates, respectively. The use of fumarate, ethanol and methanol:ethanol favored greater methane production, with P values of 2144 ± 45 μmolCH4, 2960 ± 185 μmolCH4 and 2239 ± 171 μmolCH4 for 5.1 ± 0.1 mgTCS L-1, respectively; and of 10,827 ± 185 μmolCH4, 10,946 ± 108 μmolCH4 and 10,809 ± 210 μmolCH4 for 55.0 ± 1.3 mgPRO L-1, respectively. Greater degradation of TCS (77.1 ± 0.1% for 5.1 ± 0.1 mg L-1) and PRO (24.1 ± 0.1% for 55.9 ± 1.2 mg L-1) was obtained with ethanol. However, with 28.5 ± 0.5 mg PRO L-1, greater degradation (88.4 ± 0.9%) was obtained without cosubstrates. With TCS, via sequencing of rRNA 16S gene, for Bacteria Domain, greater abundance of phylum Chloroflexi and of the genera Longilinea, Arcobacter, Mesotoga and Sulfuricurvum were identified. With PRO, the genus VadinBC27 was the most abundant. Methanosaeta was dominant in TCS with ethanol, while in PRO without cosubstrates, Methanobacterium and Methanosaeta were the most abundant. The use of metabolic cosubstrates is a favorable strategy to obtain greater methanogenic potential and degradation of TCS and PRO.
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Affiliation(s)
- Caroline F Granatto
- Department of Hydraulics and Sanitation, São Carlos School of Engineering, University of São Paulo. Ave Trabalhador São-Carlense, no. 400, Zipcode, 13566-590, São Carlos, SP, Brazil.
| | - Guilherme M Grosseli
- Federal University of São Carlos, Washington Luiz Highway, Km 235, Zipcode 13565-905, São Carlos, SP, Brazil.
| | - Isabel K Sakamoto
- Department of Hydraulics and Sanitation, São Carlos School of Engineering, University of São Paulo. Ave Trabalhador São-Carlense, no. 400, Zipcode, 13566-590, São Carlos, SP, Brazil.
| | - Pedro S Fadini
- Federal University of São Carlos, Washington Luiz Highway, Km 235, Zipcode 13565-905, São Carlos, SP, Brazil.
| | - Maria Bernadete A Varesche
- Department of Hydraulics and Sanitation, São Carlos School of Engineering, University of São Paulo. Ave Trabalhador São-Carlense, no. 400, Zipcode, 13566-590, São Carlos, SP, Brazil.
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6
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Lu Q, Liu J, He H, Liang Z, Qiu R, Wang S. Waste activated sludge stimulates in situ microbial reductive dehalogenation of organohalide-contaminated soil. JOURNAL OF HAZARDOUS MATERIALS 2021; 411:125189. [PMID: 33858119 DOI: 10.1016/j.jhazmat.2021.125189] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/14/2021] [Accepted: 01/19/2021] [Indexed: 06/12/2023]
Abstract
Due to its enriched organic matter, nutrients and growth cofactors, as well as a diverse range of microorganisms, waste activated sludge (WAS) might be an ideal additive to stimulate organohalide respiration for in situ bioremediation of organohalide-contaminated sites. In this study, we investigated the biostimulation and bioaugmentation impacts of WAS-amendment on the performance and microbiome in tetrachloroethene (PCE) and polychlorinated biphenyls (PCBs) dechlorinating microcosms. Results demonstrated that WAS-amendment increased PCE- and PCBs-dechlorination rate as much as 6.06 and 10.67 folds, respectively. The presence of WAS provided a favorable growth niche for organohalide-respiring bacteria (OHRB), including redox mediation and generation of electron donors and carbon sources. Particularly for the PCE dechlorination, indigenous Geobacter and WAS-derived Dehalococcoides were identified to play key roles in PCE-to-dichloroethene (DCE) and DCE-to-ethene dechlorination, respectively. Similar biostimulation and bioaugmentation effects of WAS-amendment were observed on both PCE- and PCBs-dechlorination in three different soils, i.e., laterite, brown loam and paddy soil. Risk assessment suggested low potential ecological risk of WAS amendment in remediation of organohalide-contaminated soil. Overall, this study provided an economic and efficient strategy to stimulate the organohalide respiration-based bioremediation in field applications.
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Affiliation(s)
- Qihong Lu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510275, China
| | - Jinting Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510275, China
| | - Haozheng He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510275, China
| | - Zhiwei Liang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510275, China
| | - Rongliang Qiu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510275, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Shanquan Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510275, China.
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High-Level Abundances of Methanobacteriales and Syntrophobacterales May Help To Prevent Corrosion of Metal Sheet Piles. Appl Environ Microbiol 2019; 85:AEM.01369-19. [PMID: 31420342 DOI: 10.1128/aem.01369-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 08/11/2019] [Indexed: 11/20/2022] Open
Abstract
Iron sheet piles are widely used in flood protection, dike construction, and river bank reinforcement. Their corrosion leads to gradual deterioration and often makes replacement necessary. Natural deposit layers on these sheet piles can prevent degradation and significantly increase their life span. However, little is known about the mechanisms of natural protective layer formation. Here, we studied the microbially diverse populations of corrosion-protective deposit layers on iron sheet piles at the Gouderak pumping station in Zuid-Holland, the Netherlands. Deposit layers, surrounding sediment and top sediment samples were analyzed for soil physicochemical parameters, microbially diverse populations, and metabolic potential. Methanogens appeared to be enriched 18-fold in the deposit layers. After sequencing, metagenome assembly and binning, we obtained four nearly complete draft genomes of microorganisms (Methanobacteriales, two Coriobacteriales, and Syntrophobacterales) that were highly enriched in the deposit layers, strongly indicating a potential role in corrosion protection. Coriobacteriales and Syntrophobacterales could be part of a microbial food web degrading organic matter to supply methanogenic substrates. Methane-producing Methanobacteriales could metabolize iron, which may initially lead to mild corrosion but potentially stimulates the formation of a carbonate-rich protective deposit layer in the long term. In addition, Methanobacteriales and Coriobacteriales have the potential to interact with metal surfaces via direct interspecies or extracellular electron transfer. In conclusion, our study provides valuable insights into microbial populations involved in iron corrosion protection and potentially enables the development of novel strategies for in situ screening of iron sheet piles in order to reduce risks and develop more sustainable replacement practices.IMPORTANCE Iron sheet piles are widely used to reinforce dikes and river banks. Damage due to iron corrosion poses a significant safety risk and has significant economic impact. Different groups of microorganisms are known to either stimulate or inhibit the corrosion process. Recently, natural corrosion-protective deposit layers were found on sheet piles. Analyses of the microbial composition indicated a potential role for methane-producing archaea. However, the full metabolic potential of the microbial communities within these protective layers has not been determined. The significance of this work lies in the reconstruction of the microbial food web of natural corrosion-protective layers isolated from noncorroding metal sheet piles. With this work, we provide insights into the microbiological mechanisms that potentially promote corrosion protection in freshwater ecosystems. Our findings could support the development of screening protocols to assess the integrity of iron sheet piles to decide whether replacement is required.
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Feng S, Hong X, Wang T, Huang X, Tong Y, Yang H. Reutilization of high COD leachate via recirculation strategy for methane production in anaerobic digestion of municipal solid waste: Performance and dynamic of methanogen community. BIORESOURCE TECHNOLOGY 2019; 288:121509. [PMID: 31195363 DOI: 10.1016/j.biortech.2019.121509] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 05/11/2019] [Accepted: 05/17/2019] [Indexed: 06/09/2023]
Abstract
The influences of reutilization of high COD leachate via recirculation strategy on methane production and dynamic of methanogen community in anaerobic digestion of Municipal Solid Waste (MSW) were revealed. With a COD concentration of 6000 mg·L-1 recirculation, the efficiency of hydrolytic acidification process was improved and alleviated the pH reduction during acidification, while the highest COD removal efficiency was achieved. The maximum methane production rate and accumulated CH4 production by the 6000 mg·L-1 group increased by 90.7% and 156.0%, respectively. Whereas the performance of the 9000 mg·L-1 group was actually below the control group. According to high-throughput sequencing, the superiority of acetotrophic Methanothrix was replaced by hydrogenotrophic Methanobacterium in the 3000- and 6000-mg·L-1 systems. Methanoculleus predominated in the 9000-mg·L-1 system, while Methanoregula, Methanolinea, and Methanospirillum suffered intensive inhibition effects. Canonical correspondence analysis verified a positive correlation between the dominant methanogens Methanobacterium and CH4 production, and a negative correlation with Methanoculleus.
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Affiliation(s)
- Shoushuai Feng
- School of Biotechnology, Jiangnan University, No. 1800 Lihu Road, Wuxi 214122, Jiangsu, China; The Key Laboratory of Industrial Biotechnology, Ministry of Education, No. 1800 Lihu Road, Wuxi 214122, Jiangsu, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology (Jiangnan University) Ministry of Education, No. 1800 Lihu Road, Wuxi 214122, Jiangsu, China
| | - Xianjing Hong
- School of Biotechnology, Jiangnan University, No. 1800 Lihu Road, Wuxi 214122, Jiangsu, China; The Key Laboratory of Industrial Biotechnology, Ministry of Education, No. 1800 Lihu Road, Wuxi 214122, Jiangsu, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology (Jiangnan University) Ministry of Education, No. 1800 Lihu Road, Wuxi 214122, Jiangsu, China
| | - Tao Wang
- School of Biotechnology, Jiangnan University, No. 1800 Lihu Road, Wuxi 214122, Jiangsu, China; The Key Laboratory of Industrial Biotechnology, Ministry of Education, No. 1800 Lihu Road, Wuxi 214122, Jiangsu, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology (Jiangnan University) Ministry of Education, No. 1800 Lihu Road, Wuxi 214122, Jiangsu, China
| | - Xing Huang
- WUXI City Environmental Technology Co., Ltd, No. 3 Tangnan Road, Liangxi District, Wuxi 214026, Jiangsu, China
| | - Yanjun Tong
- National Engineering Research Center for Functional Food, School of Food Science and Technology, Jiangnan University, No. 1800 Lihu Road, Wuxi 214122, Jiangsu, China
| | - Hailin Yang
- School of Biotechnology, Jiangnan University, No. 1800 Lihu Road, Wuxi 214122, Jiangsu, China; The Key Laboratory of Industrial Biotechnology, Ministry of Education, No. 1800 Lihu Road, Wuxi 214122, Jiangsu, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology (Jiangnan University) Ministry of Education, No. 1800 Lihu Road, Wuxi 214122, Jiangsu, China.
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Hahnke S, Langer T, Klocke M. Proteiniborus indolifex sp. nov., isolated from a thermophilic industrial-scale biogas plant. Int J Syst Evol Microbiol 2018; 68:824-828. [PMID: 29458500 DOI: 10.1099/ijsem.0.002591] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
A novel strictly anaerobic bacterium, designated strain BA2-13T, was isolated from a thermophilic industrial-scale biogas plant. Cells were rod-shaped and Gram-stain-positive. Growth occurred at temperatures of 25 to 50 °C and between pH 6.3 and 9.5. Strain BA2-13T produced indole. Cell growth was stimulated by yeast extract, peptone, meat extract, a mixture of 20 amino acids, glucose, pyruvate and ribose. When grown on peptone and yeast extract, the main fermentation products were acetic acid, H2 and CO2. The predominant cellular fatty acids were iso-C15 : 0 and iso-C14 : 0 3-OH. Major polar lipids were diphosphatidylglycerol, glycolipids, phospholipids and phosphatidylgycerol. Phylogenetic analysis based on 16S rRNA gene nucleotide sequence analysis placed strain BA2-13T within the order Clostridiales showing closest affiliation with Proteiniborusethanoligenes with 95.9 % sequence identity. Physiological, genotypic and chemotaxonomic differences of strain BA2-13T from P. ethanoligenes support the description of a new species within the genus Proteiniborus for which we suggest the name Proteiniborusindolifex sp. nov. (type strain BA2-13T=DSM 103060T=LMG 29818T).
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Affiliation(s)
- Sarah Hahnke
- Department of Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), D-14469 Potsdam, Germany
| | - Thomas Langer
- Department of Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), D-14469 Potsdam, Germany
| | - Michael Klocke
- Department of Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), D-14469 Potsdam, Germany
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Oko BJ, Tao Y, Stuckey DC. Dynamics of two methanogenic microbiomes incubated in polycyclic aromatic hydrocarbons, naphthenic acids, and oil field produced water. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:123. [PMID: 28503198 PMCID: PMC5426053 DOI: 10.1186/s13068-017-0812-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 05/04/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Oil field produced water (OFPW) is widely produced in large volumes around the world. Transforming the organic matter in OFPW into bioenergy, such as biomethane, is one promising way to sustainability. However, OFPW is difficult to biologically degrade because it contains complex compounds such as naphthenic acids (NAs), or polycyclic aromatic hydrocarbons (PAHs). Although active microbial communities have been found in many oil reservoirs, little is known about how an exotic microbiome, e.g. the one which originates from municipal wastewater treatment plants, would evolve when incubated with OFPW. RESULTS In this study, we harvested methanogenic biomass from two sources: a full-scale anaerobic digester (AD) treating oil and gas processing wastewater (named O&G sludge), and from a full-scale AD reactor treating multiple fractions of municipal solid wastes (named MS, short for mixed sludge). Both were incubated in replicate microcosms fed with PAHs, NAs, or OFPW. The results showed that the PAHs, NAs, and OFPW feeds could rapidly alter the methanogenic microbiomes, even after 14 days, while the O&G sludge adapted faster than the mixed sludge in all the incubations. Two rarely reported microorganisms, a hydrogenotrophic methanogen Candidatus methanoregula and a saccharolytic fermenter Kosmotoga, were found to be prevalent in the PAHs and OFPW microcosms, and are likely to play an important role in the syntrophic degradation of PAHs and OFPW, cooperating with methanogens such as Methanoregula, Methanosarcina, or Methanobacterium. CONCLUSIONS The dominant phyla varied in certain patterns during the incubations, depending on the biomass source, feed type, and variation in nutrients. The sludge that originated from the oil and gas processing wastewater treatment (O&G) reactor adapted faster than the one from municipal solid waste reactors, almost certainly because the O&G biomass had been "pre-selected" by the environment. This study reveals the importance of biomass selection for other crude oil-waste-related bioengineering studies, such as bioaugmentation and bioremediation.
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Affiliation(s)
- Bonahis J. Oko
- Department of Chemical Engineering, Imperial College London, Exhibition Road, South Kensington, London, SW7 2AZ UK
| | - Yu Tao
- Department of Chemical Engineering, Imperial College London, Exhibition Road, South Kensington, London, SW7 2AZ UK
| | - David C. Stuckey
- Department of Chemical Engineering, Imperial College London, Exhibition Road, South Kensington, London, SW7 2AZ UK
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11
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Phylogenomic proximity and metabolic discrepancy of Methanosarcina mazei Go1 across methanosarcinal genomes. Biosystems 2017; 155:20-28. [DOI: 10.1016/j.biosystems.2017.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 03/15/2017] [Accepted: 03/20/2017] [Indexed: 02/04/2023]
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12
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Maus I, Bremges A, Stolze Y, Hahnke S, Cibis KG, Koeck DE, Kim YS, Kreubel J, Hassa J, Wibberg D, Weimann A, Off S, Stantscheff R, Zverlov VV, Schwarz WH, König H, Liebl W, Scherer P, McHardy AC, Sczyrba A, Klocke M, Pühler A, Schlüter A. Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:264. [PMID: 29158776 PMCID: PMC5684752 DOI: 10.1186/s13068-017-0947-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 11/01/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND To elucidate biogas microbial communities and processes, the application of high-throughput DNA analysis approaches is becoming increasingly important. Unfortunately, generated data can only partialy be interpreted rudimentary since databases lack reference sequences. RESULTS Novel cellulolytic, hydrolytic, and acidogenic/acetogenic Bacteria as well as methanogenic Archaea originating from different anaerobic digestion communities were analyzed on the genomic level to assess their role in biomass decomposition and biogas production. Some of the analyzed bacterial strains were recently described as new species and even genera, namely Herbinix hemicellulosilytica T3/55T, Herbinix luporum SD1DT, Clostridium bornimense M2/40T, Proteiniphilum saccharofermentans M3/6T, Fermentimonas caenicola ING2-E5BT, and Petrimonas mucosa ING2-E5AT. High-throughput genome sequencing of 22 anaerobic digestion isolates enabled functional genome interpretation, metabolic reconstruction, and prediction of microbial traits regarding their abilities to utilize complex bio-polymers and to perform specific fermentation pathways. To determine the prevalence of the isolates included in this study in different biogas systems, corresponding metagenome fragment mappings were done. Methanoculleus bourgensis was found to be abundant in three mesophilic biogas plants studied and slightly less abundant in a thermophilic biogas plant, whereas Defluviitoga tunisiensis was only prominent in the thermophilic system. Moreover, several of the analyzed species were clearly detectable in the mesophilic biogas plants, but appeared to be only moderately abundant. Among the species for which genome sequence information was publicly available prior to this study, only the species Amphibacillus xylanus, Clostridium clariflavum, and Lactobacillus acidophilus are of importance for the biogas microbiomes analyzed, but did not reach the level of abundance as determined for M. bourgensis and D. tunisiensis. CONCLUSIONS Isolation of key anaerobic digestion microorganisms and their functional interpretation was achieved by application of elaborated cultivation techniques and subsequent genome analyses. New isolates and their genome information extend the repository covering anaerobic digestion community members.
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Affiliation(s)
- Irena Maus
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Andreas Bremges
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
- Faculty of Technology, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Brunswick, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunscheig, Inhoffenstraße 7, 38124 Brunswick, Germany
| | - Yvonne Stolze
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Sarah Hahnke
- Department Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Katharina G. Cibis
- Johannes Gutenberg-University, Institute of Microbiology and Wine Research, Johann-Joachim Becherweg 15, 55128 Mainz, Germany
| | - Daniela E. Koeck
- Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - Yong S. Kim
- Faculty Life Sciences/Research Center ‘Biomass Utilization Hamburg’, University of Applied Sciences Hamburg (HAW), Ulmenliet 20, 21033 Hamburg-Bergedorf, Germany
| | - Jana Kreubel
- Johannes Gutenberg-University, Institute of Microbiology and Wine Research, Johann-Joachim Becherweg 15, 55128 Mainz, Germany
| | - Julia Hassa
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Aaron Weimann
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Brunswick, Germany
| | - Sandra Off
- Faculty Life Sciences/Research Center ‘Biomass Utilization Hamburg’, University of Applied Sciences Hamburg (HAW), Ulmenliet 20, 21033 Hamburg-Bergedorf, Germany
| | - Robbin Stantscheff
- Johannes Gutenberg-University, Institute of Microbiology and Wine Research, Johann-Joachim Becherweg 15, 55128 Mainz, Germany
- Institut für Forensische Genetik GmbH, Im Derdel 8, 48168 Münster, Germany
| | - Vladimir V. Zverlov
- Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
- Institute of Molecular Genetics, Russian Academy of Science, Kurchatov Sq. 2, Moscow, 123182 Russia
| | - Wolfgang H. Schwarz
- Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - Helmut König
- Johannes Gutenberg-University, Institute of Microbiology and Wine Research, Johann-Joachim Becherweg 15, 55128 Mainz, Germany
| | - Wolfgang Liebl
- Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - Paul Scherer
- Faculty Life Sciences/Research Center ‘Biomass Utilization Hamburg’, University of Applied Sciences Hamburg (HAW), Ulmenliet 20, 21033 Hamburg-Bergedorf, Germany
| | - Alice C. McHardy
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Brunswick, Germany
| | - Alexander Sczyrba
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
- Faculty of Technology, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Michael Klocke
- Department Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Alfred Pühler
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
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Rahi P, Prakash O, Shouche YS. Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass-Spectrometry (MALDI-TOF MS) Based Microbial Identifications: Challenges and Scopes for Microbial Ecologists. Front Microbiol 2016; 7:1359. [PMID: 27625644 PMCID: PMC5003876 DOI: 10.3389/fmicb.2016.01359] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 08/17/2016] [Indexed: 12/29/2022] Open
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass-spectrometry (MALDI-TOF MS) based biotyping is an emerging technique for high-throughput and rapid microbial identification. Due to its relatively higher accuracy, comprehensive database of clinically important microorganisms and low-cost compared to other microbial identification methods, MALDI-TOF MS has started replacing existing practices prevalent in clinical diagnosis. However, applicability of MALDI-TOF MS in the area of microbial ecology research is still limited mainly due to the lack of data on non-clinical microorganisms. Intense research activities on cultivation of microbial diversity by conventional as well as by innovative and high-throughput methods has substantially increased the number of microbial species known today. This important area of research is in urgent need of rapid and reliable method(s) for characterization and de-replication of microorganisms from various ecosystems. MALDI-TOF MS based characterization, in our opinion, appears to be the most suitable technique for such studies. Reliability of MALDI-TOF MS based identification method depends mainly on accuracy and width of reference databases, which need continuous expansion and improvement. In this review, we propose a common strategy to generate MALDI-TOF MS spectral database and advocated its sharing, and also discuss the role of MALDI-TOF MS based high-throughput microbial identification in microbial ecology studies.
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Affiliation(s)
- Praveen Rahi
- Microbial Culture Collection, National Centre for Cell Science Pune, India
| | - Om Prakash
- Microbial Culture Collection, National Centre for Cell Science Pune, India
| | - Yogesh S Shouche
- Microbial Culture Collection, National Centre for Cell Science Pune, India
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Maus I, Koeck DE, Cibis KG, Hahnke S, Kim YS, Langer T, Kreubel J, Erhard M, Bremges A, Off S, Stolze Y, Jaenicke S, Goesmann A, Sczyrba A, Scherer P, König H, Schwarz WH, Zverlov VV, Liebl W, Pühler A, Schlüter A, Klocke M. Unraveling the microbiome of a thermophilic biogas plant by metagenome and metatranscriptome analysis complemented by characterization of bacterial and archaeal isolates. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:171. [PMID: 27525040 PMCID: PMC4982221 DOI: 10.1186/s13068-016-0581-3] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 07/27/2016] [Indexed: 05/24/2023]
Abstract
BACKGROUND One of the most promising technologies to sustainably produce energy and to mitigate greenhouse gas emissions from combustion of fossil energy carriers is the anaerobic digestion and biomethanation of organic raw material and waste towards biogas by highly diverse microbial consortia. In this context, the microbial systems ecology of thermophilic industrial-scale biogas plants is poorly understood. RESULTS The microbial community structure of an exemplary thermophilic biogas plant was analyzed by a comprehensive approach comprising the analysis of the microbial metagenome and metatranscriptome complemented by the cultivation of hydrolytic and acido-/acetogenic Bacteria as well as methanogenic Archaea. Analysis of metagenome-derived 16S rRNA gene sequences revealed that the bacterial genera Defluviitoga (5.5 %), Halocella (3.5 %), Clostridium sensu stricto (1.9 %), Clostridium cluster III (1.5 %), and Tepidimicrobium (0.7 %) were most abundant. Among the Archaea, Methanoculleus (2.8 %) and Methanothermobacter (0.8 %) were predominant. As revealed by a metatranscriptomic 16S rRNA analysis, Defluviitoga (9.2 %), Clostridium cluster III (4.8 %), and Tepidanaerobacter (1.1 %) as well as Methanoculleus (5.7 %) mainly contributed to these sequence tags indicating their metabolic activity, whereas Hallocella (1.8 %), Tepidimicrobium (0.5 %), and Methanothermobacter (<0.1 %) were transcriptionally less active. By applying 11 different cultivation strategies, 52 taxonomically different microbial isolates representing the classes Clostridia, Bacilli, Thermotogae, Methanomicrobia and Methanobacteria were obtained. Genome analyses of isolates support the finding that, besides Clostridium thermocellum and Clostridium stercorarium, Defluviitoga tunisiensis participated in the hydrolysis of hemicellulose producing ethanol, acetate, and H2/CO2. The latter three metabolites are substrates for hydrogentrophic and acetoclastic archaeal methanogenesis. CONCLUSIONS Obtained results showed that high abundance of microorganisms as deduced from metagenome analysis does not necessarily indicate high transcriptional or metabolic activity, and vice versa. Additionally, it appeared that the microbiome of the investigated thermophilic biogas plant comprised a huge number of up to now unknown and insufficiently characterized species.
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Affiliation(s)
- Irena Maus
- Center for Biotechnology (CeBiTec), Institute for Genome Research and Systems Biology, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany
| | - Daniela E. Koeck
- Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - Katharina G. Cibis
- Institute of Microbiology and Wine Research, Johannes Gutenberg-University, Becherweg 15, 55128 Mainz, Germany
| | - Sarah Hahnke
- Dept. Bioengineering, Leibniz-Institut für Agrartechnik Potsdam-Bornim e.V. (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Yong S. Kim
- Faculty Life Sciences/Research Center ‚‘Biomass Utilization Hamburg’, University of Applied Sciences Hamburg (HAW), Ulmenliet 20, 21033 Hamburg-Bergedorf, Germany
| | - Thomas Langer
- Dept. Bioengineering, Leibniz-Institut für Agrartechnik Potsdam-Bornim e.V. (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Jana Kreubel
- Institute of Microbiology and Wine Research, Johannes Gutenberg-University, Becherweg 15, 55128 Mainz, Germany
| | - Marcel Erhard
- RIPAC-LABOR GmbH, Am Mühlenberg 11, 14476 Potsdam-Golm, Germany
| | - Andreas Bremges
- Center for Biotechnology (CeBiTec), Institute for Genome Research and Systems Biology, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany
- Faculty of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Sandra Off
- Faculty Life Sciences/Research Center ‚‘Biomass Utilization Hamburg’, University of Applied Sciences Hamburg (HAW), Ulmenliet 20, 21033 Hamburg-Bergedorf, Germany
| | - Yvonne Stolze
- Center for Biotechnology (CeBiTec), Institute for Genome Research and Systems Biology, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany
| | - Sebastian Jaenicke
- Department of Bioinformatics and Systems Biology, Justus-Liebig University Gießen, Heinrich-Buff-Ring 58, 35392 Giessen, Germany
| | - Alexander Goesmann
- Department of Bioinformatics and Systems Biology, Justus-Liebig University Gießen, Heinrich-Buff-Ring 58, 35392 Giessen, Germany
| | - Alexander Sczyrba
- Center for Biotechnology (CeBiTec), Institute for Genome Research and Systems Biology, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany
- Faculty of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Paul Scherer
- Faculty Life Sciences/Research Center ‚‘Biomass Utilization Hamburg’, University of Applied Sciences Hamburg (HAW), Ulmenliet 20, 21033 Hamburg-Bergedorf, Germany
| | - Helmut König
- Institute of Microbiology and Wine Research, Johannes Gutenberg-University, Becherweg 15, 55128 Mainz, Germany
| | - Wolfgang H. Schwarz
- Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - Vladimir V. Zverlov
- Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - Wolfgang Liebl
- Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - Alfred Pühler
- Center for Biotechnology (CeBiTec), Institute for Genome Research and Systems Biology, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Institute for Genome Research and Systems Biology, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany
| | - Michael Klocke
- Dept. Bioengineering, Leibniz-Institut für Agrartechnik Potsdam-Bornim e.V. (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
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15
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Wu Y, Wang C, Liu X, Ma H, Wu J, Zuo J, Wang K. A new method of two-phase anaerobic digestion for fruit and vegetable waste treatment. BIORESOURCE TECHNOLOGY 2016; 211:16-23. [PMID: 26995617 DOI: 10.1016/j.biortech.2016.03.050] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Revised: 03/05/2016] [Accepted: 03/08/2016] [Indexed: 05/18/2023]
Abstract
A novel method of two-phase anaerobic digestion where the acid reactor is operated at low pH 4.0 was proposed and investigated. A completely stirred tank acid reactor and an up-flow anaerobic sludge bed methane reactor were operated to examine the possibility of efficient degradation of lactate and to identify their optimal operating conditions. Lactate with an average concentration of 14.8g/L was the dominant fermentative product and Lactobacillus was the predominant microorganism in the acid reactor. The effluent from the acid reactor was efficiently degraded in the methane reactor and the average methane yield was 261.4ml/gCOD removed. Organisms of Methanosaeta were the predominant methanogen in granular sludge of methane reactor, however, after acclimation hydrogenotrophic methanogens enriched, which benefited for the conversion of lactate to acetate. The two-phase AD system exhibited a low hydraulic retention time of 3.56days and high methane yield of 348.5ml/g VS removed.
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Affiliation(s)
- Yuanyuan Wu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Cuiping Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Xiaoji Liu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Hailing Ma
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Jing Wu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Jiane Zuo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Kaijun Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
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16
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Maus I, Cibis KG, Bremges A, Stolze Y, Wibberg D, Tomazetto G, Blom J, Sczyrba A, König H, Pühler A, Schlüter A. Genomic characterization of Defluviitoga tunisiensis L3, a key hydrolytic bacterium in a thermophilic biogas plant and its abundance as determined by metagenome fragment recruitment. J Biotechnol 2016; 232:50-60. [PMID: 27165504 DOI: 10.1016/j.jbiotec.2016.05.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 05/02/2016] [Accepted: 05/02/2016] [Indexed: 12/17/2022]
Abstract
The genome sequence of Defluviitoga tunisiensis L3 originating from a thermophilic biogas-production plant was established and recently published as Genome Announcement by our group. The circular chromosome of D. tunisiensis L3 has a size of 2,053,097bp and a mean GC content of 31.38%. To analyze the D. tunisiensis L3 genome sequence in more detail, a phylogenetic analysis of completely sequenced Thermotogae strains based on shared core genes was performed. It appeared that Petrotoga mobilis DSM 10674(T), originally isolated from a North Sea oil-production well, is the closest relative of D. tunisiensis L3. Comparative genome analyses of P. mobilis DSM 10674(T) and D. tunisiensis L3 showed moderate similarities regarding occurrence of orthologous genes. Both genomes share a common set of 1351 core genes. Reconstruction of metabolic pathways important for the biogas production process revealed that the D. tunisiensis L3 genome encodes a large set of genes predicted to facilitate utilization of a variety of complex polysaccharides including cellulose, chitin and xylan. Ethanol, acetate, hydrogen (H2) and carbon dioxide (CO2) were found as possible end-products of the fermentation process. The latter three metabolites are considered to represent substrates for methanogenic Archaea, the key organisms in the final step of the anaerobic digestion process. To determine the degree of relatedness between D. tunisiensis L3 and dominant biogas community members within the thermophilic biogas-production plant, metagenome sequences obtained from the corresponding microbial community were mapped onto the L3 genome sequence. This fragment recruitment revealed that the D. tunisiensis L3 genome is almost completely covered with metagenome sequences featuring high matching accuracy. This result indicates that strains highly related or even identical to the reference strain D. tunisiensis L3 play a dominant role within the community of the thermophilic biogas-production plant.
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Affiliation(s)
- Irena Maus
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Katharina Gabriela Cibis
- Institute of Microbiology and Wine Research, Johannes Gutenberg University Mainz, 55122 Mainz, Germany
| | - Andreas Bremges
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany; Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
| | - Yvonne Stolze
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Daniel Wibberg
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | | | - Jochen Blom
- Department of Bioinformatics and Systems Biology, Justus-Liebig-University Gießen, 35390 Gießen, Germany
| | - Alexander Sczyrba
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany; Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
| | - Helmut König
- Institute of Microbiology and Wine Research, Johannes Gutenberg University Mainz, 55122 Mainz, Germany
| | - Alfred Pühler
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Andreas Schlüter
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany.
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Cibis KG, Gneipel A, König H. Isolation of acetic, propionic and butyric acid-forming bacteria from biogas plants. J Biotechnol 2016; 220:51-63. [PMID: 26779817 DOI: 10.1016/j.jbiotec.2016.01.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 01/07/2016] [Accepted: 01/12/2016] [Indexed: 11/16/2022]
Abstract
In this study, acetic, propionic and butyric acid-forming bacteria were isolated from thermophilic and mesophilic biogas plants (BGP) located in Germany. The fermenters were fed with maize silage and cattle or swine manure. Furthermore, pressurized laboratory fermenters digesting maize silage were sampled. Enrichment cultures for the isolation of acid-forming bacteria were grown in minimal medium supplemented with one of the following carbon sources: Na(+)-dl-lactate, succinate, ethanol, glycerol, glucose or a mixture of amino acids. These substrates could be converted by the isolates to acetic, propionic or butyric acid. In total, 49 isolates were obtained, which belonged to the phyla Firmicutes, Tenericutes or Thermotogae. According to 16S rRNA gene sequences, most isolates were related to Clostridium sporosphaeroides, Defluviitoga tunisiensis and Dendrosporobacter quercicolus. Acetic, propionic or butyric acid were produced in cultures of isolates affiliated to Bacillus thermoamylovorans, Clostridium aminovalericum, Clostridium cochlearium/Clostridium tetani, C. sporosphaeroides, D. quercicolus, Proteiniborus ethanoligenes, Selenomonas bovis and Tepidanaerobacter sp. Isolates related to Thermoanaerobacterium thermosaccharolyticum produced acetic, butyric and lactic acid, and isolates related to D. tunisiensis formed acetic acid. Specific primer sets targeting 16S rRNA gene sequences were designed and used for real-time quantitative PCR (qPCR). The isolates were physiologically characterized and their role in BGP discussed.
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Affiliation(s)
- Katharina Gabriela Cibis
- Institute of Microbiology and Wine Research (IMW), Johannes Gutenberg-Universität of Mainz, Johann-Joachim-Becherweg 15, 55128 Mainz, Germany.
| | - Armin Gneipel
- Institute of Microbiology and Wine Research (IMW), Johannes Gutenberg-Universität of Mainz, Johann-Joachim-Becherweg 15, 55128 Mainz, Germany
| | - Helmut König
- Institute of Microbiology and Wine Research (IMW), Johannes Gutenberg-Universität of Mainz, Johann-Joachim-Becherweg 15, 55128 Mainz, Germany
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18
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Stolze Y, Bremges A, Rumming M, Henke C, Maus I, Pühler A, Sczyrba A, Schlüter A. Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:156. [PMID: 27462367 PMCID: PMC4960831 DOI: 10.1186/s13068-016-0565-3] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 07/12/2016] [Indexed: 05/19/2023]
Abstract
BACKGROUND Biofuel production from conversion of biomass is indispensable in the portfolio of renewable energies. Complex microbial communities are involved in the anaerobic digestion process of plant material, agricultural residual products and food wastes. Analysis of the genetic potential and microbiology of communities degrading biomass to biofuels is considered to be the key to develop process optimisation strategies. Hence, due to the still incomplete taxonomic and functional characterisation of corresponding communities, new and unknown species are of special interest. RESULTS Three mesophilic and one thermophilic production-scale biogas plants (BGPs) were taxonomically profiled using high-throughput 16S rRNA gene amplicon sequencing. All BGPs shared a core microbiome with the thermophilic BGP featuring the lowest diversity. However, the phyla Cloacimonetes and Spirochaetes were unique to BGPs 2 and 3, Fusobacteria were only found in BGP3 and members of the phylum Thermotogae were present only in the thermophilic BGP4. Taxonomic analyses revealed that these distinctive taxa mostly represent so far unknown species. The only exception is the dominant Thermotogae OTU featuring 16S rRNA gene sequence identity to Defluviitoga tunisiensis L3, a sequenced and characterised strain. To further investigate the genetic potential of the biogas communities, corresponding metagenomes were sequenced in a deepness of 347.5 Gbp in total. A combined assembly comprised 80.3 % of all reads and resulted in the prediction of 1.59 million genes on assembled contigs. Genome binning yielded genome bins comprising the prevalent distinctive phyla Cloacimonetes, Spirochaetes, Fusobacteria and Thermotogae. Comparative genome analyses between the most dominant Thermotogae bin and the very closely related Defluviitoga tunisiensis L3 genome originating from the same BGP revealed high genetic similarity. This finding confirmed applicability and reliability of the binning approach. The four highly covered genome bins of the other three distinct phyla showed low or very low genetic similarities to their closest phylogenetic relatives, and therefore indicated their novelty. CONCLUSIONS In this study, the 16S rRNA gene sequencing approach and a combined metagenome assembly and binning approach were used for the first time on different production-scale biogas plants and revealed insights into the genetic potential and functional role of so far unknown species.
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Affiliation(s)
- Yvonne Stolze
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Andreas Bremges
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
- Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
| | - Madis Rumming
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
- Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
| | - Christian Henke
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
- Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
| | - Irena Maus
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Alfred Pühler
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Alexander Sczyrba
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
- Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
| | - Andreas Schlüter
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
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19
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Polag D, May T, Müller L, König H, Jacobi F, Laukenmann S, Keppler F. Online monitoring of stable carbon isotopes of methane in anaerobic digestion as a new tool for early warning of process instability. BIORESOURCE TECHNOLOGY 2015; 197:161-70. [PMID: 26335284 DOI: 10.1016/j.biortech.2015.08.058] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Revised: 08/08/2015] [Accepted: 08/12/2015] [Indexed: 05/16/2023]
Abstract
Effective control of anaerobic digestion in biogas plants requires the monitoring of process sensitive and rapid response parameters in order to ensure efficient biogas production and to prevent potential process failure. In this study, stable carbon isotopes of methane (δ(13)CCH4) produced in a full-scale continuous stirred-tank reactor were investigated as a potential new monitoring tool for this purpose. Over a six-month period with variable organic loading rates, δ(13)CCH4-values were measured online by a portable high-precision laser absorption spectrometer. During a stress period of consecutive high organic loading, δ(13)CCH4-values early indicated process changes in contrast to traditionally monitored parameters where a change was observed some five to ten days later. Comparison of the stable isotope values with data from microbial analyses showed a distinct relationship between the quantity of potentially acetoclastic methanogens and δ(13)CCH4-values. This finding indicates an association between dominant methanogenic pathways and carbon isotope values.
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Affiliation(s)
- D Polag
- Institute of Earth Sciences, Im Neuenheimer Feld 236, D-69120 Heidelberg, Germany
| | - T May
- Institute of Microbiology and Wine Research, Johann-Joachim-Becherweg 15, D-55128 Mainz, Germany
| | - L Müller
- Deutsches Biomasseforschungszentrum, Torgauer St. 116, D-04347 Leipzig, Germany
| | - H König
- Institute of Microbiology and Wine Research, Johann-Joachim-Becherweg 15, D-55128 Mainz, Germany
| | - F Jacobi
- Deutsches Biomasseforschungszentrum, Torgauer St. 116, D-04347 Leipzig, Germany
| | - S Laukenmann
- Institute of Earth Sciences, Im Neuenheimer Feld 236, D-69120 Heidelberg, Germany
| | - F Keppler
- Institute of Earth Sciences, Im Neuenheimer Feld 236, D-69120 Heidelberg, Germany
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20
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Spatiotemporal variation of bacterial and archaeal communities in a pilot-scale constructed wetland for surface water treatment. Appl Microbiol Biotechnol 2015; 100:1479-1488. [DOI: 10.1007/s00253-015-7072-5] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 09/30/2015] [Accepted: 10/06/2015] [Indexed: 01/29/2023]
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21
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Isolation of methanotrophic bacteria from termite gut. Microbiol Res 2015; 179:29-37. [DOI: 10.1016/j.micres.2015.06.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 05/08/2015] [Accepted: 06/06/2015] [Indexed: 11/20/2022]
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22
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Design and application of a synthetic DNA standard for real-time PCR analysis of microbial communities in a biogas digester. Appl Microbiol Biotechnol 2015; 99:6855-63. [DOI: 10.1007/s00253-015-6721-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 05/19/2015] [Accepted: 05/23/2015] [Indexed: 11/25/2022]
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23
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Wirth R, Lakatos G, Böjti T, Maróti G, Bagi Z, Kis M, Kovács A, Ács N, Rákhely G, Kovács KL. Metagenome changes in the mesophilic biogas-producing community during fermentation of the green alga Scenedesmus obliquus. J Biotechnol 2015; 215:52-61. [PMID: 26087313 DOI: 10.1016/j.jbiotec.2015.06.396] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 06/08/2015] [Accepted: 06/12/2015] [Indexed: 01/02/2023]
Abstract
A microalgal biomass offers a potential alternative to the maize silage commonly used in biogas technology. In this study, photoautotrophically grown Scenedesmus obliquus was used as biogas substrate. This microalga has a low C/N ratio of 8.5 relative to the optimum 20-30. A significant increase in the ammonium ion content was not observed. The methane content of the biogas generated from Sc. obliquus proved to be higher than that from maize silage, but the specific biogas yield was lower. Semi-continuous steady biogas production lasted for 2 months. Because of the thick cell wall of Sc. obliquus, the biomass-degrading microorganisms require additional time to digest its biomass. The methane concentration in the biogas was also high, in co-digestion (i.e., 52-56%) as in alga-fed anaerobic digestion (i.e., 55-62%). These results may be related to the relative predominance of the order Clostridiales in co-digestion and to the more balanced C/N ratio of the mixed algal-maize biomass. Predominance of the order Methanosarcinales was observed in the domain Archaea, which supported the diversity of metabolic pathways in the process.
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Affiliation(s)
- Roland Wirth
- Department of Biotechnology, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary.
| | - Gergely Lakatos
- Institute of Biochemistry, Biological Research Center, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726 Szeged, Hungary.
| | - Tamás Böjti
- Department of Biotechnology, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary.
| | - Gergely Maróti
- Institute of Biochemistry, Biological Research Center, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726 Szeged, Hungary.
| | - Zoltán Bagi
- Department of Biotechnology, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary.
| | - Mihály Kis
- Institute of Plant Biology, Biological Research Center, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726 Szeged, Hungary.
| | - Attila Kovács
- Phytoplankton and Macrophyte Research Team, Balaton Limnological Institute, Klebersberg Kuno 3, H-8237 Tihany, Hungary.
| | - Norbert Ács
- Department of Biotechnology, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary.
| | - Gábor Rákhely
- Department of Biotechnology, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary; Institute of Biophysics, Biological Research Center, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726 Szeged, Hungary.
| | - Kornél L Kovács
- Department of Biotechnology, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary; Institute of Biophysics, Biological Research Center, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726 Szeged, Hungary; Department of Oral Biology and Experimental Dental Research, University of Szeged, Tisza L. krt. 64, H-6720 Szeged, Hungary.
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24
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Wirth R, Lakatos G, Maróti G, Bagi Z, Minárovics J, Nagy K, Kondorosi É, Rákhely G, Kovács KL. Exploitation of algal-bacterial associations in a two-stage biohydrogen and biogas generation process. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:59. [PMID: 25873997 PMCID: PMC4395902 DOI: 10.1186/s13068-015-0243-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 03/20/2015] [Indexed: 05/12/2023]
Abstract
BACKGROUND The growing concern regarding the use of agricultural land for the production of biomass for food/feed or energy is dictating the search for alternative biomass sources. Photosynthetic microorganisms grown on marginal or deserted land present a promising alternative to the cultivation of energy plants and thereby may dampen the 'food or fuel' dispute. Microalgae offer diverse utilization routes. RESULTS A two-stage energetic utilization, using a natural mixed population of algae (Chlamydomonas sp. and Scenedesmus sp.) and mutualistic bacteria (primarily Rhizobium sp.), was tested for coupled biohydrogen and biogas production. The microalgal-bacterial biomass generated hydrogen without sulfur deprivation. Algal hydrogen production in the mixed population started earlier but lasted for a shorter period relative to the benchmark approach. The residual biomass after hydrogen production was used for biogas generation and was compared with the biogas production from maize silage. The gas evolved from the microbial biomass was enriched in methane, but the specific gas production was lower than that of maize silage. Sustainable biogas production from the microbial biomass proceeded without noticeable difficulties in continuously stirred fed-batch laboratory-size reactors for an extended period of time. Co-fermentation of the microbial biomass and maize silage improved the biogas production: The metagenomic results indicated that pronounced changes took place in the domain Bacteria, primarily due to the introduction of a considerable bacterial biomass into the system with the substrate; this effect was partially compensated in the case of co-fermentation. The bacteria living in syntrophy with the algae apparently persisted in the anaerobic reactor and predominated in the bacterial population. The Archaea community remained virtually unaffected by the changes in the substrate biomass composition. CONCLUSION Through elimination of cost- and labor-demanding sulfur deprivation, sustainable biohydrogen production can be carried out by using microalgae and their mutualistic bacterial partners. The beneficial effect of the mutualistic mixed bacteria in O2 quenching is that the spent algal-bacterial biomass can be further exploited for biogas production. Anaerobic fermentation of the microbial biomass depends on the composition of the biogas-producing microbial community. Co-fermentation of the mixed microbial biomass with maize silage improved the biogas productivity.
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Affiliation(s)
- Roland Wirth
- />Department of Biotechnology, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
| | - Gergely Lakatos
- />Institute of Biochemistry, Biological Research Center, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726 Szeged, Hungary
| | - Gergely Maróti
- />Institute of Biochemistry, Biological Research Center, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726 Szeged, Hungary
| | - Zoltán Bagi
- />Department of Biotechnology, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
| | - János Minárovics
- />Department of Oral Biology and Experimental Dental Research, University of Szeged, Tisza L. krt. 64, 6720 Szeged, Hungary
| | - Katalin Nagy
- />Department of Oral Biology and Experimental Dental Research, University of Szeged, Tisza L. krt. 64, 6720 Szeged, Hungary
| | - Éva Kondorosi
- />Institute of Biochemistry, Biological Research Center, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726 Szeged, Hungary
| | - Gábor Rákhely
- />Department of Biotechnology, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
- />Institute of Biophysics, Biological Research Center, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726 Szeged, Hungary
| | - Kornél L Kovács
- />Department of Biotechnology, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
- />Institute of Biophysics, Biological Research Center, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726 Szeged, Hungary
- />Department of Oral Biology and Experimental Dental Research, University of Szeged, Tisza L. krt. 64, 6720 Szeged, Hungary
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25
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Kern T, Linge M, Rother M. Methanobacterium aggregans sp. nov., a hydrogenotrophic methanogenic archaeon isolated from an anaerobic digester. Int J Syst Evol Microbiol 2015; 65:1975-1980. [PMID: 25807978 DOI: 10.1099/ijs.0.000210] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel, strictly anaerobic, hydrogenotrophic methanogen, strain E09F.3T, was isolated from a commercial biogas plant in Germany. Cells of E09F.3T were Gram-stain-negative, non-motile, slightly curved rods, long chains of which formed large aggregates consisting of intertwined bundles of chains. Cells utilized H2+CO2 and, to a lesser extent, formate as substrates for growth and methanogenesis. The optimal growth temperature was around 40 °C; maximum growth rate was obtained at pH around 7.0 with approximately 6.8 mM NaCl. The DNA G+C content of strain E09F.3T was 39.1 mol%. Phylogenetic analyses based on 16S rRNA and mcrA gene sequences placed strain E09F.3T within the genus Methanobacterium. On the basis of 16S rRNA gene sequence similarity, strain E09F.3T was closely related to Methanobacterium congolense CT but morphological, physiological and genomic characteristics indicated that strain E09F.3T represents a novel species. The name Methanobacterium aggregans sp. nov. is proposed for this novel species, with strain E09F.3T ( = DSM 29428T = JCM 30569T) as the type strain.
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Affiliation(s)
- Tobias Kern
- Institut für Mikrobiologie, Technische Universität Dresden, 01062 Dresden, Germany
| | - Mary Linge
- Institut für Mikrobiologie, Technische Universität Dresden, 01062 Dresden, Germany
| | - Michael Rother
- Institut für Mikrobiologie, Technische Universität Dresden, 01062 Dresden, Germany
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26
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Chen R, Yu XL, Gao XB, Xue CY, Song CX, Li Y, Cao YC. Bead-based suspension array for simultaneous differential detection of five major swine viruses. Appl Microbiol Biotechnol 2015; 99:919-28. [PMID: 25557628 DOI: 10.1007/s00253-014-6337-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 12/14/2014] [Accepted: 12/17/2014] [Indexed: 02/02/2023]
Abstract
A novel multiplex detection array based on Luminex xMAP technology was developed and validated for simultaneous detection of five major viruses causing swine reproductive diseases. By combining one-step asymmetric multiplex reverse transcription polymerase chain reaction (RT-PCR) with xMAP bead-based hybridization and flow cytometry analysis, the resulting multiplex assay was capable of detecting single and mixed infections of PRRSV, PCV-2, PRV, CSFV, and PPV in a single reaction. The assay accurately detected and differentiated 23 viral strains used in this study. The low detection limit was determined as 2.2-22 copies/μL (corresponding to 0.5-6.8 fg/μL DNA template) on plasmid constructs containing viral fragments. The intra-assay and inter-assay variances (CV%) were low that ranged from 2.5 to 5.4 % and 4.1 to 7.6 %, respectively. The assay was applied to test field samples and detected single and mixed viral infections. The detection rate was higher than that of uniplex conventional PCR and RT-PCR methods. The detection of PRRSV by the bead-based multiplex assay was comparable with a commercially available real time RT-PCR kit. The test procedure on purified DNA or RNA samples could be completed within 2 h. In conclusion, the bead-based suspension array presented here proved to be a high-throughput practical tool that provided highly specific and sensitive identification of single and multiple infections of five major viruses in pigs and boar semen.
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Affiliation(s)
- Ru Chen
- Animal Inspection and Quarantine Laboratory, Technical Center, Guangdong Entry-Exit Inspection and Quarantine Bureau, No.66 Huacheng Dadao Ave., Zhujiangxincheng, Guangzhou, 510623, China,
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27
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Lebuhn M, Weiß S, Munk B, Guebitz GM. Microbiology and Molecular Biology Tools for Biogas Process Analysis, Diagnosis and Control. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2015; 151:1-40. [PMID: 26337842 DOI: 10.1007/978-3-319-21993-6_1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Many biotechnological processes such as biogas production or defined biotransformations are carried out by microorganisms or tightly cooperating microbial communities. Process breakdown is the maximum credible accident for the operator. Any time savings that can be provided by suitable early-warning systems and allow for specific countermeasures are of great value. Process disturbance, frequently due to nutritional shortcomings, malfunction or operational deficits, is evidenced conventionally by process chemistry parameters. However, knowledge on systems microbiology and its function has essentially increased in the last two decades, and molecular biology tools, most of which are directed against nucleic acids, have been developed to analyze and diagnose the process. Some of these systems have been shown to indicate changes of the process status considerably earlier than the conventionally applied process chemistry parameters. This is reasonable because the triggering catalyst is determined, activity changes of the microbes that perform the reaction. These molecular biology tools have thus the potential to add to and improve the established process diagnosis system. This chapter is dealing with the actual state of the art of biogas process analysis in practice, and introduces molecular biology tools that have been shown to be of particular value in complementing the current systems of process monitoring and diagnosis, with emphasis on nucleic acid targeted molecular biology systems.
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Affiliation(s)
- Michael Lebuhn
- Department for Quality Assurance and Analytics, Bavarian State Research Center for Agriculture (LfL), Lange Point 6, 85354, Freising, Germany
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28
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Ghasimi DSM, Tao Y, de Kreuk M, Zandvoort MH, van Lier JB. Microbial population dynamics during long-term sludge adaptation of thermophilic and mesophilic sequencing batch digesters treating sewage fine sieved fraction at varying organic loading rates. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:171. [PMID: 26500697 PMCID: PMC4618146 DOI: 10.1186/s13068-015-0355-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 10/09/2015] [Indexed: 05/16/2023]
Abstract
BACKGROUND In this research, the feasibility of, and population dynamics in, one-step anaerobic sequencing batch reactor systems treating the fine sieved fraction (FSF) from raw municipal wastewater was studied under thermophilic (55 °C) and mesophilic (35 °C) conditions. FSF was sequestered from raw municipal wastewater, in the Netherlands, using a rotating belt filter (mesh size 350 micron). FSF is a heterogeneous substrate that mainly consists of fibres originating from toilet paper and thus contains a high cellulosic fraction (60-80 % of total solids content), regarded as an energy-rich material. RESULTS Results of the 656-day fed-batch operation clearly showed that thermophilic digestion was more stable, applying high organic loading rates (OLR) up to 22 kg COD/(m(3) day). In contrast, the mesophilic digester already failed applying an OLR of 5.5 kg COD/(m(3) day), indicated by a drop in pH and increase in volatile fatty acids (VFAs). The observed viscosity values of the mesophilic sludge were more than tenfold higher than the thermophilic sludge. 454-pyrosequencing of eight mesophilic and eight thermophilic biomass samples revealed that Bacteroides and aceticlastic methanogen Methanosaeta were the dominant genera in the mesophilic digester, whereas OP9 lineages, Clostridium and the hydrogenotrophic methanogen Methanothermobacter dominated the thermophilic one. CONCLUSIONS Our study suggests that applying thermophilic conditions for FSF digestion would result in a higher biogas production rate and/or a smaller required reactor volume, comparing to mesophilic conditions.
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Affiliation(s)
- Dara S. M. Ghasimi
- />Sanitary Engineering Section, Department of Water Management, Faculty of Civil Engineering and Geosciences, Delft University of Technology, Stevinweg 1, 2628 CN Delft, The Netherlands
| | - Yu Tao
- />Sanitary Engineering Section, Department of Water Management, Faculty of Civil Engineering and Geosciences, Delft University of Technology, Stevinweg 1, 2628 CN Delft, The Netherlands
- />Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, SW7 2AZ the UK
| | - Merle de Kreuk
- />Sanitary Engineering Section, Department of Water Management, Faculty of Civil Engineering and Geosciences, Delft University of Technology, Stevinweg 1, 2628 CN Delft, The Netherlands
| | - Marcel H. Zandvoort
- />Waternet, Korte Ouderkerkerdijk 7, P.O. Box 94370, 1090 GJ Amsterdam, The Netherlands
| | - Jules B. van Lier
- />Sanitary Engineering Section, Department of Water Management, Faculty of Civil Engineering and Geosciences, Delft University of Technology, Stevinweg 1, 2628 CN Delft, The Netherlands
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29
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Maus I, Wibberg D, Stantscheff R, Stolze Y, Blom J, Eikmeyer FG, Fracowiak J, König H, Pühler A, Schlüter A. Insights into the annotated genome sequence of Methanoculleus bourgensis MS2(T), related to dominant methanogens in biogas-producing plants. J Biotechnol 2014; 201:43-53. [PMID: 25455016 DOI: 10.1016/j.jbiotec.2014.11.020] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 11/18/2014] [Accepted: 11/21/2014] [Indexed: 01/13/2023]
Abstract
The final step of the biogas production process, the methanogenesis, is frequently dominated by members of the genus Methanoculleus. In particular, the species Methanoculleus bourgensis was identified to play a role in different biogas reactor systems. The genome of the type strain M. bourgensis MS2(T), originally isolated from a sewage sludge digestor, was completely sequenced to analyze putative adaptive genome features conferring competitiveness within biogas reactor environments to the strain. Sequencing and assembly of the M. bourgensis MS2(T) genome yielded a chromosome with a size of 2,789,773 bp. Comparative analysis of M. bourgensis MS2(T) and Methanoculleus marisnigri JR1 revealed significant similarities. The absence of genes for a putative ammonium uptake system may indicate that M. bourgensis MS2(T) is adapted to environments rich in ammonium/ammonia. Specific genes featuring predicted functions in the context of osmolyte production were detected in the genome of M. bourgensis MS2(T). Mapping of metagenome sequences derived from a production-scale biogas plant revealed that M. bourgensis MS2(T) almost completely comprises the genetic information of dominant methanogens present in the biogas reactor analyzed. Hence, availability of the M. bourgensis MS2(T) genome sequence may be valuable regarding further research addressing the performance of Methanoculleus species in agricultural biogas plants.
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Affiliation(s)
- Irena Maus
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Daniel Wibberg
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Robbin Stantscheff
- Institute of Microbiology and Wine Research, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Yvonne Stolze
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Jochen Blom
- Department of Bioinformatics and Systems Biology, Justus-Liebig-University Gießen, Gießen, Germany
| | | | - Jochen Fracowiak
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Helmut König
- Institute of Microbiology and Wine Research, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Alfred Pühler
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Andreas Schlüter
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany.
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30
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Maus I, Stantscheff R, Wibberg D, Stolze Y, Winkler A, Pühler A, König H, Schlüter A. Complete genome sequence of the methanogenic neotype strain Methanobacterium formicicum MF(T.). J Biotechnol 2014; 192 Pt A:40-1. [PMID: 25270020 DOI: 10.1016/j.jbiotec.2014.09.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 09/19/2014] [Indexed: 12/27/2022]
Abstract
The neotype strain Methanobacterium formicicum MF(T) (DSM1535), a hydrogenotrophic methanogenic Archaeon, was isolated from a domestic sewage sludge digestor in Urbana (IL, USA). Here, the complete genome sequence of the methanogen is reported. The genome is 2,478,074bp in size, featuring a GC content of 41.23%. M. formicicum MF(T) encodes several genes predicted to be involved in adaptation to abiotic stress such as high osmolarity. The strain MF(T) is of biotechnological importance since M. formicicum strains are often found in production-scale biogas plants and it is suggested as a starter culture for the anaerobic biomethanation process.
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Affiliation(s)
- Irena Maus
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Robbin Stantscheff
- Institute of Microbiology and Wine Research, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Daniel Wibberg
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Yvonne Stolze
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Anika Winkler
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Alfred Pühler
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Helmut König
- Institute of Microbiology and Wine Research, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Andreas Schlüter
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany.
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