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Shi Z, Zhang C, Tan X, Xie L, Luo G. Syntrophic microbes involved in the oxidation of short-chain fatty acids in continuous-flow anaerobic digesters treating waste activated sludge with hydrochar. Appl Environ Microbiol 2024; 90:e0204723. [PMID: 38205997 PMCID: PMC10880590 DOI: 10.1128/aem.02047-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 12/12/2023] [Indexed: 01/12/2024] Open
Abstract
The rapid degradation of short-chain fatty acids (SCFAs) is an essential issue of anaerobic digestion (AD), in which SCFA oxidizers could generally metabolize in syntrophy with methanogens. The dynamic responses of active metagenome-assembled genomes to low concentrations of propionate and acetate were analyzed to identify specific syntrophic SCFA oxidizers and their metabolic characteristics in continuous-flow AD systems treating waste activated sludge with and without hydrochar. In this study, hydrochar increased methane production by 19%, possibly due to hydrochar enhancing acidification and methanogenesis processes. A putative syntrophic propionate oxidizer and two acetate oxidizers contributed substantially to the syntrophic degradation of SCFAs, and hydrochar positively regulated their functional gene expressions. A significant relationship was established between the replication rate of SCFA oxidizers and their stimulation-related transcriptional activity. Acetate was degraded in the hydrochar group, which might be mainly through the syntrophic acetate oxidizer from the genus Desulfallas and methanogens from the genus Methanosarcina.IMPORTANCEShort-chain fatty acid (SCFA) degradation is an important process in the methanogenic ecosystem. However, current knowledge of this microbial mechanism is mainly based on studies on a few model organisms incubated as mono- or co-cultures or in enrichments, which cannot provide appropriate evidence in complex environments. Here, this study revealed the microbial mechanism of a hydrochar-mediated anaerobic digestion (AD) system promoting SCFA degradation at the species level and identified key SCFA oxidizing bacteria. Our analysis provided new insights into the SCFA oxidizers involved in the AD of waste activated sludge facilitated by hydrochar.
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Affiliation(s)
- Zhijian Shi
- Department of Environmental Science and Engineering, Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Fudan University, Shanghai, China
- Shanghai Municipal Engineering Design Institute (Group) Co., Ltd., Shanghai, China
| | - Chen Zhang
- Department of Environmental Science and Engineering, Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Fudan University, Shanghai, China
- Shanghai Municipal Engineering Design Institute (Group) Co., Ltd., Shanghai, China
| | - Xuejun Tan
- Shanghai Municipal Engineering Design Institute (Group) Co., Ltd., Shanghai, China
| | - Li Xie
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai, China
| | - Gang Luo
- Department of Environmental Science and Engineering, Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Fudan University, Shanghai, China
- Shanghai Technical Service Platform for Pollution Control and Resource Utilization of Organic Wastes, Shanghai, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai, China
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Moon J, Schubert A, Waschinger LM, Müller V. Reprogramming the metabolism of an acetogenic bacterium to homoformatogenesis. THE ISME JOURNAL 2023:10.1038/s41396-023-01411-2. [PMID: 37061584 DOI: 10.1038/s41396-023-01411-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/30/2023] [Accepted: 04/04/2023] [Indexed: 04/17/2023]
Abstract
Methyl groups are abundant in anoxic environments and their utilization as carbon and energy sources by microorganisms involves oxidation of the methyl groups to CO2, followed by transfer of the electrons to an acceptor. In acetogenic bacteria, the electron acceptor is CO2 that is reduced to enzyme bound carbon monoxide, the precursor of the carboxyl group in acetate. Here, we describe the generation of a mutant of the acetogen Acetobacterium woodii in which the last step in methyl group oxidation, formate oxidation to CO2 catalyzed by the HDCR enzyme, has been genetically deleted. The mutant grew on glycine betaine as methyl group donor, and in contrast to the wild type, formed formate alongside acetate, in a 1:2 ratio, demonstrating that methyl group oxidation stopped at the level of formate and reduced electron carriers were reoxidized by CO2 reduction to acetate. In the presence of the alternative electron acceptor caffeate, CO2 was no longer reduced to acetate, formate was the only product and all the carbon went to formate. Apparently, acetogenesis was not required to sustain formatogenic growth. This is the first demonstration of a genetic reprogramming of an acetogen into a formatogen that grows by homoformatogenesis from methyl groups. Formate production from methyl groups is not only of biotechnological interest but also for the mechanism of electron transfer in syntrophic interactions in anoxic environments.
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Affiliation(s)
- Jimyung Moon
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438, Frankfurt, Germany
| | - Anja Schubert
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438, Frankfurt, Germany
| | - Lara M Waschinger
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438, Frankfurt, Germany
| | - Volker Müller
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438, Frankfurt, Germany.
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Mlinar S, Weig AR, Freitag R. Influence of NH 3 and NH 4+ on anaerobic digestion and microbial population structure at increasing total ammonia nitrogen concentrations. BIORESOURCE TECHNOLOGY 2022; 361:127638. [PMID: 35853595 DOI: 10.1016/j.biortech.2022.127638] [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: 05/04/2022] [Revised: 07/10/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
Despite the extensive research dedicated to ammonia inhibition, the effect of NH3 and NH4+ on each anaerobic digestion stage and the associated microorganisms is still not completely understood. In the past, the focus was mainly on methanogenesis and either on NH3 or total ammonia nitrogen (TAN). Here, anaerobic digestion of two defined substrates, namely starch/NH4Cl and casein, was investigated particularly regarding the effects of different NH3/NH4+ ratios on the involved microorganisms. TAN affected bacteria, primarily gram-positive ones, whereas archaea responded largely to the NH3 concentration. These sensitivity differences are attributed to differences in the corresponding cell-membrane structures. A TAN decrease via stripping performed in two full-scale agricultural biogas plants resulted in increased bacterial diversity, with a pronounced increase in the propionate acetogens' abundance. Based on these data, it is suggested that inhibition can be avoided and processes stabilized in biogas plants by adjusting the NH3/NH4+ ratio, when feeding nitrogen-rich substrates.
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Affiliation(s)
- Stanislava Mlinar
- Process Biotechnology and Center for Energy Technology (ZET), University of Bayreuth, 95447 Bayreuth, Germany
| | - Alfons R Weig
- Genomics & Bioinformatics, University of Bayreuth, 95447 Bayreuth, Germany
| | - Ruth Freitag
- Process Biotechnology and Center for Energy Technology (ZET), University of Bayreuth, 95447 Bayreuth, Germany.
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Garcia-Lopez E, Moreno A, Bartolomé M, Leunda M, Sancho C, Cid C. Glacial Ice Age Shapes Microbiome Composition in a Receding Southern European Glacier. Front Microbiol 2021; 12:714537. [PMID: 34867842 PMCID: PMC8636055 DOI: 10.3389/fmicb.2021.714537] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 10/08/2021] [Indexed: 11/13/2022] Open
Abstract
Glaciers and their microbiomes are exceptional witnesses of the environmental conditions from remote times. Climate change is threatening mountain glaciers, and especially those found in southern Europe, such as the Monte Perdido Glacier (northern Spain, Central Pyrenees). This study focuses on the reconstruction of the history of microbial communities over time. The microorganisms that inhabit the Monte Perdido Glacier were identified using high-throughput sequencing, and the microbial communities were compared along an altitudinal transect covering most of the preserved ice sequence in the glacier. The results showed that the glacial ice age gradient did shape the diversity of microbial populations, which presented large differences throughout the last 2000 years. Variations in microbial community diversity were influenced by glacial conditions over time (nutrient concentration, chemical composition, and ice age). Some groups were exclusively identified in the oldest samples as the bacterial phyla Fusobacteria and Calditrichaeota, or the eukaryotic class Rhodophyceae. Among groups only found in modern samples, the green sulfur bacteria (phylum Chlorobi) stood out, as well as the bacterial phylum Gemmatimonadetes and the eukaryotic class Tubulinea. A patent impact of human contamination was also observed on the glacier microbiome. The oldest samples, corresponding to the Roman Empire times, were influenced by the beginning of mining exploitation in the Pyrenean area, with the presence of metal-tolerant microorganisms. The most recent samples comprise 600-year-old ancient ice in which current communities are living.
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Affiliation(s)
- Eva Garcia-Lopez
- Molecular Evolution Department, Centro de Astrobiologia (CSIC-INTA), Madrid, Spain
| | - Ana Moreno
- Departamento de Procesos Geoambientales y Cambio Global, Instituto Pirenaico de Ecología-CSIC, Zaragoza, Spain
| | - Miguel Bartolomé
- Departamento de Geología, Museo de Ciencias Naturales-CSIC, Madrid, Spain
| | - Maria Leunda
- Oeschger Centre for Climate Change Research, Institute of Plant Sciences, University of Bern, Bern, Switzerland.,Swiss Federal Research Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Carlos Sancho
- Departamento de Ciencias de la Tierra, Universidad de Zaragoza, Zaragoza, Spain
| | - Cristina Cid
- Molecular Evolution Department, Centro de Astrobiologia (CSIC-INTA), Madrid, Spain
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Hardy J, Bonin P, Lazuka A, Gonidec E, Guasco S, Valette C, Lacroix S, Cabrol L. Similar Methanogenic Shift but Divergent Syntrophic Partners in Anaerobic Digesters Exposed to Direct versus Successive Ammonium Additions. Microbiol Spectr 2021; 9:e0080521. [PMID: 34612672 PMCID: PMC8510171 DOI: 10.1128/spectrum.00805-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 08/02/2021] [Indexed: 01/04/2023] Open
Abstract
During anaerobic digestion (AD) of protein-rich wastewater, ammonium (NH4+) is released by amino acid degradation. High NH4+ concentrations disturb the AD microbiome balance, leading to process impairments. The sensitivity of the AD microbiome to NH4+ and the inhibition threshold depend on multiple parameters, especially the previous microbial acclimation to ammonium stress. However, little is known about the effect of different NH4+ acclimation strategies on the differential expression of key active microbial taxa. Here, we applied NH4+ inputs of increasing intensity (from 1.7 to 15.2 g N-NH4+ liters-1) in batch assays fed with synthetic wastewater, according to two different strategies: (i) direct independent inputs at a unique target concentration and (ii) successive inputs in a stepwise manner. In both strategies, along the NH4+ gradient, the active methanogens shifted from acetoclastic Methanosaeta to Methanosarcina and eventually hydrogenotrophic Methanoculleus. Despite shorter latency times, the successive input modality led to lower methane production rate, lower soluble chemical oxygen demand (sCOD) removal efficiency, and lower half maximal inhibitory concentration, together with higher volatile fatty acid (VFA) accumulation, compared to the independent input modality. These differential performances were associated with a drastically distinct succession pattern of the active bacterial partners in both experiments. In particular, the direct exposure modality was characterized by a progressive enrichment of VFA producers (mainly Tepidimicrobium) and syntrophic VFA oxidizers (mainly Syntrophaceticus) with increasing NH4+ concentration, while the successive exposure modality was characterized by a more dynamic succession of VFA producers (mainly Clostridium, Sporanaerobacter, Terrisporobacter) and syntrophic VFA oxidizers (mainly Tepidanaerobacter, Syntrophomonas). These results bring relevant insights for improved process management through inoculum adaptation, bioaugmentation, or community-driven optimization. IMPORTANCE Anaerobic digestion (AD) is an attractive biotechnological process for wastewater bioremediation and bioenergy production in the form of methane-rich biogas. However, AD can be inhibited by ammonium generated by protein-rich effluent, commonly found in agro-industrial activities. Insights in the microbial community composition and identification of AD key players are crucial for anticipating process impairments in response to ammonium stress. They can also help in defining an optimal microbiome adapted to high ammonium levels. Here, we compared two strategies for acclimation of AD microbiome to increasing ammonium concentration to better understand the effect of this stress on the methanogens and their bacterial partners. Our results suggest that long-term cumulative exposure to ammonia disrupted the AD microbiome more strongly than direct (independent) ammonium additions. We identified bioindicators with different NH4+ tolerance capacity among VFA producers and syntrophic VFA oxidizers.
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Affiliation(s)
- Julie Hardy
- MIO, Aix Marseille University, University of Toulon, CNRS, IRD, Marseille, France
- Scientific & Technological Expertise Department, Veolia, Maisons-Laffitte, France
| | - Patricia Bonin
- MIO, Aix Marseille University, University of Toulon, CNRS, IRD, Marseille, France
| | - Adele Lazuka
- Scientific & Technological Expertise Department, Veolia, Maisons-Laffitte, France
| | - Estelle Gonidec
- Scientific & Technological Expertise Department, Veolia, Maisons-Laffitte, France
| | - Sophie Guasco
- MIO, Aix Marseille University, University of Toulon, CNRS, IRD, Marseille, France
| | - Corinne Valette
- MIO, Aix Marseille University, University of Toulon, CNRS, IRD, Marseille, France
| | - Sébastien Lacroix
- Scientific & Technological Expertise Department, Veolia, Maisons-Laffitte, France
| | - Léa Cabrol
- MIO, Aix Marseille University, University of Toulon, CNRS, IRD, Marseille, France
- Instituto de Ecologia y Biodiversidad (IEB) Facultad de Ciencias, Universidad de Chile Las Palmeras, Nunoa, Santiago, Chile
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6
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Pan X, Zhao L, Li C, Angelidaki I, Lv N, Ning J, Cai G, Zhu G. Deep insights into the network of acetate metabolism in anaerobic digestion: focusing on syntrophic acetate oxidation and homoacetogenesis. WATER RESEARCH 2021; 190:116774. [PMID: 33387947 DOI: 10.1016/j.watres.2020.116774] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/18/2020] [Accepted: 12/21/2020] [Indexed: 06/12/2023]
Abstract
Acetate is a pivotal intermediate product during anaerobic decomposition of organic matter. Its generation and consumption network is quite complex, which almost covers the most steps in anaerobic digestion (AD) process. Besides acidogenesis, acetogenesis and methanogenesis, syntrophic acetate oxidation (SAO) replaced acetoclastic methanogenesis to release the inhibition of AD at some special conditions, and the importance of considering homoacetogenesis had also been proved when analysing anaerobic fermentations. Syntrophic acetate-oxidizing bacteria (SAOB), with function of SAO, can survive under high temperature and ammonia/ volatile fatty acids (VFAs) concentrations, while, homoacetogens, performed homoacetogenesis, are more active under acidic, alkaline and low temperature (10°C-20°C) conditions, This review summarized the roles of SAO and homoacetogenesis in AD process, which contains the biochemical reactions, metabolism pathways, physiological characteristics and energy conservation of functional bacteria. The specific roles of these two processes in the subprocess of AD (i.e., acidogenesis, acetogenesis and methanogenesis) were also analyzed in detail. A two phases anaerobic digester is proposed for protein-rich waste(water) treatment by enhancing the functions of homoacetogens and SAOB compared to the traditional two-phases anaerobic digesters, in which the first phase is fermentation phase including acidogens and homoacetogens for acetate production, and second phase is a mixed culture coupling syntrophic fatty acids bacteria, SAOB and hydrogenotrophic methanogens for methane production. This review provides a new insight into the network on production and consumption of acetate in AD process.
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Affiliation(s)
- Xiaofang Pan
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen361021, China
| | - Lixin Zhao
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agriculture Sciences, Beijing100081, China
| | - Chunxing Li
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Irini Angelidaki
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Nan Lv
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen361021, China
| | - Jing Ning
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen361021, China
| | - Guanjing Cai
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen361021, China
| | - Gefu Zhu
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen361021, China.
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Sakamoto S, Nobu MK, Mayumi D, Tamazawa S, Kusada H, Yonebayashi H, Iwama H, Ikarashi M, Wakayama T, Maeda H, Sakata S, Tamura T, Nomura N, Kamagata Y, Tamaki H. Koleobacter methoxysyntrophicus gen. nov., sp. nov., a novel anaerobic bacterium isolated from deep subsurface oil field and proposal of Koleobacteraceae fam. nov. and Koleobacterales ord. nov. within the class Clostridia of the phylum Firmicutes. Syst Appl Microbiol 2020; 44:126154. [PMID: 33227632 DOI: 10.1016/j.syapm.2020.126154] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/28/2020] [Accepted: 11/02/2020] [Indexed: 11/16/2022]
Abstract
An anaerobic thermophilic, rod-shaped bacterium possessing a unique non-lipid sheathed-like structure enveloping a single-membraned cell, designated strain NRmbB1T was isolated from at the deep subsurface oil field located in Yamagata Prefecture, Japan. Growth occurred with 40-60°C (optimum, 55°C), 0-2% (2%), NaCl and pH 6.0-8.5 (8.0). Fermentative growth with various sugars was observed. Glucose-grown cells generated acetate, hydrogen, pyruvate and lactate as the main end products. Syntrophic growth occurred with glucose, pyruvate and 3,4,5-trimethoxybenzoate in the presence of an H2-scavenging partner, and growth on 3,4,5-trimethoxybenzoate was only observed under syntrophic condition. The predominant cellular fatty acids were C16:0, iso-C16:0, anteiso-C15:0, and iso-C14:0. Respiratory quinone was not detected. The genomic G+C content was 40.8mol%. Based on 16S rRNA gene phylogeny, strain NRmbB1T belongs to a distinct order-level clade in the class Clostridia of the phylum Firmicutes, sharing low similarity with other isolated organisms (i.e., 87.5% for top hit Moorella thermoacetica DSM 2955T). In total, chemotaxonomic, phylogenetic and genomic characterization revealed that strain NRmbB1T (=KCTC 25035T, =JCM 39120T) represents a novel species of a new genus. In addition, we also propose the associated family and order as Koleobacteraceae fam. nov and Koleobacterales ord. nov., respectively.
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Affiliation(s)
- Sachiko Sakamoto
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan; JST ERATO Nomura Microbial Community Control Project, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Masaru K Nobu
- Bioproduction Research Institute, AIST, 1-1-1 Higashi, Tsukuba 305-8566, Japan.
| | - Daisuke Mayumi
- Institute for Geo-Resources and Environment, Geological Survey of Japan, AIST, 1-1-1, Higashi, Tsukuba 305-8566, Ibaraki, Japan
| | - Satoshi Tamazawa
- Bioproduction Research Institute, AIST, 1-1-1 Higashi, Tsukuba 305-8566, Japan; Northern Advancement Center for Science & Technology, H-RISE, 5-3 Sakae-machi, Horonobe-cho, Teshio-gun, BPRI, Hokkaido 098-3221, Japan
| | - Hiroyuki Kusada
- JST ERATO Nomura Microbial Community Control Project, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan; Bioproduction Research Institute, AIST, 1-1-1 Higashi, Tsukuba 305-8566, Japan
| | - Hideharu Yonebayashi
- Technical Research Center, INPEX CORPORATION, 9-23-30, Kitakarasuyama, Setagaya, 157-0061, Tokyo, Japan
| | - Hiroki Iwama
- Technical Research Center, INPEX CORPORATION, 9-23-30, Kitakarasuyama, Setagaya, 157-0061, Tokyo, Japan
| | - Masayuki Ikarashi
- Technical Research Center, INPEX CORPORATION, 9-23-30, Kitakarasuyama, Setagaya, 157-0061, Tokyo, Japan
| | - Tatsuki Wakayama
- Technical Research Center, INPEX CORPORATION, 9-23-30, Kitakarasuyama, Setagaya, 157-0061, Tokyo, Japan
| | - Haruo Maeda
- Institute for Geo-Resources and Environment, Geological Survey of Japan, AIST, 1-1-1, Higashi, Tsukuba 305-8566, Ibaraki, Japan; Technical Research Center, INPEX CORPORATION, 9-23-30, Kitakarasuyama, Setagaya, 157-0061, Tokyo, Japan
| | - Susumu Sakata
- Institute for Geo-Resources and Environment, Geological Survey of Japan, AIST, 1-1-1, Higashi, Tsukuba 305-8566, Ibaraki, Japan
| | - Tomohiro Tamura
- Bioproduction Research Institute, AIST, 1-1-1 Higashi, Tsukuba 305-8566, Japan; Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), AIST, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan
| | - Nobuhiko Nomura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan; JST ERATO Nomura Microbial Community Control Project, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Yoichi Kamagata
- Bioproduction Research Institute, AIST, 1-1-1 Higashi, Tsukuba 305-8566, Japan
| | - Hideyuki Tamaki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan; JST ERATO Nomura Microbial Community Control Project, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan; Bioproduction Research Institute, AIST, 1-1-1 Higashi, Tsukuba 305-8566, Japan.
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Westerholm M, Dolfing J, Schnürer A. Growth Characteristics and Thermodynamics of Syntrophic Acetate Oxidizers. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:5512-5520. [PMID: 30990997 DOI: 10.1021/acs.est.9b00288] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Syntrophic acetate oxidation (SAO) plays a pivotal role in biogas production processes when aceticlastic methanogens are inhibited. Despite the importance of SAO, the metabolic interactions and syntrophic growth of the organisms involved are still poorly understood. Therefore, we studied growth parameters and interactions within constructed defined cocultures comprising the methanogen Methanoculleus bourgensis and one, or several, of the syntrophic acetate oxidizers Syntrophaceticus schinkii, [ Clostridium] ultunense, and Tepidanaerobacter acetatoxydans and a novel, uncharacterized bacterium. Cultivation experiments in a design-of-experiment approach revealed positive effects on methane production rate of increased ammonium levels (up to 0.2 M), temperature (up to 45 °C), and acetate concentrations (0.15-0.30 M). Molecular analyses and thermodynamic calculations demonstrated close interlinkages between the microorganisms, with available energies of -10 kJ/mol for acetate oxidation and -20 kJ/mol for hydrogenotrophic methanogenesis. The estimated generation time varied between 3 and 20 days for all syntrophic microorganisms involved, and the acetate minimum threshold level was 0.40-0.45 mM. The rate of methanogenesis depended on the SAO bacteria present in the culture. These data are beneficial for interpretation of SAO prevalence and competiveness against aceticlastic methanogens in anaerobic environments.
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Affiliation(s)
- Maria Westerholm
- Department of Microbiology , Swedish University of Agricultural Sciences , Uppsala BioCenter, Box 7025, SE-750 07 Uppsala , Sweden
| | - Jan Dolfing
- School of Engineering , Newcastle University , Newcastle-upon-Tyne NE1 7RU United Kingdom
| | - Anna Schnürer
- Department of Microbiology , Swedish University of Agricultural Sciences , Uppsala BioCenter, Box 7025, SE-750 07 Uppsala , Sweden
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9
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Timmers PHA, Vavourakis CD, Kleerebezem R, Damsté JSS, Muyzer G, Stams AJM, Sorokin DY, Plugge CM. Metabolism and Occurrence of Methanogenic and Sulfate-Reducing Syntrophic Acetate Oxidizing Communities in Haloalkaline Environments. Front Microbiol 2018; 9:3039. [PMID: 30619130 PMCID: PMC6295475 DOI: 10.3389/fmicb.2018.03039] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 11/26/2018] [Indexed: 01/31/2023] Open
Abstract
Anaerobic syntrophic acetate oxidation (SAO) is a thermodynamically unfavorable process involving a syntrophic acetate oxidizing bacterium (SAOB) that forms interspecies electron carriers (IECs). These IECs are consumed by syntrophic partners, typically hydrogenotrophic methanogenic archaea or sulfate reducing bacteria. In this work, the metabolism and occurrence of SAOB at extremely haloalkaline conditions were investigated, using highly enriched methanogenic (M-SAO) and sulfate-reducing (S-SAO) cultures from south-western Siberian hypersaline soda lakes. Activity tests with the M-SAO and S-SAO cultures and thermodynamic calculations indicated that H2 and formate are important IECs in both SAO cultures. Metagenomic analysis of the M-SAO cultures showed that the dominant SAOB was ‘Candidatus Syntrophonatronum acetioxidans,’ and a near-complete draft genome of this SAOB was reconstructed. ‘Ca. S. acetioxidans’ has all genes necessary for operating the Wood–Ljungdahl pathway, which is likely employed for acetate oxidation. It also encodes several genes essential to thrive at haloalkaline conditions; including a Na+-dependent ATP synthase and marker genes for ‘salt-out‘ strategies for osmotic homeostasis at high soda conditions. Membrane lipid analysis of the M-SAO culture showed the presence of unusual bacterial diether membrane lipids which are presumably beneficial at extreme haloalkaline conditions. To determine the importance of SAO in haloalkaline environments, previously obtained 16S rRNA gene sequencing data and metagenomic data of five different hypersaline soda lake sediment samples were investigated, including the soda lakes where the enrichment cultures originated from. The draft genome of ‘Ca. S. acetioxidans’ showed highest identity with two metagenome-assembled genomes (MAGs) of putative SAOBs that belonged to the highly abundant and diverse Syntrophomonadaceae family present in the soda lake sediments. The 16S rRNA gene amplicon datasets of the soda lake sediments showed a high similarity of reads to ‘Ca. S. acetioxidans’ with abundance as high as 1.3% of all reads, whereas aceticlastic methanogens and acetate oxidizing sulfate-reducers were not abundant (≤0.1%) or could not be detected. These combined results indicate that SAO is the primary anaerobic acetate oxidizing pathway at extreme haloalkaline conditions performed by haloalkaliphilic syntrophic consortia.
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Affiliation(s)
- Peer H A Timmers
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands.,European Centre of Excellence for Sustainable Water Technology, Wetsus, Leeuwarden, Netherlands
| | - Charlotte D Vavourakis
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Robbert Kleerebezem
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Jaap S Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Netherlands Institute for Sea Research, Utrecht University, Utrecht, Netherlands.,Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
| | - Gerard Muyzer
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands.,Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Dimity Y Sorokin
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands.,Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Caroline M Plugge
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands.,European Centre of Excellence for Sustainable Water Technology, Wetsus, Leeuwarden, Netherlands
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10
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Fontana A, Campanaro S, Treu L, Kougias PG, Cappa F, Morelli L, Angelidaki I. Performance and genome-centric metagenomics of thermophilic single and two-stage anaerobic digesters treating cheese wastes. WATER RESEARCH 2018; 134:181-191. [PMID: 29427960 DOI: 10.1016/j.watres.2018.02.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 01/31/2018] [Accepted: 02/01/2018] [Indexed: 05/25/2023]
Abstract
The present research is the first comprehensive study regarding the thermophilic anaerobic degradation of cheese wastewater, which combines the evaluation of different reactor configurations (i.e. single and two-stage continuous stirred tank reactors) on the process efficiency and the in-depth characterization of the microbial community structure using genome-centric metagenomics. Both reactor configurations showed acidification problems under the tested organic loading rates (OLRs) of 3.6 and 2.4 g COD/L-reactor day and the hydraulic retention time (HRT) of 15 days. However, the two-stage design reached a methane yield equal to 95% of the theoretical value, in contrast with the single stage configuration, which reached a maximum of 33% of the theoretical methane yield. The metagenomic analysis identified 22 new population genomes and revealed that the microbial compositions between the two configurations were remarkably different, demonstrating a higher methanogenic biodiversity in the two-stage configuration. In fact, the acidogenic reactor of the serial configuration was almost solely composed by the lactose degrader Bifidobacterium crudilactis UC0001. The predictive functional analyses of the main population genomes highlighted specific metabolic pathways responsible for the AD process and the mechanisms of main intermediates production. Particularly, the acetate accumulation experienced by the single stage configuration was mainly correlated to the low abundant syntrophic acetate oxidizer Tepidanaerobacter acetatoxydans UC0018 and to the absence of aceticlastic methanogens.
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Affiliation(s)
- Alessandra Fontana
- Department for Sustainable Food Process - DiSTAS, Catholic University of the Sacred Heart, 29122 Piacenza, Italy; Department of Environmental Engineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | | | - Laura Treu
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Panagiotis G Kougias
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
| | - Fabrizio Cappa
- Department for Sustainable Food Process - DiSTAS, Catholic University of the Sacred Heart, 29122 Piacenza, Italy
| | - Lorenzo Morelli
- Department for Sustainable Food Process - DiSTAS, Catholic University of the Sacred Heart, 29122 Piacenza, Italy
| | - Irini Angelidaki
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
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11
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Manzoor S, Schnürer A, Bongcam-Rudloff E, Müller B. Genome-Guided Analysis of Clostridium ultunense and Comparative Genomics Reveal Different Strategies for Acetate Oxidation and Energy Conservation in Syntrophic Acetate-Oxidising Bacteria. Genes (Basel) 2018; 9:genes9040225. [PMID: 29690652 PMCID: PMC5924567 DOI: 10.3390/genes9040225] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 04/15/2018] [Accepted: 04/16/2018] [Indexed: 01/04/2023] Open
Abstract
Syntrophic acetate oxidation operates close to the thermodynamic equilibrium and very little is known about the participating organisms and their metabolism. Clostridium ultunense is one of the most abundant syntrophic acetate-oxidising bacteria (SAOB) that are found in engineered biogas processes operating with high ammonia concentrations. It has been proven to oxidise acetate in cooperation with hydrogenotrophic methanogens. There is evidence that the Wood-Ljungdahl (WL) pathway plays an important role in acetate oxidation. In this study, we analysed the physiological and metabolic capacities of C. ultunense strain Esp and strain BST on genome scale and conducted a comparative study of all the known characterised SAOB, namely Syntrophaceticus schinkii, Thermacetogenium phaeum, Tepidanaerobacter acetatoxydans, and Pseudothermotoga lettingae. The results clearly indicated physiological robustness to be beneficial for anaerobic digestion environments and revealed unexpected metabolic diversity with respect to acetate oxidation and energy conservation systems. Unlike S. schinkii and Th. phaeum, C. ultunense clearly does not employ the oxidative WL pathway for acetate oxidation, as its genome (and that of P. lettingae) lack important key genes. In both of those species, a proton motive force is likely formed by chemical protons involving putative electron-bifurcating [Fe-Fe] hydrogenases rather than proton pumps. No genes encoding a respiratory Ech (energy-converting hydrogenase), as involved in energy conservation in Th. phaeum and S. schinkii, were identified in C. ultunense and P. lettingae. Moreover, two respiratory complexes sharing similarities to the proton-translocating ferredoxin:NAD⁺ oxidoreductase (Rnf) and the Na⁺ pumping NADH:quinone hydrogenase (NQR) were predicted. These might form a respiratory chain that is involved in the reduction of electron acceptors rather than protons. However, involvement of these complexes in acetate oxidation in C. ultunense and P. lettingae needs further study. This genome-based comparison provides a solid platform for future meta-proteomics and meta-transcriptomics studies and for metabolic engineering, control, and monitoring of SAOB.
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Affiliation(s)
- Shahid Manzoor
- Department of Information Technology, University of the Punjab, Lahore 54 590, Pakistan.
| | - Anna Schnürer
- BioCenter, Department of Molecular Sciences, Box 7015, Swedish University of Agricultural Sciences, SE 750 07 Uppsala, Sweden.
| | - Erik Bongcam-Rudloff
- SLU-Global Bioinformatics Centre, Department of Animal Breeding and Genetics Science, Swedish University of Agricultural Sciences, SE 750 07 Uppsala, Sweden.
| | - Bettina Müller
- BioCenter, Department of Molecular Sciences, Box 7015, Swedish University of Agricultural Sciences, SE 750 07 Uppsala, Sweden.
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12
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Figueroa IA, Barnum TP, Somasekhar PY, Carlström CI, Engelbrektson AL, Coates JD. Metagenomics-guided analysis of microbial chemolithoautotrophic phosphite oxidation yields evidence of a seventh natural CO 2 fixation pathway. Proc Natl Acad Sci U S A 2018; 115:E92-E101. [PMID: 29183985 PMCID: PMC5776814 DOI: 10.1073/pnas.1715549114] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Dissimilatory phosphite oxidation (DPO), a microbial metabolism by which phosphite (HPO32-) is oxidized to phosphate (PO43-), is the most energetically favorable chemotrophic electron-donating process known. Only one DPO organism has been described to date, and little is known about the environmental relevance of this metabolism. In this study, we used 16S rRNA gene community analysis and genome-resolved metagenomics to characterize anaerobic wastewater treatment sludge enrichments performing DPO coupled to CO2 reduction. We identified an uncultivated DPO bacterium, Candidatus Phosphitivorax (Ca. P.) anaerolimi strain Phox-21, that belongs to candidate order GW-28 within the Deltaproteobacteria, which has no known cultured isolates. Genes for phosphite oxidation and for CO2 reduction to formate were found in the genome of Ca. P. anaerolimi, but it appears to lack any of the known natural carbon fixation pathways. These observations led us to propose a metabolic model for autotrophic growth by Ca. P. anaerolimi whereby DPO drives CO2 reduction to formate, which is then assimilated into biomass via the reductive glycine pathway.
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Affiliation(s)
- Israel A Figueroa
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Tyler P Barnum
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Pranav Y Somasekhar
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Charlotte I Carlström
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Anna L Engelbrektson
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - John D Coates
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
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13
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Westerholm M, Müller B, Singh A, Karlsson Lindsjö O, Schnürer A. Detection of novel syntrophic acetate-oxidizing bacteria from biogas processes by continuous acetate enrichment approaches. Microb Biotechnol 2017; 11:680-693. [PMID: 29239113 PMCID: PMC6011928 DOI: 10.1111/1751-7915.13035] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 11/11/2017] [Accepted: 11/12/2017] [Indexed: 11/27/2022] Open
Abstract
To enrich syntrophic acetate‐oxidizing bacteria (SAOB), duplicate chemostats were inoculated with sludge from syntrophic acetate oxidation (SAO)‐dominated systems and continuously supplied with acetate (0.4 or 7.5 g l−1) at high‐ammonia levels. The chemostats were operated under mesophilic (37°C) or thermophilic (52°C) temperature for about six hydraulic retention times (HRT 28 days) and were sampled over time. Irrespective of temperature, a methane content of 64–69% and effluent acetate level of 0.4–1.0 g l−1 were recorded in chemostats fed high acetate. Low methane production in the low‐acetate chemostats indicated that the substrate supply was below the threshold for methanization of acetate via SAO. Novel representatives within the family Clostridiales and genus Syntrophaceticus (class Clostridia) were identified to represent putative SAOB candidates in mesophilic and thermophilic conditions respectively. Known SAOB persisted at low relative abundance in all chemostats. The hydrogenotrophic methanogens Methanoculleus bourgensis (mesophilic) and Methanothermobacter thermautotrophicus (thermophilic) dominated archaeal communities in the high‐acetate chemostats. In line with the restricted methane production in the low‐acetate chemostats, methanogens persisted at considerably lower abundance in these chemostats. These findings strongly indicate involvement in SAO and tolerance to high ammonia levels of the species identified here, and have implications for understanding community function in stressed anaerobic processes.
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Affiliation(s)
- Maria Westerholm
- Uppsala BioCenter, Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7025, SE-750 07, Uppsala, Sweden
| | - Bettina Müller
- Uppsala BioCenter, Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7025, SE-750 07, Uppsala, Sweden
| | - Abhijeet Singh
- Uppsala BioCenter, Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7025, SE-750 07, Uppsala, Sweden
| | - Oskar Karlsson Lindsjö
- Uppsala BioCenter, Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7025, SE-750 07, Uppsala, Sweden
| | - Anna Schnürer
- Uppsala BioCenter, Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7025, SE-750 07, Uppsala, Sweden
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14
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Schink B, Montag D, Keller A, Müller N. Hydrogen or formate: Alternative key players in methanogenic degradation. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:189-202. [PMID: 28205388 DOI: 10.1111/1758-2229.12524] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Hydrogen and formate are important electron carriers in methanogenic degradation in anoxic environments such as sediments, sewage sludge digestors and biogas reactors. Especially in the terminal steps of methanogenesis, they determine the energy budgets of secondary (syntrophically) fermenting bacteria and their methanogenic partners. The literature provides considerable data on hydrogen pool sizes in such habitats, but little data exist for formate concentrations due to technical difficulties in formate determination at low concentration. Recent evidence from biochemical and molecular biological studies indicates that several secondary fermenters can use both hydrogen and formate for electron release, and may do so even simultaneously. Numerous strictly anaerobic bacteria contain enzymes which equilibrate hydrogen and formate pools to energetically equal values, and recent measurements in sewage digestors and biogas reactors indicate that - beyond occasional fluctuations - the pool sizes of hydrogen and formate are indeed energetically nearly equivalent. Nonetheless, a thermophilic archaeon from a submarine hydrothermal vent, Thermococcus onnurineus, can obtain ATP from the conversion of formate to hydrogen plus bicarbonate at 80°C, indicating that at least in this extreme environment the pools of formate and hydrogen are likely to be sufficiently different to support such an unusual type of energy conservation.
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Affiliation(s)
- Bernhard Schink
- Department of Biology, Microbial Ecology, University of Konstanz, Konstanz, D-78457, Germany
| | - Dominik Montag
- Department of Biology, Microbial Ecology, University of Konstanz, Konstanz, D-78457, Germany
| | - Anja Keller
- Department of Biology, Microbial Ecology, University of Konstanz, Konstanz, D-78457, Germany
| | - Nicolai Müller
- Department of Biology, Microbial Ecology, University of Konstanz, Konstanz, D-78457, Germany
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15
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Manzoor S, Bongcam-Rudloff E, Schnürer A, Müller B. Genome-Guided Analysis and Whole Transcriptome Profiling of the Mesophilic Syntrophic Acetate Oxidising Bacterium Syntrophaceticus schinkii. PLoS One 2016; 11:e0166520. [PMID: 27851830 PMCID: PMC5113046 DOI: 10.1371/journal.pone.0166520] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 10/31/2016] [Indexed: 01/29/2023] Open
Abstract
Syntrophaceticus schinkii is a mesophilic, anaerobic bacterium capable of oxidising acetate to CO2 and H2 in intimate association with a methanogenic partner, a syntrophic relationship which operates close to the energetic limits of microbial life. Syntrophaceticus schinkii has been identified as a key organism in engineered methane-producing processes relying on syntrophic acetate oxidation as the main methane-producing pathway. However, due to strict cultivation requirements and difficulties in reconstituting the thermodynamically unfavourable acetate oxidation, the physiology of this functional group is poorly understood. Genome-guided and whole transcriptome analyses performed in the present study provide new insights into habitat adaptation, syntrophic acetate oxidation and energy conservation. The working draft genome of Syntrophaceticus schinkii indicates limited metabolic capacities, with lack of organic nutrient uptake systems, chemotactic machineries, carbon catabolite repression and incomplete biosynthesis pathways. Ech hydrogenase, [FeFe] hydrogenases, [NiFe] hydrogenases, F1F0-ATP synthase and membrane-bound and cytoplasmic formate dehydrogenases were found clearly expressed, whereas Rnf and a predicted oxidoreductase/heterodisulphide reductase complex, both found encoded in the genome, were not expressed under syntrophic growth condition. A transporter sharing similarities to the high-affinity acetate transporters of aceticlastic methanogens was also found expressed, suggesting that Syntrophaceticus schinkii can potentially compete with methanogens for acetate. Acetate oxidation seems to proceed via the Wood-Ljungdahl pathway as all genes involved in this pathway were highly expressed. This study shows that Syntrophaceticus schinkii is a highly specialised, habitat-adapted organism relying on syntrophic acetate oxidation rather than metabolic versatility. By expanding its complement of respiratory complexes, it might overcome limiting bioenergetic barriers, and drive efficient energy conservation from reactions operating close to the thermodynamic equilibrium, which might enable S. schinkii to occupy the same niche as the aceticlastic methanogens. The knowledge gained here will help specify process conditions supporting efficient and robust biogas production and will help identify mechanisms important for the syntrophic lifestyle.
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Affiliation(s)
- Shahid Manzoor
- Department of Information Technology, University of the Punjab, Lahore, Pakistan
| | - Erik Bongcam-Rudloff
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Science, SLU-Global Bioinformatics Centre, Uppsala, SE 750 07, Sweden
| | - Anna Schnürer
- Department of Microbiology, Swedish University of Agricultural Sciences, BioCenter, Uppsala, SE 750 07, Sweden
| | - Bettina Müller
- Department of Microbiology, Swedish University of Agricultural Sciences, BioCenter, Uppsala, SE 750 07, Sweden
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16
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Novel Syntrophic Populations Dominate an Ammonia-Tolerant Methanogenic Microbiome. mSystems 2016; 1:mSystems00092-16. [PMID: 27822555 PMCID: PMC5080403 DOI: 10.1128/msystems.00092-16] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 08/18/2016] [Indexed: 12/31/2022] Open
Abstract
The microbial production of methane or “biogas” is an attractive renewable energy technology that can recycle organic waste into biofuel. Biogas reactors operating with protein-rich substrates such as household municipal or agricultural wastes have significant industrial and societal value; however, they are highly unstable and frequently collapse due to the accumulation of ammonia. We report the discovery of a novel uncultured phylotype (unFirm_1) that is highly detectable in metaproteomic data generated from an ammonia-tolerant commercial reactor. Importantly, unFirm_1 is proposed to perform a key metabolic step in biogas microbiomes, whereby it syntrophically oxidizes acetate to hydrogen and carbon dioxide, which methanogens then covert to methane. Only very few culturable syntrophic acetate-oxidizing bacteria have been described, and all were detected at low in situ levels compared to unFirm_1. Broader comparisons produced the hypothesis that unFirm_1 is a key mediator toward the successful long-term stable operation of biogas production using protein-rich substrates. Biogas reactors operating with protein-rich substrates have high methane potential and industrial value; however, they are highly susceptible to process failure because of the accumulation of ammonia. High ammonia levels cause a decline in acetate-utilizing methanogens and instead promote the conversion of acetate via a two-step mechanism involving syntrophic acetate oxidation (SAO) to H2 and CO2, followed by hydrogenotrophic methanogenesis. Despite the key role of syntrophic acetate-oxidizing bacteria (SAOB), only a few culturable representatives have been characterized. Here we show that the microbiome of a commercial, ammonia-tolerant biogas reactor harbors a deeply branched, uncultured phylotype (unFirm_1) accounting for approximately 5% of the 16S rRNA gene inventory and sharing 88% 16S rRNA gene identity with its closest characterized relative. Reconstructed genome and quantitative metaproteomic analyses imply unFirm_1’s metabolic dominance and SAO capabilities, whereby the key enzymes required for acetate oxidation are among the most highly detected in the reactor microbiome. While culturable SAOB were identified in genomic analyses of the reactor, their limited proteomic representation suggests that unFirm_1 plays an important role in channeling acetate toward methane. Notably, unFirm_1-like populations were found in other high-ammonia biogas installations, conjecturing a broader importance for this novel clade of SAOB in anaerobic fermentations. IMPORTANCE The microbial production of methane or “biogas” is an attractive renewable energy technology that can recycle organic waste into biofuel. Biogas reactors operating with protein-rich substrates such as household municipal or agricultural wastes have significant industrial and societal value; however, they are highly unstable and frequently collapse due to the accumulation of ammonia. We report the discovery of a novel uncultured phylotype (unFirm_1) that is highly detectable in metaproteomic data generated from an ammonia-tolerant commercial reactor. Importantly, unFirm_1 is proposed to perform a key metabolic step in biogas microbiomes, whereby it syntrophically oxidizes acetate to hydrogen and carbon dioxide, which methanogens then covert to methane. Only very few culturable syntrophic acetate-oxidizing bacteria have been described, and all were detected at low in situ levels compared to unFirm_1. Broader comparisons produced the hypothesis that unFirm_1 is a key mediator toward the successful long-term stable operation of biogas production using protein-rich substrates.
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17
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Draft Genome Sequence of the Syntrophic Lactate-Degrading Bacterium Tepidanaerobacter syntrophicus JLT. GENOME ANNOUNCEMENTS 2016; 4:4/1/e01712-15. [PMID: 26868399 PMCID: PMC4751323 DOI: 10.1128/genomea.01712-15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report here a high-quality draft genome sequence of the type strain (JL) of Tepidanaerobacter syntrophicus, an obligately anaerobic and moderately thermophilic bacterium, which is able to perform syntrophic lactate degradation with hydrogenotrophic methanogens. The genome comprises 2.43 Mb in 9 scaffolds, with a G+C content of 38.6%.
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18
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Müller B, Sun L, Westerholm M, Schnürer A. Bacterial community composition and fhs profiles of low- and high-ammonia biogas digesters reveal novel syntrophic acetate-oxidising bacteria. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:48. [PMID: 26925165 PMCID: PMC4769498 DOI: 10.1186/s13068-016-0454-9] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 02/08/2016] [Indexed: 05/04/2023]
Abstract
BACKGROUND Syntrophic acetate oxidation (SAO) is the predominant pathway for methane production in high ammonia anaerobic digestion processes. The bacteria (SAOB) occupying this niche and the metabolic pathway are poorly understood. Phylogenetic diversity and strict cultivation requirements hinder comprehensive research and discovery of novel SAOB. Most SAOB characterised to date are affiliated to the physiological group of acetogens. Formyltetrahydrofolate synthetase is a key enzyme of both acetogenic and SAO metabolism. The encoding fhs gene has therefore been identified as a suitable functional marker, using a newly designed primer pair. In this comparative study, we used a combination of terminal restriction fragment length polymorphism profiling, clone-based comparison, qPCR and Illumina amplicon sequencing to assess the bacterial community and acetogenic sub-community prevailing in high- and low-ammonia laboratory-scale digesters in order to delineate potential SAOB communities. Potential candidates identified were further tracked in a number of low-ammonia and high-ammonia laboratory-scale and large-scale digesters in order to reveal a potential function in SAO. RESULTS All methodical approaches revealed significant changes in the bacterial community composition concurrently with increasing ammonia and predominance of SAO. The acetogenic community under high ammonia conditions was revealed to be generally heterogeneous, but formed distinct phylogenetic clusters. The clusters differed clearly from those found under low-ammonia conditions and represented an acetogenic assemblage unique for biogas processes and recurring in a number of high-ammonia processes, indicating potential involvement in SAO. CONCLUSIONS The phylogenetic affiliation and population dynamics observed point to a key community, belonging mainly to the Clostridia class, in particular to the orders Clostridiales and Thermoanaerobacterales, which appear to specialise in SAO rather than being metabolically versatile. Overall, the results reported here provide evidence of functional importance of the bacterial families identified in high-ammonia systems and extend existing knowledge of bacterial and acetogenic assemblages at low and high ammonia levels. This information will be of help in monitoring and assessing the impacts on the SAOB community in order to identify characteristics of robust and productive high ammonia biogas processes.
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Affiliation(s)
- Bettina Müller
- Department of Microbiology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Box 7025, 750 07 Uppsala, Sweden
| | - Li Sun
- Department of Microbiology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Box 7025, 750 07 Uppsala, Sweden
| | - Maria Westerholm
- Department of Microbiology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Box 7025, 750 07 Uppsala, Sweden
| | - Anna Schnürer
- Department of Microbiology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Box 7025, 750 07 Uppsala, Sweden
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19
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Manzoor S, Müller B, Niazi A, Schnürer A, Bongcam-Rudloff E. Working draft genome sequence of the mesophilic acetate oxidizing bacterium Syntrophaceticus schinkii strain Sp3. Stand Genomic Sci 2015; 10:99. [PMID: 26566424 PMCID: PMC4642661 DOI: 10.1186/s40793-015-0092-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Accepted: 10/29/2015] [Indexed: 11/10/2022] Open
Abstract
Syntrophaceticus schinkii strain Sp3 is a mesophilic syntrophic acetate oxidizing bacterium, belonging to the Clostridia class within the phylum Firmicutes, originally isolated from a mesophilic methanogenic digester. It has been shown to oxidize acetate in co-cultivation with hydrogenotrophic methanogens forming methane. The draft genome shows a total size of 3,196,921 bp, encoding 3,688 open reading frames, which includes 3,445 predicted protein-encoding genes and 55 RNA genes. Here, we are presenting assembly and annotation features as well as basic genomic properties of the type strain Sp3.
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Affiliation(s)
- Shahid Manzoor
- />Department of Animal Breeding and Genetics Science, Swedish University of Agricultural Science, SLU-Global Bioinformatics Centre, Uppsala, SE 750 07 Sweden
- />University of the Punjab, Lahore, Pakistan
| | - Bettina Müller
- />Department of Microbiology, Swedish University of Agricultural Sciences, BioCenter, Uppsala, SE 750 07 Sweden
| | - Adnan Niazi
- />Department of Animal Breeding and Genetics Science, Swedish University of Agricultural Science, SLU-Global Bioinformatics Centre, Uppsala, SE 750 07 Sweden
| | - Anna Schnürer
- />Department of Microbiology, Swedish University of Agricultural Sciences, BioCenter, Uppsala, SE 750 07 Sweden
| | - Erik Bongcam-Rudloff
- />Department of Animal Breeding and Genetics Science, Swedish University of Agricultural Science, SLU-Global Bioinformatics Centre, Uppsala, SE 750 07 Sweden
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