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Choudhury PK, Jena R, Puniya AK, Tomar SK. Isolation and characterization of reductive acetogens from rumen fluid samples of Murrah buffaloes. 3 Biotech 2023; 13:265. [PMID: 37415727 PMCID: PMC10319699 DOI: 10.1007/s13205-023-03688-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 06/27/2023] [Indexed: 07/08/2023] Open
Abstract
In the present study, attempts have been made to isolate reductive acetogens from the rumen fluid samples of Murrah buffaloes (Bubalus bubalis). Out of 32 rumen samples 51 isolates were isolated, and based on autotrophic growth for production of acetate and presence of formyltetrahydrofolate synthetase gene (FTHFS) 12 isolates were confirmed as reductive acetogens. Microscopic observations showed that ten isolates as Gram-positive rods (ACB28, ACB29, ACB66, ACB73, ACB81, ACB91, ACB133, ACB229, ACB52, ACB95) and two isolates as Gram-positive cocci (ACB19, ACB89). All isolates tested negative for catalase, oxidase, and gelatin liquefaction, whereas the production of H2S was detected for two (ACB52 and ACB95) of the above isolates. All these isolates showed autotrophic growth from H2 and CO2, and heterotrophic growth with different fermentable sugars, viz., d-glucose, D-fructose, and D-trehalose but failed to grow on salicin, raffinose, and l-rhamnose. Out of the isolates, two showed amylase activity (ACB28 and ACB95), five showed CMCase activity (ACB19, ACB28, ACB29, ACB73 and ACB91), three showed pectinase activity (ACB29, ACB52 and ACB89), whereas none of the isolates was found positive for avicellase and xylanase activity. Based on 16S rDNA gene sequence analysis, the isolates showed their phylogenetic relationship with maximum similarity up to 99% to different strains of earlier reported known acetogens of clostridia group including Clostridium sp. (6), Eubacterium limosum (1), Ruminococcus sp. (1) and Acetobacterium woodii (1) except one, i.e., Vagococcus fluvialis. The results indicate that reductive acetogens isolated from the rumen fluid samples of Murrah buffalos are both autotrophic and heterotrophic in nature and further investigations are required to exploit and explore their potential as an alternate hydrogen sink.
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Affiliation(s)
- Prasanta Kumar Choudhury
- Dairy Microbiology Division, ICAR-National Dairy Research Institute, Karnal, Haryana 132001 India
- Department of Dairy Technology, School of Agricultural and Bioengineering, Centurion University of Technology and Management, Paralakhemundi, Odisha 761211 India
| | - Rajashree Jena
- Dairy Microbiology Division, ICAR-National Dairy Research Institute, Karnal, Haryana 132001 India
- Department of Dairy Technology, School of Agricultural and Bioengineering, Centurion University of Technology and Management, Paralakhemundi, Odisha 761211 India
| | - Anil Kumar Puniya
- Dairy Microbiology Division, ICAR-National Dairy Research Institute, Karnal, Haryana 132001 India
| | - Sudhir Kumar Tomar
- Dairy Microbiology Division, ICAR-National Dairy Research Institute, Karnal, Haryana 132001 India
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2
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Singh A, Schnürer A. AcetoBase Version 2: a database update and re-analysis of formyltetrahydrofolate synthetase amplicon sequencing data from anaerobic digesters. Database (Oxford) 2022; 2022:6609150. [PMID: 35708586 PMCID: PMC9216588 DOI: 10.1093/database/baac041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 05/03/2022] [Accepted: 05/04/2022] [Indexed: 11/14/2022]
Abstract
AcetoBase is a public repository and database of formyltetrahydrofolate synthetase (FTHFS) sequences. It is the first systematic collection of bacterial FTHFS nucleotide and protein sequences from genomes and metagenome-assembled genomes and of sequences generated by clone library sequencing. At its publication in 2019, AcetoBase (Version 1) was also the first database to establish connections between the FTHFS gene, the Wood–Ljungdahl pathway and 16S ribosomal RNA genes. Since the publication of AcetoBase, there have been significant improvements in the taxonomy of many bacterial lineages and accessibility/availability of public genomics and metagenomics data. The update to the AcetoBase reference database described here (Version 2) provides new sequence data and taxonomy, along with improvements in web functionality and user interface. The evaluation of this latest update by re-analysis of publicly accessible FTHFS amplicon sequencing data previously analysed with AcetoBase Version 1 revealed significant improvements in the taxonomic assignment of FTHFS sequences. Database URL: https://acetobase.molbio.slu.se
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Affiliation(s)
- Abhijeet Singh
- Department of Molecular Sciences, BioCenter, Anaerobic Microbiology and Biotechnology Group, Swedish University of Agricultural Sciences , Almas Allé 5, Uppsala SE-750 07, Sweden
| | - Anna Schnürer
- Department of Molecular Sciences, BioCenter, Anaerobic Microbiology and Biotechnology Group, Swedish University of Agricultural Sciences , Almas Allé 5, Uppsala SE-750 07, Sweden
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3
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Fuentes L, Palomo-Briones R, de Jesús Montoya-Rosales J, Braga L, Castelló E, Vesga A, Tapia-Venegas E, Razo-Flores E, Ecthebehere C. Knowing the enemy: homoacetogens in hydrogen production reactors. Appl Microbiol Biotechnol 2021; 105:8989-9002. [PMID: 34716461 DOI: 10.1007/s00253-021-11656-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 09/17/2021] [Accepted: 10/18/2021] [Indexed: 11/29/2022]
Abstract
One of the bottlenecks of the hydrogen production by dark fermentation is the low yields obtained because of the homoacetogenesis persistence, a metabolic pathway where H2 and CO2 are consumed to produce acetate. The central reactions of H2 production and homoacetogenesis are catalyzed by enzyme hydrogenase and the formyltetrahydrofolate synthetase, respectively. In this work, genes encoding for the formyltetrahydrofolate synthetase (fthfs) and hydrogenase (hydA) were used to investigate the diversity of homoacetogens as well as their phylogenetic relationships through quantitative PCR (qPCR) and next-generation amplicon sequencing. A total of 70 samples from 19 different H2-producing bioreactors with different configurations and operating conditions were analyzed. Quantification through qPCR showed that the abundance of fthfs and hydA was strongly associated with the type of substrate, organic loading rate, and H2 production performance. In particular, fthfs sequencing revealed that homoacetogens diversity was low with one or two dominant homoacetogens in each sample. Clostridium carboxivorans was detected in the reactors fed with agave hydrolisates; Acetobacterium woodii dominated in systems fed with glucose; Blautia coccoides and unclassified Sporoanaerobacter species were present in reactors fed with cheese whey; finally, Eubacterium limosum and Selenomonas sp. were co-dominant in reactors fed with glycerol. Altogether, quantification and sequencing analysis revealed that the occurrence of homoacetogenesis could take place due to (1) metabolic changes of H2-producing bacteria towards homoacetogenesis or (2) the displacement of H2-producing bacteria by homoacetogens. Overall, it was demonstrated that the fthfs gene was a suitable marker to investigate homoacetogens in H2-producing reactors. KEY POINTS: • qPCR and sequencing analysis revealed two homoacetogenesis phenomena. • fthfs gene was a suitable marker to investigate homoacetogens in H2 reactors.
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Affiliation(s)
- Laura Fuentes
- Laboratorio de Ecología Microbiana, Departamento de Bioquímica Y Genómica Microbiana, Instituto de Investigaciones Biológicas Clemente Estable, Av. Italia, 3318, Montevideo, Uruguay
| | - Rodolfo Palomo-Briones
- División de Ciencias Ambientales, Instituto Potosino de Investigación Científica Y Tecnológica A.C, Camino a La Presa San José No, 2055, Col. Lomas 4a Sección, C.P., 78216, San Luis Potosí, SLP, México
| | - José de Jesús Montoya-Rosales
- División de Ciencias Ambientales, Instituto Potosino de Investigación Científica Y Tecnológica A.C, Camino a La Presa San José No, 2055, Col. Lomas 4a Sección, C.P., 78216, San Luis Potosí, SLP, México
| | - Lucía Braga
- Laboratorio Bioprocesos Ambientales, Facultad de Ingeniería, Instituto de Ingeniería Química, Universidad de La República, Herrera Y Reissig, 565, Montevideo, Uruguay
| | - Elena Castelló
- Laboratorio Bioprocesos Ambientales, Facultad de Ingeniería, Instituto de Ingeniería Química, Universidad de La República, Herrera Y Reissig, 565, Montevideo, Uruguay
| | - Alejandra Vesga
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, 2085, Valparaíso, Av. Brasil, Chile
| | - Estela Tapia-Venegas
- Departamento de Medio Ambiente, Facultad de Ingeniería, Universidad de Playa Ancha Av, Leopoldo Carvallo 270, Valparaíso, Chile
| | - Elías Razo-Flores
- División de Ciencias Ambientales, Instituto Potosino de Investigación Científica Y Tecnológica A.C, Camino a La Presa San José No, 2055, Col. Lomas 4a Sección, C.P., 78216, San Luis Potosí, SLP, México
| | - Claudia Ecthebehere
- Laboratorio de Ecología Microbiana, Departamento de Bioquímica Y Genómica Microbiana, Instituto de Investigaciones Biológicas Clemente Estable, Av. Italia, 3318, Montevideo, Uruguay.
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4
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Singh A, Moestedt J, Berg A, Schnürer A. Microbiological Surveillance of Biogas Plants: Targeting Acetogenic Community. Front Microbiol 2021; 12:700256. [PMID: 34484143 PMCID: PMC8415747 DOI: 10.3389/fmicb.2021.700256] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 07/21/2021] [Indexed: 11/15/2022] Open
Abstract
Acetogens play a very important role in anaerobic digestion and are essential in ensuring process stability. Despite this, targeted studies of the acetogenic community in biogas processes remain limited. Some efforts have been made to identify and understand this community, but the lack of a reliable molecular analysis strategy makes the detection of acetogenic bacteria tedious. Recent studies suggest that screening of bacterial genetic material for formyltetrahydrofolate synthetase (FTHFS), a key marker enzyme in the Wood-Ljungdahl pathway, can give a strong indication of the presence of putative acetogens in biogas environments. In this study, we applied an acetogen-targeted analyses strategy developed previously by our research group for microbiological surveillance of commercial biogas plants. The surveillance comprised high-throughput sequencing of FTHFS gene amplicons and unsupervised data analysis with the AcetoScan pipeline. The results showed differences in the acetogenic community structure related to feed substrate and operating parameters. They also indicated that our surveillance method can be helpful in the detection of community changes before observed changes in physico-chemical profiles, and that frequent high-throughput surveillance can assist in management towards stable process operation, thus improving the economic viability of biogas plants. To our knowledge, this is the first study to apply a high-throughput microbiological surveillance approach to visualise the potential acetogenic population in commercial biogas digesters.
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Affiliation(s)
- Abhijeet Singh
- Anaerobic Microbiology and Biotechnology Group, Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jan Moestedt
- Tekniska Verken i Linköping AB, Department R&D, Linköping, Sweden
| | | | - Anna Schnürer
- Anaerobic Microbiology and Biotechnology Group, Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
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5
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Singh A, Nylander JAA, Schnürer A, Bongcam-Rudloff E, Müller B. High-Throughput Sequencing and Unsupervised Analysis of Formyltetrahydrofolate Synthetase (FTHFS) Gene Amplicons to Estimate Acetogenic Community Structure. Front Microbiol 2020; 11:2066. [PMID: 32983047 PMCID: PMC7481360 DOI: 10.3389/fmicb.2020.02066] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 08/05/2020] [Indexed: 11/17/2022] Open
Abstract
The formyltetrahydrofolate synthetase (FTHFS) gene is a molecular marker of choice to study the diversity of acetogenic communities. However, current analyses are limited due to lack of a high-throughput sequencing approach for FTHFS gene amplicons and a dedicated bioinformatics pipeline for data analysis, including taxonomic annotation and visualization of the sequence data. In the present study, we combined the barcode approach for multiplexed sequencing with unsupervised data analysis to visualize acetogenic community structure. We used samples from a biogas digester to develop proof-of-principle for our combined approach. We successfully generated high-throughput sequence data for the partial FTHFS gene and performed unsupervised data analysis using the novel bioinformatics pipeline “AcetoScan” presented in this study, which resulted in taxonomically annotated OTUs, phylogenetic tree, abundance plots and diversity indices. The results demonstrated that high-throughput sequencing can be used to sequence the FTHFS amplicons from a pool of samples, while the analysis pipeline AcetoScan can be reliably used to process the raw sequence data and visualize acetogenic community structure. The method and analysis pipeline described in this paper can assist in the identification and quantification of known or potentially new acetogens. The AcetoScan pipeline is freely available at https://github.com/abhijeetsingh1704/AcetoScan.
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Affiliation(s)
- Abhijeet Singh
- Anaerobic Microbiology and Biotechnology Group, Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Johan A A Nylander
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,National Bioinformatics Infrastructure Sweden, SciLifeLab, Uppsala, Sweden
| | - Anna Schnürer
- Anaerobic Microbiology and Biotechnology Group, Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Erik Bongcam-Rudloff
- SLU-Global Bioinformatics Centre, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Bettina Müller
- Anaerobic Microbiology and Biotechnology Group, Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
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6
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Kim SH, Mamuad LL, Islam M, Lee SS. Reductive acetogens isolated from ruminants and their effect on in vitro methane mitigation and milk performance in Holstein cows. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2020; 62:1-13. [PMID: 32082593 PMCID: PMC7008121 DOI: 10.5187/jast.2020.62.1.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/05/2019] [Accepted: 11/22/2019] [Indexed: 11/20/2022]
Abstract
This study was designed to evaluate the in vitro and in
vivo effects of reductive acetogens isolated from ruminants on
methane mitigation, and milk performance, respectively. Four acetogens,
Proteiniphilum acetatigenes DA02, P.
acetatigenes GA01, Alkaliphilus crotonatoxidans
GA02, and P. acetatigenes GA03 strains were isolated from
ruminants and used in in vitro experiment. A control (without
acetogen) and a positive group (with Eubacterium limosum ATCC
8486) were also included in in vitro experiment. Based on
higher acetate as well as lower methane producing ability in in
vitro trial, P. acetatigenes GA03 was used as
inoculum for in vivo experiment. Holstein dairy cows (n = 14)
were divided into two groups viz. control (without) and GA03 group (diet
supplied with P. acetatigenes GA03 at a feed rate of 1%
supplementation). Milk performance and blood parameters were checked for both
groups. In in vitro, the total volatile fatty acids and acetate
production were higher (p < 0.05) in all 4 isolated
acetogens than the control and positive treatment. Also, all acetogens
significantly lowered (p < 0.05) methane production in
comparison to positive and control groups however, GA03 had the lowest
(p < 0.05) methane production among 4 isolates. In
in vivo, the rate of milk yield reduction was higher
(p < 0.05) in the control than GA03 treated group
(5.07 vs 2.4 kg). Similarly, the decrease in milk fat was also higher in control
(0.14% vs 0.09%) than treatment. The somatic cell counts (SCC;
×103/mL) was decreased from 128.43 to 107.00 in acetogen
treated group however, increased in control from 138.14 to 395.71. In addition,
GA03 increased blood glucose and decreased non-esterified fatty acids. Our
results suggest that the isolated acetogens have the potential for in
vitro methane reduction and P. acetatigenes GA03
strain could be a candidate probiotic strain for improving milk yield and milk
fat in lactating cows with lowering SCCs.
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Affiliation(s)
- Seon-Ho Kim
- Ruminant Nutrition and Anaerobe Laboratory, Department of Animal Science and Technology, Sunchon National University, Suncheon 57922, Korea
| | - Lovelia L Mamuad
- Ruminant Nutrition and Anaerobe Laboratory, Department of Animal Science and Technology, Sunchon National University, Suncheon 57922, Korea
| | - Mahfuzul Islam
- Ruminant Nutrition and Anaerobe Laboratory, Department of Animal Science and Technology, Sunchon National University, Suncheon 57922, Korea
| | - Sang-Suk Lee
- Ruminant Nutrition and Anaerobe Laboratory, Department of Animal Science and Technology, Sunchon National University, Suncheon 57922, Korea
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7
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Deciphering mixotrophic Clostridium formicoaceticum metabolism and energy conservation: Genomic analysis and experimental studies. Genomics 2019; 111:1687-1694. [DOI: 10.1016/j.ygeno.2018.11.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 11/07/2018] [Accepted: 11/16/2018] [Indexed: 01/01/2023]
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8
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Fischer MA, Ulbricht A, Neulinger SC, Refai S, Waßmann K, Künzel S, Schmitz RA. Immediate Effects of Ammonia Shock on Transcription and Composition of a Biogas Reactor Microbiome. Front Microbiol 2019; 10:2064. [PMID: 31555248 PMCID: PMC6742706 DOI: 10.3389/fmicb.2019.02064] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 08/21/2019] [Indexed: 12/22/2022] Open
Abstract
The biotechnological process of biogas production from organic material is carried out by a diverse microbial community under anaerobic conditions. However, the complex and sensitive microbial network present in anaerobic degradation of organic material can be disturbed by increased ammonia concentration introduced into the system by protein-rich substrates and imbalanced feeding. Here, we report on a simulated increase of ammonia concentration in a fed batch lab-scale biogas reactor experiment. Two treatment conditions were used simulating total ammonia nitrogen concentrations of 4.9 and 8.0 g/L with four replicate reactors. Each reactor was monitored concerning methane generation and microbial composition using 16S rRNA gene amplicon sequencing, while the transcriptional activity of the overall process was investigated by metatranscriptomic analysis. This allowed investigating the response of the microbial community in terms of species composition and transcriptional activity to a rapid upshift to high ammonia conditions. Clostridia and Methanomicrobiales dominated the microbial community throughout the entire experiment under both experimental conditions, while Methanosarcinales were only present in minor abundance. Transcription analysis demonstrated clostridial dominance with respect to genes encoding for enzymes of the hydrolysis step (cellulase, EC 3.2.1.4) as well as dominance of key genes for enzymes of the methanogenic pathway (methyl-CoM reductase, EC 2.8.4.1; heterodisulfide reductase, EC 1.8.98.1). Upon ammonia shock, the selected marker genes showed significant changes in transcriptional activity. Cellulose hydrolysis as well as methanogenesis were significantly reduced at high ammonia concentrations as indicated by reduced transcription levels of the corresponding genes. Based on these experiments we concluded that, apart from the methanogenic archaea, hydrolytic cellulose-degrading microorganisms are negatively affected by high ammonia concentrations. Further, Acholeplasma and Erysipelotrichia showed lower abundance under increased ammonia concentrations and thus might serve as indicator species for an earlier detection in order to counteract against ammonia crises.
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Affiliation(s)
- Martin A. Fischer
- Department of Biology, Institute of General Microbiology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Andrea Ulbricht
- Department of Biology, Institute of General Microbiology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Sven C. Neulinger
- Department of Biology, Institute of General Microbiology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Sarah Refai
- Department of Biology, Institut für Mikrobiologie und Biotechnologie, University Bonn, Bonn, Germany
| | - Kati Waßmann
- Department of Biology, Institut für Mikrobiologie und Biotechnologie, University Bonn, Bonn, Germany
| | - Sven Künzel
- Department for Evolutionary Genetics, Max-Planck-Institute for Evolutionary Biology, Plön, Germany
| | - Ruth A. Schmitz
- Department of Biology, Institute of General Microbiology, Christian-Albrechts-University Kiel, Kiel, Germany
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9
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Guo N, Ma X, Ren S, Wang S, Wang Y. Mechanisms of metabolic performance enhancement during electrically assisted anaerobic treatment of chloramphenicol wastewater. WATER RESEARCH 2019; 156:199-207. [PMID: 30917300 DOI: 10.1016/j.watres.2019.03.032] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 03/15/2019] [Accepted: 03/17/2019] [Indexed: 06/09/2023]
Abstract
The anaerobic process is a favorable alternative for the treatment of antibiotic pharmaceutical wastewater. The electrically assisted anaerobic process can be used to accelerate contaminant removal, especially for persistent organic pollutants such as antibiotics. In this study, an electrically assisted anaerobic system for chloramphenicol (CAP) wastewater treatment was developed. The system performance and the underlying metabolic mechanisms were evaluated under different applied voltages. With the increase of applied voltage from 0 to 2 V, the CAP removal efficiencies increased from 53.3% to 89.7%, while the methane production increased more than three times. The microbial community structure and correlation analysis showed that electrical stimulation selected the dominant functional bacteria and increased antibiotic resistance in dominant functional bacteria, both of which enhanced CAP removal and methane production. The improved CAP removal was a result of the presence of dechlorination-related bacteria (Acidovorax, Sedimentibacter, Thauera, and Flavobacterium) and potential electroactive bacteria (Shewanella and Comamonas), both of which carried ARGs and therefore could survive the biotoxicity of CAP. The enhanced methane production could be partly attributed to the surviving fermentative-related bacteria (Paludibacter, Proteiniclasticum, and Macellibacteroides) in the anaerobic bioreactor. The increased abundances of methanogenic genes (mcrA and ACAS genes) under high voltage further confirmed the enhanced methane production of this electrically assisted anaerobic system. The fundamental understanding of the mechanisms underlying metabolic performance enhancement is critical for the further development of anaerobic wastewater treatment.
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Affiliation(s)
- Ning Guo
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, China
| | - Xiaofang Ma
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, China
| | - Shaojie Ren
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, China
| | - Shuguang Wang
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, China
| | - Yunkun Wang
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, China.
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Planý M, Czolderová M, Kraková L, Puškárová A, Bučková M, Šoltys K, Budiš J, Szemes T, Mackulak T, Wu JH, Pangallo D. Biogas production: evaluation of the influence of K2FeO4 pretreatment of maple leaves (Acer platanoides) on microbial consortia composition. Bioprocess Biosyst Eng 2019; 42:1151-1163. [DOI: 10.1007/s00449-019-02112-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 03/20/2019] [Indexed: 10/27/2022]
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11
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Matsui H, Mimura A, Maekawa S, Ban-Tokuda T. Effects of feed intake on the diversity and population density of homoacetogens in the large intestine of pigs. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2019; 32:1907-1913. [PMID: 31010997 PMCID: PMC6819677 DOI: 10.5713/ajas.18.0512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 02/12/2019] [Indexed: 11/27/2022]
Abstract
Objective Homoacetogens play important roles in the production of acetate in the large intestine of monogastric mammals. However, their diversity in the porcine large intestine is still unknown. Marker gene analysis was performed to assess the effects of energy level on the diversity and population densities of homoacetogens in porcine feces. Methods Crossbred pigs were fed high or low energy-level diets. The high-intake (HI) diet was sufficient to allow a daily gain of 1.2 kg. The low-intake (LI) diet provided 0.6 times the amount of energy as the HI diet. Genetic diversity was analyzed using formyltetrahydrofolate synthetase gene (FHS) clone libraries derived from fecal DNA samples. FHS DNA copy numbers were quantified using real-time polymerase chain reaction. Results A wide variety of FHS sequences was recovered from animals in both treatments. No differences in FHS clone libraries between the HI and LI groups were found. During the experimental period, no significant differences in the proportion of FHS copy numbers were observed between the two treatment groups. Conclusion This is the first reported molecular diversity analysis using specific homoacetogen marker genes from the large intestines of pigs. There was no observable effect of feed intake on acetogen diversity.
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Affiliation(s)
- Hiroki Matsui
- Graduate School of Bioresources, Mie University, Tsu, Mie 514-8507, Japan
| | - Ayumi Mimura
- Graduate School of Bioresources, Mie University, Tsu, Mie 514-8507, Japan.,Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan
| | - Sakiko Maekawa
- Graduate School of Bioresources, Mie University, Tsu, Mie 514-8507, Japan
| | - Tomomi Ban-Tokuda
- Graduate School of Bioresources, Mie University, Tsu, Mie 514-8507, Japan
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12
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Singh A, Müller B, Fuxelius HH, Schnürer A. AcetoBase: a functional gene repository and database for formyltetrahydrofolate synthetase sequences. Database (Oxford) 2019; 2019:baz142. [PMID: 31832668 PMCID: PMC6908459 DOI: 10.1093/database/baz142] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 11/01/2019] [Accepted: 11/14/2019] [Indexed: 01/01/2023]
Abstract
Acetogenic bacteria are imperative to environmental carbon cycling and diverse biotechnological applications, but their extensive physiological and taxonomical diversity is an impediment to systematic taxonomic studies. Acetogens are chemolithoautotrophic bacteria that perform reductive carbon fixation under anaerobic conditions through the Wood-Ljungdahl pathway (WLP)/acetyl-coenzyme A pathway. The gene-encoding formyltetrahydrofolate synthetase (FTHFS), a key enzyme of this pathway, is highly conserved and can be used as a molecular marker to probe acetogenic communities. However, there is a lack of systematic collection of FTHFS sequence data at nucleotide and protein levels. In an attempt to streamline investigations on acetogens, we developed AcetoBase - a repository and database for systematically collecting and organizing information related to FTHFS sequences. AcetoBase also provides an opportunity to submit data and obtain accession numbers, perform homology searches for sequence identification and access a customized blast database of submitted sequences. AcetoBase provides the prospect to identify potential acetogenic bacteria, based on metadata information related to genome content and the WLP, supplemented with FTHFS sequence accessions, and can be an important tool in the study of acetogenic communities. AcetoBase can be publicly accessed at https://acetobase.molbio.slu.se.
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Affiliation(s)
- Abhijeet Singh
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala BioCenter, Box 7025, SE-750 07 Uppsala, Sweden
| | - Bettina Müller
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala BioCenter, Box 7025, SE-750 07 Uppsala, Sweden
| | - Hans-Henrik Fuxelius
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala BioCenter, Box 7025, SE-750 07 Uppsala, Sweden
| | - Anna Schnürer
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala BioCenter, Box 7025, SE-750 07 Uppsala, Sweden
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13
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Acetogen Communities in the Gut of Herbivores and Their Potential Role in Syngas Fermentation. FERMENTATION-BASEL 2018. [DOI: 10.3390/fermentation4020040] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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14
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Li Y, Hu Q, Chen CH, Wang XL, Gao DW. Performance and microbial community structure in an integrated anaerobic fluidized-bed membrane bioreactor treating synthetic benzothiazole contaminated wastewater. BIORESOURCE TECHNOLOGY 2017; 236:1-10. [PMID: 28390271 DOI: 10.1016/j.biortech.2017.03.189] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/29/2017] [Accepted: 03/30/2017] [Indexed: 06/07/2023]
Abstract
This study investigated the impact of benzothiazole on the performance and microbial community structures in an integrated anaerobic fluidized-bed membrane bioreactor fed with synthetic benzothiazole wastewater (with gradually increasing doses of benzothiazole (1-50mg/L)). The addition of benzothiazole had an adverse effect on volatile fatty acids accumulation (from 10.86mg/L to 57.83mg/L), and membrane fouling (service period from 5.9d to 5.3d). The removal efficiency of benzothiazole was 96.0%. Biodegradation was the major benzothiazole removal route and the biodegradation efficiency obviously improved from 25.7% to 98.3% after adaptation. Sludge 1 (collected on day 58 without benzothiazole) and sludge 2 (collected on day 185 with 50mg/L benzothiazole) were analyzed using the Illumina®MiSeq platform. The most abundant genera were Trichococcus (43.1% in sludge 1) and Clostridium sensu stricto (23.9% in sludge 2). The dominant genus of archaea was Methanosaeta (90.3% in sludge 1 and 80.8% in sludge 2).
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Affiliation(s)
- Yue Li
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Qi Hu
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China; School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Chun-Hong Chen
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Xiao-Long Wang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Da-Wen Gao
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China; School of Forestry, Northeast Forestry University, Harbin 150040, China.
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15
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Sagheddu V, Patrone V, Miragoli F, Morelli L. Abundance and Diversity of Hydrogenotrophic Microorganisms in the Infant Gut before the Weaning Period Assessed by Denaturing Gradient Gel Electrophoresis and Quantitative PCR. Front Nutr 2017; 4:29. [PMID: 28695121 PMCID: PMC5483434 DOI: 10.3389/fnut.2017.00029] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 06/09/2017] [Indexed: 12/17/2022] Open
Abstract
Delivery mode (natural vs. cesarean) and feeding type (breast vs. formula feeding) are relevant factors for neonatal gut colonization. Biomolecular methods have shown that the ecological structure of infant microbiota is more complex than previously proposed, suggesting a relevant presence of unculturable bacteria. It has also been postulated that among unculturable bacteria, hydrogenotrophic populations might play a key role in infant health. Sulfate-reducing bacteria (SRB), acetogens, and methanogenic archaea use hydrogenotrophic pathways within the human colon. However, to date, few studies have reported detection of hydrogenotrophic microorganisms in newborns, possibly because of limitations on available group-specific, culture-independent quantification procedures. In the present work, we analyzed 16 fecal samples of healthy babies aged 1-6 months by means of quantitative PCR (qPCR) targeting the 16S rRNA or metabolic functional genes and by denaturing gradient gel electrophoresis (DGGE). qPCR data showed quantifiable levels of methanogens, SRB, and acetogens in all samples, indicating that the relative abundances of these microbial groups were not affected by delivery mode (natural vs. caesarian). DGGE revealed a high prevalence of the Blautia genus within the acetogenic bacteria despite strong interindividual variability. Our preliminary results suggest that hydrogenotrophic microorganisms, which have been a neglected group to date, should be included in future ecological and metabolic studies evaluating the infant intestinal microbiota.
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Affiliation(s)
- Valeria Sagheddu
- Facoltà di Scienze Agrarie, Alimentari e Ambientali, Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Vania Patrone
- Facoltà di Scienze Agrarie, Alimentari e Ambientali, Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Francesco Miragoli
- Facoltà di Scienze Agrarie, Alimentari e Ambientali, Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Lorenzo Morelli
- Facoltà di Scienze Agrarie, Alimentari e Ambientali, Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Piacenza, Italy
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16
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Li Z, Henderson G, Yang Y, Li G. Diversity of formyltetrahydrofolate synthetase genes in the rumens of roe deer (Capreolus pygargus) and sika deer (Cervus nippon) fed different diets. Can J Microbiol 2016; 63:11-19. [PMID: 27819479 DOI: 10.1139/cjm-2016-0424] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Reductive acetogenesis by homoacetogens represents an alternative pathway to methanogenesis to remove metabolic hydrogen during rumen fermentation. In this study, we investigated the occurrence of homoacetogen in the rumens of pasture-fed roe deer (Capreolus pygargus) and sika deer (Cervus nippon) fed either oak-leaf-based (tannin-rich, 100 mg/kg dried matter), corn-stover-based, or corn-silage-based diets, by using formyltetrahydrofolate synthetase (FTHFS) gene sequences as a marker. The diversity and richness of FTHFS sequences was lowest in animals fed oak leaf, indicating that tannin-containing plants may affect rumen homoacetogen diversity. FTHFS amino acid sequences in the rumen of roe deer significantly differed from those of sika deer. The phylogenetic analyses showed that 44.8% of sequences in pasture-fed roe deer, and 72.1%, 81.1%, and 37.5% of sequences in sika deer fed oak-leaf-, corn-stover-, and corn-silage-based diets, respectively, may represent novel bacteria that have not yet been cultured. These results demonstrate that the rumens of roe deer and sika deer harbor potentially novel homoacetogens and that diet may influence homoacetogen community structure.
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Affiliation(s)
- Zhipeng Li
- a Jilin Provincial Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, Jilin, People's Republic of China
| | - Gemma Henderson
- b AgResearch, Grasslands Research Centre, Palmerston North 4442, New Zealand
| | - Yahan Yang
- a Jilin Provincial Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, Jilin, People's Republic of China
| | - Guangyu Li
- a Jilin Provincial Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, Jilin, People's Republic of China
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17
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De Vrieze J, Verstraete W. Perspectives for microbial community composition in anaerobic digestion: from abundance and activity to connectivity. Environ Microbiol 2016; 18:2797-809. [DOI: 10.1111/1462-2920.13437] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Jo De Vrieze
- Center for Microbial Ecology and Technology (CMET), Ghent University; Coupure Links 653 Gent B-9000 Belgium
| | - Willy Verstraete
- Center for Microbial Ecology and Technology (CMET), Ghent University; Coupure Links 653 Gent B-9000 Belgium
- Avecom NV, Industrieweg 122P; Wondelgem 9032 Belgium
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18
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Yang C, Mi L, Hu X, Liu J, Wang J. Investigation into Host Selection of the Cecal Acetogen Population in Rabbits after Weaning. PLoS One 2016; 11:e0158768. [PMID: 27379387 PMCID: PMC4933399 DOI: 10.1371/journal.pone.0158768] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 06/18/2016] [Indexed: 01/13/2023] Open
Abstract
Homoacetogenic bacteria have received attention as a hydrogenotrophic population that offers a significant energetic advantage to the host animal. Reductive acetogenesis is likely an important hydrogen disposal mechanism in the cecum of rabbits. However, molecular ecology information about cecal acetogen candidates has rarely been reported. To better understand the effect of host selection in the rabbit cecal acetogen community with respect to growth, rabbits at four different age stages (30, 60, 120 and 180 days) with the same diet were studied. Although the abundance of potential acetogens and methanogens was high in the cecum of rabbits undergoing growth, many novel potential acetogen populations were observed in the cecum of rabbits across all age groups. Young and adult rabbits had their own distinct acetogen community although they received the same diet, which suggests that as the rabbit ages, acetogens in the cecum undergo developmental changes because of host selection that are independent of diet, and perhaps the different acetogen communities result in different hydrogenotrophic characteristics. The within-group similarity increased with age, indicating that the acetogen community converges to a more homogeneous and stable arrangement with aging.
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Affiliation(s)
- Chunlei Yang
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lan Mi
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xialu Hu
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jianxin Liu
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jiakun Wang
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
- * E-mail:
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19
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Biogas generation in anaerobic wastewater treatment under tetracycline antibiotic pressure. Sci Rep 2016; 6:28336. [PMID: 27341657 PMCID: PMC4920035 DOI: 10.1038/srep28336] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 06/01/2016] [Indexed: 11/22/2022] Open
Abstract
The effect of tetracycline (TC) antibiotic on biogas generation in anaerobic wastewater treatment was studied. A lab-scale Anaerobic Baffled Reactor (ABR) with three compartments was used. The reactor was operated with synthetic wastewater in the absence of TC and in the presence of 250 μg/L TC for 90 days, respectively. The removal rate of TC, volatile fatty acids (VFAs), biogas compositions (hydrogen (H2), methane (CH4), carbon dioxide (CO2)), and total biogas production in each compartment were monitored in the two operational conditions. Results showed that the removal rate of TC was 14.97–67.97% in the reactor. The presence of TC had a large negative effect on CH4 and CO2 generation, but appeared to have a positive effect on H2 production and VFAs accumulation. This response indicated that the methanogenesis process was sensitive to TC presence, but the acidogenesis process was insensitive. This suggested that the presence of TC had less influence on the degradation of organic matter but had a strong influence on biogas generation. Additionally, the decrease of CH4 and CO2 generation and the increase of H2 and VFAs accumulation suggest a promising strategy to help alleviate global warming and improve resource recovery in an environmentally friendly approach.
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20
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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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21
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Denman SE, Martinez Fernandez G, Shinkai T, Mitsumori M, McSweeney CS. Metagenomic analysis of the rumen microbial community following inhibition of methane formation by a halogenated methane analog. Front Microbiol 2015; 6:1087. [PMID: 26528253 PMCID: PMC4602129 DOI: 10.3389/fmicb.2015.01087] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 09/22/2015] [Indexed: 12/29/2022] Open
Abstract
Japanese goats fed a diet of 50% Timothy grass and 50% concentrate with increasing levels of the anti-methanogenic compound, bromochloromethane (BCM) were investigated with respect to the microbial population and functional shifts in the rumen. Microbial ecology methods identified species that exhibited positive and negative responses to the increasing levels of BCM. The methane-inhibited rumen appeared to adapt to the higher H2 levels by shifting fermentation to propionate which was mediated by an increase in the population of H2-consuming Prevotella and Selenomonas spp. Metagenomic analysis of propionate production pathways was dominated by genomic content from these species. Reductive acetogenic marker gene libraries and metagenomics analysis indicate that reductive acetogenic species do not play a major role in the BCM treated rumen.
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Affiliation(s)
- Stuart E Denman
- CSIRO, Agriculture Flagship, Queensland Bioscience Precinct St. Lucia, QLD, Australia
| | | | - Takumi Shinkai
- National Institute of Livestock and Grassland Science Tsukuba, Japan
| | - Makoto Mitsumori
- National Institute of Livestock and Grassland Science Tsukuba, Japan
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22
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Gagen EJ, Padmanabha J, Denman SE, McSweeney CS. Hydrogenotrophic culture enrichment reveals rumenLachnospiraceaeandRuminococcaceaeacetogens and hydrogen-responsiveBacteroidetesfrom pasture-fed cattle. FEMS Microbiol Lett 2015; 362:fnv104. [DOI: 10.1093/femsle/fnv104] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/19/2015] [Indexed: 11/13/2022] Open
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Aydin S, Ince B, Ince O. Application of real-time PCR to determination of combined effect of antibiotics on Bacteria, Methanogenic Archaea, Archaea in anaerobic sequencing batch reactors. WATER RESEARCH 2015; 76:88-98. [PMID: 25792437 DOI: 10.1016/j.watres.2015.02.043] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Revised: 02/19/2015] [Accepted: 02/20/2015] [Indexed: 06/04/2023]
Abstract
This study evaluated the long-term effects of erythromycin-tetracycline-sulfamethoxazole (ETS) and sulfamethoxazole-tetracycline (ST) antibiotic combinations on the microbial community and examined the ways in which these antimicrobials impact the performance of anaerobic reactors. Quantitative real-time PCR was used to determine the effect that different antibiotic combinations had on the total and active Bacteria, Archae and Methanogenic Archae. Three primer sets that targeted metabolic genes encoding formylterahydrofolate synthetase, methyl-coenzyme M reductase and acetyl-coA synthetase were also used to determine the inhibition level on the mRNA expression of the homoacetogens, methanogens and specifically acetoclastic methanogens, respectively. These microorganisms play a vital role in the anaerobic degradation of organic waste and targeting these gene expressions offers operators or someone at a treatment plant the potential to control and the improve the anaerobic system. The results of the investigation revealed that acetogens have a competitive advantage over Archaea in the presence of ETS and ST combinations. Although the efficiency with which methane production takes place and the quantification of microbial populations in both the ETS and ST reactors decreased as antibiotic concentrations increased, the ETS batch reactor performed better than the ST batch reactor. According to the expression of genes results, the syntrophic interaction of acetogens and methanogens is critical to the performance of the ETS and ST reactors. Failure to maintain the stability of these microorganisms resulted in a decrease in the performance and stability of the anaerobic reactors.
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Affiliation(s)
- Sevcan Aydin
- Environmental Engineering Department, Istanbul Technical University, Maslak, Istanbul, Turkey.
| | - Bahar Ince
- Institutes of Environmental Sciences, Bogazici University, Bebek, Istanbul, Turkey
| | - Orhan Ince
- Environmental Engineering Department, Istanbul Technical University, Maslak, Istanbul, Turkey
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Xu S, Fu B, Zhang L, Liu H. Bioconversion of H2/CO 2 by acetogen enriched cultures for acetate and ethanol production: the impact of pH. World J Microbiol Biotechnol 2015; 31:941-50. [PMID: 25838196 DOI: 10.1007/s11274-015-1848-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 03/11/2015] [Indexed: 12/29/2022]
Abstract
Syngas fermentation into ethanol and other bioproducts by mixed cultures is considered a promising biotechnology. Effects of pH on product generation and microbial community during H2/CO2 utilization by acetogen enrichment cultures were investigated in this work. The maximum acetate concentration reached 95.41 mmol L(-1) at pH 7, which was 71.7, 21.8 and 50.9% higher than at pH 5, 9 and 11, respectively. The maximum ethanol concentration at pH 7 was 45.7, 50, 72% higher than that at pH 5, 9 and 11, respectively. The CO dehydrogenase (CODH) gene copy number was highest at pH 7, indicating that metabolically active acetogens reached their highest level at pH 7. The CODH gene copy number at pH 9 was lower than at pH 7, but higher than at pH 5 and 11. Correspondingly, the enrichment cultures at pH 7 had the highest species richness and diversity, while those at pH 9 had the second highest diversity, and those at pH 5 and 11 had the lowest diversity. The shift in microbial community structure and the different active acetogen contents resulting from different pHs were responsible for the differences in acetate and ethanol production.
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Affiliation(s)
- Shuyun Xu
- Laboratory of Environmental Biotechnology, School of Environmental and Civil Engineering, Jiangnan University, Wuxi, 214122, Jiangsu Province, China
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25
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Liu JF, Sun XB, Yang GC, Mbadinga SM, Gu JD, Mu BZ. Analysis of microbial communities in the oil reservoir subjected to CO2-flooding by using functional genes as molecular biomarkers for microbial CO2 sequestration. Front Microbiol 2015; 6:236. [PMID: 25873911 PMCID: PMC4379918 DOI: 10.3389/fmicb.2015.00236] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Accepted: 03/10/2015] [Indexed: 11/13/2022] Open
Abstract
Sequestration of CO2 in oil reservoirs is considered to be one of the feasible options for mitigating atmospheric CO2 building up and also for the in situ potential bioconversion of stored CO2 to methane. However, the information on these functional microbial communities and the impact of CO2 storage on them is hardly available. In this paper a comprehensive molecular survey was performed on microbial communities in production water samples from oil reservoirs experienced CO2-flooding by analysis of functional genes involved in the process, including cbbM, cbbL, fthfs, [FeFe]-hydrogenase, and mcrA. As a comparison, these functional genes in the production water samples from oil reservoir only experienced water-flooding in areas of the same oil bearing bed were also analyzed. It showed that these functional genes were all of rich diversity in these samples, and the functional microbial communities and their diversity were strongly affected by a long-term exposure to injected CO2. More interestingly, microorganisms affiliated with members of the genera Methanothemobacter, Acetobacterium, and Halothiobacillus as well as hydrogen producers in CO2 injected area either increased or remained unchanged in relative abundance compared to that in water-flooded area, which implied that these microorganisms could adapt to CO2 injection and, if so, demonstrated the potential for microbial fixation and conversion of CO2 into methane in subsurface oil reservoirs.
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Affiliation(s)
- Jin-Feng Liu
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology Shanghai, China
| | - Xiao-Bo Sun
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology Shanghai, China
| | - Guang-Chao Yang
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology Shanghai, China
| | - Serge M Mbadinga
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology Shanghai, China
| | - Ji-Dong Gu
- School of Biological Sciences, University of Hong Kong Hong Kong, China
| | - Bo-Zhong Mu
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology Shanghai, China
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26
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Gagen EJ, Wang J, Padmanabha J, Liu J, de Carvalho IPC, Liu J, Webb RI, Al Jassim R, Morrison M, Denman SE, McSweeney CS. Investigation of a new acetogen isolated from an enrichment of the tammar wallaby forestomach. BMC Microbiol 2014; 14:314. [PMID: 25495654 PMCID: PMC4275979 DOI: 10.1186/s12866-014-0314-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 11/26/2014] [Indexed: 02/01/2023] Open
Abstract
Background Forestomach fermentation in Australian marsupials such as wallabies and kangaroos, though analogous to rumen fermentation, results in lower methane emissions. Insights into hydrogenotrophy in these systems could help in devising strategies to reduce ruminal methanogenesis. Reductive acetogenesis may be a significant hydrogen sink in these systems and previous molecular analyses have revealed a novel diversity of putative acetogens in the tammar wallaby forestomach. Results Methanogen-inhibited enrichment cultures prepared from tammar wallaby forestomach contents consumed hydrogen and produced primarily acetate. Functional gene (formyltetrahydrofolate synthetase and acetyl-CoA synthase) analyses revealed a restricted diversity of Clostridiales species as the putative acetogens in the cultures. A new acetogen (growth on H2/CO2 with acetate as primary end product) designated isolate TWA4, was obtained from the cultures. Isolate TWA4 classified within the Lachnospiraceae and demonstrated >97% rrs identity to previously isolated kangaroo acetogens. Isolate TWA4 was a potent hydrogenotroph and demonstrated excellent mixotrophic growth (concomitant consumption of hydrogen during heterotrophic growth) with glycerol. Mixotrophic growth of isolate TWA4 on glycerol resulted in increased cell densities and acetate production compared to autotrophic growth. Co-cultures with an autotrophic methanogen Methanobrevibacter smithii revealed that isolate TWA4 performed reductive acetogenesis under high hydrogen concentration (>5 mM), but not at low concentrations. Under heterotrophic growth conditions, isolate TWA4 did not significantly stimulate methanogenesis in a co-culture with M. smithii contrary to the expectation for organisms growing fermentatively. Conclusions The unique properties of tammar wallaby acetogens might be contributing factors to reduced methanogen numbers and methane emissions from tammar wallaby forestomach fermentation, compared to ruminal fermentation. The macropod forestomach may be a useful source of acetogens for future strategies to reduce methane emissions from ruminants, particularly if these strategies also include some level of methane suppression and/or acetogen stimulation, for example by harnessing mixotrophic growth capabilities Electronic supplementary material The online version of this article (doi:10.1186/s12866-014-0314-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Emma J Gagen
- CSIRO Agriculture, St Lucia, Australia. .,School of Agriculture and Food Sciences, The University of Queensland, Gatton, Australia.
| | - Jiakun Wang
- CSIRO Agriculture, St Lucia, Australia. .,Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China.
| | | | - Jing Liu
- CSIRO Agriculture, St Lucia, Australia. .,Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China.
| | | | - Jianxin Liu
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China.
| | - Richard I Webb
- Centre for Microscopy and Microanalysis, The University of Queensland, St Lucia, Australia.
| | - Rafat Al Jassim
- School of Agriculture and Food Sciences, The University of Queensland, Gatton, Australia.
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Diversity of the Formyltetrahydrofolate Synthetase Gene (fhs), a Key Enzyme for Reductive Acetogenesis, in the Bovine Rumen. Biosci Biotechnol Biochem 2014; 72:3273-6. [DOI: 10.1271/bbb.70375] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Tun HM, Mauroo NF, Yuen CS, Ho JCW, Wong MT, Leung FCC. Microbial diversity and evidence of novel homoacetogens in the gut of both geriatric and adult giant pandas (Ailuropoda melanoleuca). PLoS One 2014; 9:e79902. [PMID: 24475017 PMCID: PMC3901650 DOI: 10.1371/journal.pone.0079902] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 09/25/2013] [Indexed: 12/20/2022] Open
Abstract
Recent studies have described the bacterial community residing in the guts of giant pandas, together with the presence of lignocellulolytic enzymes. However, a more comprehensive understanding of the intestinal microbial composition and its functional capacity in giant pandas remains a major goal. Here, we conducted a comparison of bacterial, fungal and homoacetogenic microbial communities from fecal samples taken from two geriatric and two adult captive giant pandas. 16S rDNA amplicon pyrosequencing revealed that Firmicutes and Proteobacteria are the most abundant microbiota in both geriatric and adult giant pandas. However, members of phylum Actinobacteria found in adult giant pandas were absent in their geriatric counterparts. Similarly, ITS1 amplicon pyrosequencing identified developmental changes in the most abundant fungal classes from Sordariomycetes in adult pandas to Saccharomycetes in geriatric pandas. Geriatric pandas exhibited significantly higher abundance of a potential probiotic fungus (Candida tropicalis) as compared to adult pandas, indicating their importance in the normal digestive physiology of aged pandas. Our study also reported the presence of a lignocellulolytic white-rot fungus, Perenniporia medulla-panis, and the evidence of novel homoacetogens residing in the guts of giant pandas.
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Affiliation(s)
- Hein Min Tun
- School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Nathalie France Mauroo
- Department of Pathology, The University of Hong Kong, Hong Kong, Hong Kong SAR
- Hong Kong Wildlife Health Foundation, Hong Kong, Hong Kong SAR
| | - Chan San Yuen
- Clinical Laboratory, Veterinary Center, Ocean Park Corporation, Hong Kong, Hong Kong SAR
| | - John Chi Wang Ho
- School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Mabel Ting Wong
- School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Frederick Chi-Ching Leung
- School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR
- Bioinformatics Center, Nanjing Agricultural University, Nanjing, China
- * E-mail:
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29
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Li YF, Wei S, Yu Z. Feedstocks affect the diversity and distribution of propionate CoA-transferase genes (pct) in anaerobic digesters. MICROBIAL ECOLOGY 2013; 66:351-62. [PMID: 23640276 DOI: 10.1007/s00248-013-0234-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 04/15/2013] [Indexed: 05/18/2023]
Abstract
Anaerobic digestion (AD) is an attractive microbiological technology for both waste treatment and energy production. Syntrophic acetogenic bacteria are an important guild because they are essential for maintaining efficient and stable AD operation. However, this guild is poorly understood due to difficulties to culture them. In this study, we developed specific PCR assays targeting the propionate-CoA transferase genes (pct) to investigate their diversity and distribution in several mesophilic anaerobic digesters and a bench-scale temperature-phased AD (TPAD) system. Phylogenetic analysis of sequenced pct amplicons revealed the occurrence of Syntrophobacter fumaroxidans and six other clusters of putative pct genes. Principal coordinate analysis (PCoA) showed that pct diversity and abundance were largely correlated to the feedstocks of the digesters, while little difference was seen between the granular and the liquid fractions of each digester or between the two digesters of the TPAD system. Cluster-specific qPCR analysis revealed major impact of feedstocks and fractions on the abundance of pct genes. Readily fermentable substrates such as sugar- or starch-rich feedstocks selected for pct genes (Cluster I) related to Syntrophobacter, while manure feedstock selected for pct clusters related to pct of Clostridium spp. These results suggest that propionate metabolism can be affected by feedstocks and partition differently between solid and liquid phases in digesters. The PCR assays developed in this study may serve as a tool to investigate propionate-oxidizing bacteria in anaerobic digesters and other anaerobic environments.
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Affiliation(s)
- Yueh-Fen Li
- Environmental Science Graduate Program, The Ohio State University, Columbus, OH 43210, USA
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30
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Ma J, Nossa CW, Xiu Z, Rixey WG, Alvarez PJJ. Adaptive microbial population shifts in response to a continuous ethanol blend release increases biodegradation potential. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2013; 178:419-425. [PMID: 23628885 DOI: 10.1016/j.envpol.2013.03.057] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 03/26/2013] [Accepted: 03/28/2013] [Indexed: 06/02/2023]
Abstract
The fate of fuel releases largely depends on the poorly-understood response in microbial community structure and function. Here, we evaluate the impacts to the microbial community resulting from a pilot-scale continuous release (10 months) of a 10% v:v ethanol solution mixed with benzene and toluene (50 mg/L each). Microbial population shifts were characterized by pyrosequencing-based 16S rRNA analysis and by quantitative PCR targeting Bacteria, Archaea, and functional genes for methanogenesis (mcrA), acetogenesis (fhs) and aerobic degradation of aromatic hydrocarbons (PHE), which could occur in hypoxic micro-environments. The release stimulated microbial growth, increased species richness and diversity, and selected for genotypes involved in fermentative degradation (the relative abundance of mcrA and fhs increased 18- and 6-fold, respectively). The growth of putative hydrocarbon degraders and commensal anaerobes, and increases in microbial diversity and in degradation rates suggest an adaptive response that increases the potential for natural attenuation of ethanol blend releases.
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Affiliation(s)
- Jie Ma
- Department of Civil and Environmental Engineering, Rice University, 6100 Main St., Houston, TX 77005, USA
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31
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Bengelsdorf FR, Straub M, Dürre P. Bacterial synthesis gas (syngas) fermentation. ENVIRONMENTAL TECHNOLOGY 2013; 34:1639-51. [PMID: 24350425 DOI: 10.1080/09593330.2013.827747] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Acetogenic bacteria employing the Wood-Ljungdahl pathway can be used as biocatalysts in syngas fermentation for the production ofbiofuels such as ethanol or butanol as well as biocommodities such as acetate, lactate, butyrate, 2,3 butanediol, and acetone. The potential of such processes can be projected by the global syngas output, which was 70,817 megawatts thermal in 2010 and is expected to increase up to 72% in 2016. To date, different acetogens are used as commercial production strains for industrial syngas fermentations in pilot or demonstration plants (Coskata, INEOS Bio, LanzaTech) and first commercial units are expected to launch operation in the near future (INEOS Bio, LanzaTech). Considerations on potential yields are quite promising for fermentative production. New methods for metabolic engineering were established to construct novel recombinant acetogenic biocatalysts. Synthetic biology will certainly play a major role in constructing strains for commercial operations. This way, a cheap and abundant carbon source most probably replace, processes based on crude oil or sugar in the near future.
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Affiliation(s)
- Frank R Bengelsdorf
- Institute of Microbiology and Biotechnology, University of Ulm, Albert-Einstein-Allee 11, Ulm D-89081, Germany.
| | - Melanie Straub
- Institute of Microbiology and Biotechnology, University of Ulm, Albert-Einstein-Allee 11, Ulm D-89081, Germany
| | - Peter Dürre
- Institute of Microbiology and Biotechnology, University of Ulm, Albert-Einstein-Allee 11, Ulm D-89081, Germany
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32
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Amato KR, Yeoman CJ, Kent A, Righini N, Carbonero F, Estrada A, Rex Gaskins H, Stumpf RM, Yildirim S, Torralba M, Gillis M, Wilson BA, Nelson KE, White BA, Leigh SR. Habitat degradation impacts black howler monkey (Alouatta pigra) gastrointestinal microbiomes. THE ISME JOURNAL 2013; 7:1344-53. [PMID: 23486247 PMCID: PMC3695285 DOI: 10.1038/ismej.2013.16] [Citation(s) in RCA: 752] [Impact Index Per Article: 68.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 11/16/2012] [Accepted: 01/06/2013] [Indexed: 02/08/2023]
Abstract
The gastrointestinal (GI) microbiome contributes significantly to host nutrition and health. However, relationships involving GI microbes, their hosts and host macrohabitats remain to be established. Here, we define clear patterns of variation in the GI microbiomes of six groups of Mexican black howler monkeys (Alouatta pigra) occupying a gradation of habitats including a continuous evergreen rainforest, an evergreen rainforest fragment, a continuous semi-deciduous forest and captivity. High throughput microbial 16S ribosomal RNA gene sequencing indicated that diversity, richness and composition of howler GI microbiomes varied with host habitat in relation to diet. Howlers occupying suboptimal habitats consumed less diverse diets and correspondingly had less diverse gut microbiomes. Quantitative real-time PCR also revealed a reduction in the number of genes related to butyrate production and hydrogen metabolism in the microbiomes of howlers occupying suboptimal habitats, which may impact host health.
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Affiliation(s)
- Katherine R Amato
- Program in Ecology, Evolution and Conservation Biology, University of Illinois, Urbana, IL, USA
- Department of Anthropology, University of Illinois, Urbana, IL, USA
| | - Carl J Yeoman
- Department of Animal and Range Sciences, Montana State University, Bozeman, MT, USA
- Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
| | - Angela Kent
- Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana, IL, USA
| | | | - Franck Carbonero
- Department of Animal Sciences, University of Illinois, Urbana, IL, USA
| | - Alejandro Estrada
- Estacion de Biologia Tropical Los Tuxtlas, Instituto de Biologia, Universidad Nacional Autonoma de Mexico, San Andrés Tuxtla, Mexico
| | - H Rex Gaskins
- Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
- Department of Animal Sciences, University of Illinois, Urbana, IL, USA
| | - Rebecca M Stumpf
- Department of Anthropology, University of Illinois, Urbana, IL, USA
- Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
| | - Suleyman Yildirim
- Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
| | | | | | - Brenda A Wilson
- Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
- Department of Microbiology, University of Illinois, Urbana, IL, USA
| | | | - Bryan A White
- Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
- Department of Animal Sciences, University of Illinois, Urbana, IL, USA
| | - Steven R Leigh
- Department of Anthropology, University of Illinois, Urbana, IL, USA
- Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
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Mitsumori M, Matsui H, Tajima K, Shinkai T, Takenaka A, Denman SE, McSweeney CS. Effect of bromochloromethane and fumarate on phylogenetic diversity of the formyltetrahydrofolate synthetase gene in bovine rumen. Anim Sci J 2013; 85:25-31. [PMID: 23638678 DOI: 10.1111/asj.12072] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Accepted: 02/25/2013] [Indexed: 11/30/2022]
Abstract
Effect of the methane inhibitor, bromochloromethane (BCM) and dietary substrate, fumarate, on microbial community structure of acetogen bacteria in the bovine rumen was investigated through analysis of the formyltetrahydrofolate synthetase gene (fhs). The fhs sequences obtained from BCM-untreated, BCM-treated, fumarate-untreated and fumarate-treated bovine rumen were categorized into homoacetogens and nonhomoacetogenic bacteria by homoacetogen similarity scores. Phylogenetic tree analysis indicated that most of the fhs sequences categorized into homoacetogens were divided into nine clusters, which were in close agreement with a result shown in a self-organizing map. The diversity of the fhs sequences from the BCM-treated rumen was significantly different from those from BCM-non-treated rumen. Principal component analysis also showed that addition of BCM to the rumen altered the population structure of acetogenic bacteria significantly but the effect of fumarate was comparatively minor. These results indicate that BCM affects diversity of actogens in the bovine rumen, and changes in acetogenic community structure in response to methane inhibitors may be caused by different mechanisms.
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Affiliation(s)
- Makoto Mitsumori
- National Institute of Livestock and Grassland Science, Tsukuba, Japan
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34
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Li X, Deng Y, Li Q, Lu C, Wang J, Zhang H, Zhu J, Zhou J, He Z. Shifts of functional gene representation in wheat rhizosphere microbial communities under elevated ozone. THE ISME JOURNAL 2013; 7:660-71. [PMID: 23151639 PMCID: PMC3578556 DOI: 10.1038/ismej.2012.120] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 08/21/2012] [Accepted: 08/21/2012] [Indexed: 11/08/2022]
Abstract
Although the influence of ozone (O(3)) on plants has been well studied in agroecosystems, little is known about the effect of elevated O(3) (eO(3)) on soil microbial functional communities. Here, we used a comprehensive functional gene array (GeoChip 3.0) to investigate the functional composition, and structure of rhizosphere microbial communities of Yannong 19 (O(3)-sensitive) and Yangmai 16 (O(3)-relatively sensitive) wheat (Triticum aestivum L.) cultivars under eO(3). Compared with ambient O(3) (aO(3)), eO(3) led to an increase in soil pH and total carbon (C) percentages in grain and straw of wheat plants, and reduced grain weight and soil dissolved organic carbon (DOC). Based on GeoChip hybridization signal intensities, although the overall functional structure of rhizosphere microbial communities did not significantly change by eO(3) or cultivars, the results showed that the abundance of specific functional genes involved in C fixation and degradation, nitrogen (N) fixation, and sulfite reduction did significantly (P<0.05) alter in response to eO(3) and/or wheat cultivars. Also, Yannong 19 appeared to harbor microbial functional communities in the rhizosphere more sensitive in response to eO(3) than Yangmai 16. Additionally, canonical correspondence analysis suggested that the functional structure of microbial community involved in C cycling was largely shaped by soil and plant properties including pH, DOC, microbial biomass C, C/N ratio and grain weight. This study provides new insight into our understanding of the influence of eO(3) and wheat cultivars on soil microbial communities.
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Affiliation(s)
- Xinyu Li
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- Department of Botany and Microbiology, Institute for Environmental Genomics, The University of Oklahoma, Norman, OK, USA
| | - Ye Deng
- Department of Botany and Microbiology, Institute for Environmental Genomics, The University of Oklahoma, Norman, OK, USA
| | - Qi Li
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Caiyan Lu
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Jingjing Wang
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Huiwen Zhang
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Jianguo Zhu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, The Chinese Academy of Sciences, Nanjing, China
| | - Jizhong Zhou
- Department of Botany and Microbiology, Institute for Environmental Genomics, The University of Oklahoma, Norman, OK, USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
- Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Zhili He
- Department of Botany and Microbiology, Institute for Environmental Genomics, The University of Oklahoma, Norman, OK, USA
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35
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Müller B, Sun L, Schnürer A. First insights into the syntrophic acetate-oxidizing bacteria--a genetic study. Microbiologyopen 2012; 2:35-53. [PMID: 23239474 PMCID: PMC3584212 DOI: 10.1002/mbo3.50] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Revised: 10/18/2012] [Accepted: 11/05/2012] [Indexed: 11/10/2022] Open
Abstract
Syntrophic acetate-oxidizing bacteria have been identified as key organisms for efficient biogas production from protein-rich materials. They normally grow as lithotrophs or heterotrophs, producing acetate through the Wood–Ljungdahl pathway, but when growing in syntrophy with methanogens, they reportedly reverse this pathway and oxidize acetate to hydrogen and carbon dioxide. However, the biochemical and regulatory mechanisms behind the shift and the way in which the bacteria regain energy remain unknown. In a genome-walking approach, starting with degenerated primers, we identified those gene clusters in Syntrophaceticus schinkii, Clostridium ultunense, and Tepidanaerobacter acetatoxydans that comprise the formyltetrahydrofolate synthetase gene (fhs), encoding a key enzyme of the Wood–Ljungdahl pathway. We also discovered that the latter two harbor two fhs alleles. The fhs genes are phylogenetically separated and in the case of S. schinkii functionally linked to sulfate reducers. The T. acetatoxydansfhs1 cluster combines features of acetogens, sulfate reducers, and carbon monoxide oxidizers and is organized as a putative operon. The T. acetatoxydansfhs2 cluster encodes Wood–Ljungdahl pathway enzymes, which are also known to be involved in C1 carbon metabolism. Isolation of the enzymes illustrated that both formyltetrahydrofolate synthetases of T. acetatoxydans were functionally active. However, only fhs1 was expressed, confirming bidirectional usage of the pathway.
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Affiliation(s)
- Bettina Müller
- Department of Microbiology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, SE 750 07, Sweden.
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36
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Gagen EJ, Mosoni P, Denman SE, Al Jassim R, McSweeney CS, Forano E. Methanogen colonisation does not significantly alter acetogen diversity in lambs isolated 17 h after birth and raised aseptically. MICROBIAL ECOLOGY 2012; 64:628-640. [PMID: 22383121 DOI: 10.1007/s00248-012-0024-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Accepted: 02/03/2012] [Indexed: 05/31/2023]
Abstract
Reductive acetogenesis is not competitive with methanogenesis in adult ruminants, whereas acetogenic bacteria are the dominant hydrogenotrophs in the early rumen microbiota. The ecology of hydrogenotrophs in the developing rumen was investigated using young lambs, raised in sterile isolators, and conventional adult sheep. Two lambs were born naturally, left with their dams for 17 h and then placed into a sterile isolator and reared aseptically. They were inoculated with cellulolytic bacteria and later with Methanobrevibacter sp. 87.7 to investigate the effect of methanogen establishment on the rumen acetogen population since they lacked cultivable representatives of methanogens. Putative acetogens were investigated by acetyl-CoA synthase and formyltetrahydrofolate synthetase gene analysis and methanogens by methyl coenzyme reductase A gene analysis. Unexpectedly, a low abundant but diverse population of methanogens (predominantly Methanobrevibacter spp.) was identified in isolated lambs pre-inoculation with Mbb. sp 87.7, which was similar to the community structure in conventional sheep. In contrast, potential acetogen diversity in isolated lambs and conventional sheep was different. Potential acetogens affiliated between the Lachnospiraceae and Clostridiaceae in conventional sheep and with the Blautia genus and the Lachnospiraceae in isolated lambs. The establishment of Mbb. sp. 87.7 (1,000-fold increase in methanogens) did not substantially affect acetogen diversity.
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Affiliation(s)
- Emma J Gagen
- CSIRO Livestock Industries, St. Lucia, QLD 4067, Australia.
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37
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Hydrogenotrophic methanogens dominate in biogas reactors fed with defined substrates. Syst Appl Microbiol 2012; 35:404-13. [DOI: 10.1016/j.syapm.2012.07.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Revised: 07/15/2012] [Accepted: 07/16/2012] [Indexed: 11/20/2022]
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38
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Köhler T, Dietrich C, Scheffrahn RH, Brune A. High-resolution analysis of gut environment and bacterial microbiota reveals functional compartmentation of the gut in wood-feeding higher termites (Nasutitermes spp.). Appl Environ Microbiol 2012; 78:4691-701. [PMID: 22544239 PMCID: PMC3370480 DOI: 10.1128/aem.00683-12] [Citation(s) in RCA: 152] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Accepted: 04/13/2012] [Indexed: 11/20/2022] Open
Abstract
Higher termites are characterized by a purely prokaryotic gut microbiota and an increased compartmentation of their intestinal tract. In soil-feeding species, each gut compartment has different physicochemical conditions and is colonized by a specific microbial community. Although considerable information has accumulated also for wood-feeding species of the genus Nasutitermes, including cellulase activities and metagenomic data, a comprehensive study linking physicochemical gut conditions with the structure of the microbial communities in the different gut compartments is lacking. In this study, we measured high-resolution profiles of H(2), O(2), pH, and redox potential in the gut of Nasutitermes corniger termites, determined the fermentation products accumulating in the individual gut compartments, and analyzed the bacterial communities in detail by pyrotag sequencing of the V3-V4 region of the 16S rRNA genes. The dilated hindgut paunch (P3 compartment) was the only anoxic gut region, showed the highest density of bacteria, and accumulated H(2) to high partial pressures (up to 12 kPa). Molecular hydrogen is apparently produced by a dense community of Spirochaetes and Fibrobacteres, which also dominate the gut of other Nasutitermes species. All other compartments, such as the alkaline P1 compartment (average pH, 10.0), showed high redox potentials and comprised small but distinct populations characteristic for each gut region. In the crop and the posterior hindgut compartments, the community was even more diverse than in the paunch. Similarities in the communities of the posterior hindgut and crop suggested that proctodeal trophallaxis or coprophagy also occurs in higher termites. The large sampling depths of pyrotag sequencing in combination with the determination of important physicochemical parameters allow cautious conclusions concerning the functions of particular bacterial lineages in the respective gut sections to be drawn.
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Affiliation(s)
- Tim Köhler
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Carsten Dietrich
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Rudolf H. Scheffrahn
- Fort Lauderdale Research and Education Center, University of Florida, Davie, Florida, USA
| | - Andreas Brune
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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39
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Hädrich A, Heuer VB, Herrmann M, Hinrichs KU, Küsel K. Origin and fate of acetate in an acidic fen. FEMS Microbiol Ecol 2012; 81:339-54. [DOI: 10.1111/j.1574-6941.2012.01352.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Revised: 02/16/2012] [Accepted: 02/26/2012] [Indexed: 11/28/2022] Open
Affiliation(s)
- Anke Hädrich
- Aquatic Geomicrobiology Group; Institute of Ecology; Friedrich Schiller University Jena; Jena; Germany
| | - Verena B. Heuer
- Organic Geochemistry Group; Department of Geosciences and MARUM Center for Marine Environmental Sciences; University of Bremen; Bremen; Germany
| | - Martina Herrmann
- Aquatic Geomicrobiology Group; Institute of Ecology; Friedrich Schiller University Jena; Jena; Germany
| | - Kai-Uwe Hinrichs
- Organic Geochemistry Group; Department of Geosciences and MARUM Center for Marine Environmental Sciences; University of Bremen; Bremen; Germany
| | - Kirsten Küsel
- Aquatic Geomicrobiology Group; Institute of Ecology; Friedrich Schiller University Jena; Jena; Germany
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40
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Nakamura N, Lin HC, McSweeney CS, Mackie RI, Gaskins HR. Mechanisms of microbial hydrogen disposal in the human colon and implications for health and disease. Annu Rev Food Sci Technol 2012; 1:363-95. [PMID: 22129341 DOI: 10.1146/annurev.food.102308.124101] [Citation(s) in RCA: 128] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In the human gastrointestinal tract, dietary components, including fiber, that reach the colon are fermented principally to short-chain fatty acids, hydrogen, and carbon dioxide. Microbial disposal of the hydrogen generated during anaerobic fermentation in the human colon is critical to optimal functioning of this ecosystem. However, our understanding of microbial hydrogenotrophy is fragmented and, at least as it occurs in the colon, is mostly theoretical in nature. Thorough investigation and integration of knowledge on the diversity of hydrogenotrophic microbes, their metabolic variation and activities as a functional group, as well as the nature of their interactions with fermentative bacteria, are necessary to understand hydrogen metabolism in the human colon. Here, we review the limited data available on the three major groups of H(2)-consuming microorganisms found in the human colon [methanogens, sulfate-reducing bacteria (SRB), and acetogens] as well as evidence that end products of their metabolism have an important impact on colonic health.
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Affiliation(s)
- Noriko Nakamura
- Department of Animal Sciences and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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41
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On the relationship between sialomucin and sulfomucin expression and hydrogenotrophic microbes in the human colonic mucosa. PLoS One 2011; 6:e24447. [PMID: 21931721 PMCID: PMC3170330 DOI: 10.1371/journal.pone.0024447] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Accepted: 08/10/2011] [Indexed: 11/19/2022] Open
Abstract
The colonic mucus layer is comprised primarily of acidomucins, which provide viscous properties and can be broadly classified into sialomucins or sulfomucins based on the presence of terminating sialic acid or sulfate groups. Differences in acidomucin chemotypes have been observed in diseases such as colorectal cancer and inflammatory bowel disease, and variation in sialo- and sulfomucin content may influence microbial colonization. For example, sulfate derived from sulfomucin degradation may promote the colonization of sulfate-reducing bacteria (SRB), which through sulfate respiration generate the genotoxic gas hydrogen sulfide. Here, paired biopsies from right colon, left colon, and rectum of 20 subjects undergoing routine screening colonoscopies were collected to enable parallel histochemical and microbiological studies. Goblet cell sialo- and sulfomucins in each biopsy were distinguished histochemically and quantified. Quantitative PCR and multivariate analyses were used to examine the abundance of hydrogenotrophic microbial groups and SRB genera relative to acidomucin profiles. Regional variation was observed in sialomucins and sulfomucins with the greatest abundance of each found in the rectum. Mucin composition did not appear to influence the abundance of SRB or other hydrogenotrophic microbiota but correlated with the composition of different SRB genera. A higher sulfomucin proportion correlated with higher quantities of Desulfobacter, Desulfobulbus and Desulfotomaculum, relative to the predominant Desulfovibrio genus. Thus, acidomucin composition may influence bacterial sulfate respiration in the human colon, which may in turn impact mucosal homeostasis. These results stress the need to consider mucus characteristics in the context of studies of the microbiome that target intestinal diseases.
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42
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Hunger S, Gößner AS, Drake HL. Trophic links between the acetogen Clostridium glycolicum KHa and the fermentative anaerobe Bacteroides xylanolyticus KHb, isolated from Hawaiian forest soil. Appl Environ Microbiol 2011; 77:6281-5. [PMID: 21764978 PMCID: PMC3165425 DOI: 10.1128/aem.05519-11] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Accepted: 07/02/2011] [Indexed: 11/20/2022] Open
Abstract
Isolate KH was obtained from Hawaiian forest soil and found to be composed of two functionally linked anaerobes, KHa and KHb. Gene analyses (16S rRNA, fhs, cooS) identified KHa as an acetogenic strain of Clostridium glycolicum and KHb as Bacteroides xylanolyticus. KHb fermented xylan and other saccharides that KHa could not utilize and formed products (e.g., ethanol and H(2)) that supported the acetogenic growth of KHa.
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Affiliation(s)
| | | | - Harold L. Drake
- Department of Ecological Microbiology, University of Bayreuth, 95440 Bayreuth, Germany
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Westerholm M, Müller B, Arthurson V, Schnürer A. Changes in the acetogenic population in a mesophilic anaerobic digester in response to increasing ammonia concentration. Microbes Environ 2011; 26:347-53. [PMID: 21869569 DOI: 10.1264/jsme2.me11123] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Changes in the acetogenic population were investigated in an experimental laboratory-scale biogas reactor (37°C) subjected to gradually elevated ammonia levels (0.8 to 6.9 g NH(4)(+)-N L(-1)). A shift from aceticlastic acetate degradation to syntrophic acetate oxidation had previously been confirmed in this reactor. In a parallel control reactor, operating at constant ammonia levels (0.65-0.90 g NH(4)(+)-N L(-1)), acetate degradation proceeded via the aceticlastic pathway throughout the operating period (660 d). The acetogenic populations in the reactors were analysed using degenerated primers designed to target the functional gene encoding a key enzyme of the acetyl-CoA pathway, 10-formyltetrahydrofolate synthetase (FTHFS). The analysis consisted of terminal restriction fragment length polymorphism (T-RFLP) analysis coupled with the construction of clone libraries, and quantitative PCR (qPCR) analysis. The T-RFLP data obtained were statistically analysed by non-metric multidimensional scaling. The most abundant FTHFS genes recovered in the clone libraries were assigned to terminal restriction fragments of the T-RFLP profile. The results of the investigation clearly indicated that increased ammonia concentration substantially influenced the putative acetogenic population structure and caused two distinct shifts of the most abundant members; however, the identity of the dominating species remains unknown, as none of the genes had been identified previously. Despite the shifts in the population, the qPCR analysis revealed a relatively stable abundance of the acetogenic population throughout the operation.
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Affiliation(s)
- Maria Westerholm
- Department of Microbiology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Carbonero F, Nava GM, Benefiel AC, Greenberg E, Gaskins HR. Microbial DNA extraction from intestinal biopsies is improved by avoiding mechanical cell disruption. J Microbiol Methods 2011; 87:125-7. [PMID: 21820015 DOI: 10.1016/j.mimet.2011.07.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Revised: 07/14/2011] [Accepted: 07/16/2011] [Indexed: 12/28/2022]
Abstract
Currently, standard protocols for microbial DNA extraction from intestinal tissues do not exist. We assessed the efficiency of a commercial kit with and without mechanical disruption. Better quality DNA was obtained without mechanical disruption. Thus, it appears that bead-beating is not required for efficient microbial DNA extraction from intestinal biopsies.
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Affiliation(s)
- Franck Carbonero
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, IL 61801, USA
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Abundance and diversity of mucosa-associated hydrogenotrophic microbes in the healthy human colon. ISME JOURNAL 2011; 6:57-70. [PMID: 21753800 DOI: 10.1038/ismej.2011.90] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Hydrogenotrophic microbiota have a significant impact on colonic health; however, little is known about their diversity and ecology in situ. Here, molecular-based methods and multivariate analyses were used to examine the abundance and diversity of mucosa-associated hydrogenotrophic microbes in 90 biopsies collected from right colon, left colon and rectum of 25 healthy subjects. Functional genes of all three hydrogenotrophic groups were detected in at least one colonic region of all subjects. Methanogenic archaea (MA) constituted approximately one half of the hydrogenotrophic microbiota in each colonic region. Sulfate-reducing bacteria (SRB) were more abundant than acetogens in right colon, while acetogens were more abundant than SRB in left colon and rectum. MA genotypes exhibited low diversity, whereas SRB genotypes were diverse and generally similar across the three regions within subject but significantly variable among subjects. Multivariate cluster analysis defined subject-specific patterns for the diversity of SRB genotypes; however, neither subject- nor region-specific clusters were observed for the abundance of hydrogenotrophic functional genes. Sequence analyses of functional gene clones revealed that mucosa-associated SRB were phylogenetically related to Desulfovibrio piger, Desulfovibrio desulfuricans and Bilophila wadsworthia; whereas MA were related to Methanobrevibacter spp., Mb. smithii and the order Methanomicrobiales. Together these data demonstrate for the first time that the human colonic mucosa is persistently colonized by all three groups of hydrogenotrophic microbes, which exhibit segmental and interindividual variation in abundance and diversity.
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Hunger S, Schmidt O, Hilgarth M, Horn MA, Kolb S, Conrad R, Drake HL. Competing formate- and carbon dioxide-utilizing prokaryotes in an anoxic methane-emitting fen soil. Appl Environ Microbiol 2011; 77:3773-85. [PMID: 21478308 PMCID: PMC3127604 DOI: 10.1128/aem.00282-11] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Accepted: 03/29/2011] [Indexed: 11/20/2022] Open
Abstract
Methanogenesis in wetlands is dependent on intermediary substrates derived from the degradation of biopolymers. Formate is one such substrate and is stimulatory to methanogenesis and acetogenesis in anoxic microcosms of soil from the fen Schlöppnerbrunnen. Formate dissimilation also yields CO(2) as a potential secondary substrate. The objective of this study was to resolve potential differences between anaerobic formate- and CO(2)-utilizing prokaryotes of this fen by stable isotope probing. Anoxic soil microcosms were pulsed daily with low concentrations of [(13)C]formate or (13)CO(2) (i.e., [(13)C]bicarbonate). Taxa were evaluated by assessment of 16S rRNA genes, mcrA (encoding the alpha-subunit of methyl-coenzyme M reductase), and fhs (encoding formyltetrahydrofolate synthetase). Methanogens, acetogens, and formate-hydrogen lyase-containing taxa appeared to compete for formate. Genes affiliated with Methanocellaceae, Methanobacteriaceae, Acetobacteraceae, and Rhodospirillaceae were (13)C enriched (i.e., labeled) in [(13)C]formate treatments, whereas genes affiliated with Methanosarcinaceae, Conexibacteraceae, and Solirubrobacteraceae were labeled in (13)CO(2) treatments. [(13)C]acetate was enriched in [(13)C]formate treatments, but labeling of known acetogenic taxa was not detected. However, several phylotypes were affiliated with acetogen-containing taxa (e.g., Sporomusa). Methanosaetaceae-affiliated methanogens appeared to participate in the consumption of acetate. Twelve and 58 family-level archaeal and bacterial 16S rRNA phylotypes, respectively, were detected, approximately half of which had no isolated representatives. Crenarchaeota constituted half of the detected archaeal 16S rRNA phylotypes. The results highlight the unresolved microbial diversity of the fen Schlöppnerbrunnen, suggest that differing taxa competed for the same substrate, and indicate that Methanocellaceae, Methanobacteriaceae, Methanosarcinaceae, and Methanosaetaceae were linked to the production of methane, but they do not clearly resolve the taxa responsible for the apparent conversion of formate to acetate.
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MESH Headings
- Anaerobiosis
- Biodiversity
- Carbon Dioxide/metabolism
- Carbon Isotopes/metabolism
- Cluster Analysis
- DNA, Archaeal/chemistry
- DNA, Archaeal/genetics
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Formates/metabolism
- Genes, rRNA
- Methane/metabolism
- Molecular Sequence Data
- Phylogeny
- RNA, Archaeal/genetics
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Soil Microbiology
- Wetlands
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Affiliation(s)
- Sindy Hunger
- Department of Ecological Microbiology, University of Bayreuth, 95440 Bayreuth, Germany
| | - Oliver Schmidt
- Department of Ecological Microbiology, University of Bayreuth, 95440 Bayreuth, Germany
| | - Maik Hilgarth
- Department of Ecological Microbiology, University of Bayreuth, 95440 Bayreuth, Germany
| | - Marcus A. Horn
- Department of Ecological Microbiology, University of Bayreuth, 95440 Bayreuth, Germany
| | - Steffen Kolb
- Department of Ecological Microbiology, University of Bayreuth, 95440 Bayreuth, Germany
| | - Ralf Conrad
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Harold L. Drake
- Department of Ecological Microbiology, University of Bayreuth, 95440 Bayreuth, Germany
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Ottesen EA, Leadbetter JR. Formyltetrahydrofolate synthetase gene diversity in the guts of higher termites with different diets and lifestyles. Appl Environ Microbiol 2011; 77:3461-7. [PMID: 21441328 PMCID: PMC3126463 DOI: 10.1128/aem.02657-10] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Accepted: 03/17/2011] [Indexed: 11/20/2022] Open
Abstract
In this study, we examine gene diversity for formyl-tetrahydrofolate synthetase (FTHFS), a key enzyme in homoacetogenesis, recovered from the gut microbiota of six species of higher termites. The "higher" termites (family Termitidae), which represent the majority of extant termite species and genera, engage in a broader diversity of feeding and nesting styles than the "lower" termites. Previous studies of termite gut homoacetogenesis have focused on wood-feeding lower termites, from which the preponderance of FTHFS sequences recovered were related to those from acetogenic treponemes. While sequences belonging to this group were present in the guts of all six higher termites examined, treponeme-like FTHFS sequences represented the majority of recovered sequences in only two species (a wood-feeding Nasutitermes sp. and a palm-feeding Microcerotermes sp.). The remaining four termite species analyzed (a Gnathamitermes sp. and two Amitermes spp. that were recovered from subterranean nests with indeterminate feeding strategies and a litter-feeding Rhynchotermes sp.) yielded novel FTHFS clades not observed in lower termites. These termites yielded two distinct clusters of probable purinolytic Firmicutes and a large group of potential homoacetogens related to sequences previously recovered from the guts of omnivorous cockroaches. These findings suggest that the gut environments of different higher termite species may select for different groups of homoacetogens, with some species hosting treponeme-dominated homoacetogen populations similar to those of wood-feeding, lower termites while others host Firmicutes-dominated communities more similar to those of omnivorous cockroaches.
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Affiliation(s)
| | - Jared R. Leadbetter
- Environmental Science & Engineering, W. M. Keck Laboratories, M/C 138-78, California Institute of Technology, Pasadena, California 91125
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Westerholm M, Roos S, Schnürer A. Tepidanaerobacter acetatoxydans sp. nov., an anaerobic, syntrophic acetate-oxidizing bacterium isolated from two ammonium-enriched mesophilic methanogenic processes. Syst Appl Microbiol 2011; 34:260-6. [PMID: 21498020 DOI: 10.1016/j.syapm.2010.11.018] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Revised: 11/10/2010] [Accepted: 11/12/2010] [Indexed: 11/26/2022]
Abstract
Four anaerobic syntrophic acetate-oxidizing bacteria, the thermotolerant strains Re1(T), Re2, T1 and T2, were isolated from two different mesophilic methanogenic systems. The strains originate from sludge of a continuously stirred laboratory-scale reactor containing high levels of ammonium and from a high ammonium enrichment culture. Comparative 16S rRNA gene sequence analysis confirmed that the strains belong to the Firmicutes-Clostridia class. The most closely related species to strains Re1(T), Re2, T1 and T2 was Tepidanaerobacter syntrophicus, with a 16S rRNA gene sequence identity of 96%. The DNA-DNA relatedness of strains Re2, T1 and T2 to strain Re1(T) was 92, 102, 81%, respectively. The gene encoding the acetogen key enzyme formyltetrahydrofolate synthetase (FTHFS) was detected and partly sequenced from the strains. In pure culture the bacteria used different organic compounds as carbon and energy source, such as organic acids, alcohols, sugars and amino acids. Furthermore, acetate-oxidizing ability was observed during co-cultivation with a hydrogen-consuming Methanoculleus sp. The bacteria were found to be spore-forming, rod-shaped and motile, and possessed Gram-positive cell walls. The four strains were thermotolerant and grew at temperatures between 25 and 55°C. Strain Re1(T) had a DNA G+C content of 38.4% and the major fatty acids were C(18:1) w7c, C(18:1) w9c, anteiso-C(17:0), C(16:1) w7c and C(18:0). The genetic and phenotypic properties of strains Re1(T), Re2, T1 and T2 suggest classification as representatives of a novel species of the genus Tepidanaerobacter; the name Tepidanaerobacter acetatoxydans sp. nov. is suggested. The type strain of T. acetatoxydans is Re1(T) (=DSM 21804(T)=JCM 16047(T)).
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Affiliation(s)
- Maria Westerholm
- Department of Microbiology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Hori T, Sasaki D, Haruta S, Shigematsu T, Ueno Y, Ishii M, Igarashi Y. Detection of active, potentially acetate-oxidizing syntrophs in an anaerobic digester by flux measurement and formyltetrahydrofolate synthetase (FTHFS) expression profiling. MICROBIOLOGY-SGM 2011; 157:1980-1989. [PMID: 21474532 DOI: 10.1099/mic.0.049189-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Syntrophic oxidation of acetate, so-called reversed reductive acetogenesis, is one of the most important degradation steps in anaerobic digesters. However, little is known about the genetic diversity of the micro-organisms involved. Here we investigated the activity and composition of potentially acetate-oxidizing syntrophs using a combinatorial approach of flux measurement and transcriptional profiling of the formyltetrahydrofolate synthetase (FTHFS) gene, an ecological biomarker for reductive acetogenesis. During the operation of a thermophilic anaerobic digester, volatile fatty acids were mostly depleted, suggesting a high turnover rate for dissolved H(2), and hydrogenotrophic methanogens were the dominant archaeal members. Batch cultivation of the digester microbiota with (13)C-labelled acetate indicated that syntrophic oxidation accounted for 13.1-21.3 % of methane production from acetate. FTHFS genes were transcribed in the absence of carbon monoxide, methoxylated compounds and inorganic electron acceptors other than CO(2), which is implicated in the activity of reversed reductive acetogenesis; however, expression itself does not distinguish whether biosynthesis or biodegradation is functioning. The mRNA- and DNA-based terminal RFLP and clone library analyses indicated that, out of nine FTHFS phylotypes detected, the FTHFS genes from the novel phylotypes I-IV in addition to the known syntroph Thermacetogenium phaeum (i.e. phylotype V) were specifically expressed. These transcripts arose from phylogenetically presumed homoacetogens. The results of this study demonstrate that hitherto unidentified phylotypes of homoacetogens are responsible for syntrophic acetate oxidation in an anaerobic digester.
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Affiliation(s)
- Tomoyuki Hori
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukisamu-Higashi 2-17-2-1, Toyohira-ku, Sapporo 062-8517, Japan.,Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Daisuke Sasaki
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Shin Haruta
- Graduate School of Science and Engineering, Tokyo Metropolitan University, Minami-Osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan.,Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Toru Shigematsu
- Department of Food Science, Faculty of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata 956-8603, Japan
| | - Yoshiyuki Ueno
- Kajima Technical Research Institute, Tobitakyu 2-19-1, Chofu-shi, Tokyo 182-0036, Japan
| | - Masaharu Ishii
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yasuo Igarashi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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Parameswaran P, Torres CI, Lee HS, Rittmann BE, Krajmalnik-Brown R. Hydrogen consumption in microbial electrochemical systems (MXCs): the role of homo-acetogenic bacteria. BIORESOURCE TECHNOLOGY 2011; 102:263-271. [PMID: 20430615 DOI: 10.1016/j.biortech.2010.03.133] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Revised: 03/23/2010] [Accepted: 03/29/2010] [Indexed: 05/29/2023]
Abstract
Homo-acetogens in the anode of a microbial electrolysis cell (MEC) fed with H(2) as sole electron donor allowed current densities similar to acetate-fed biofilm anodes (∼10 A/m(2)). Evidence for homo-acetogens included accumulation of acetate at high concentrations (up to 18 mM) in the anode compartment; detection of formate, a known intermediate during reductive acetogenesis by the acetyl-CoA pathway; and detection of formyl tetrahydrofolate synthetase (FTHFS) genes by quantitative real-time PCR. Current production and acetate accumulation increased in parallel in batch and continuous mode, while both values decreased simultaneously at short hydraulic retention times (1h) in the anode compartment, which limited suspended homo-acetogens. Acetate produced by homo-acetogens accounted for about 88% of the current density of 10A/m(2), but the current density was sustained at 4A/m(2) at short hydraulic retention time because of a robust partnership of homo-acetogens and anode respiring bacteria (ARB) in the biofilm anode.
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Affiliation(s)
- Prathap Parameswaran
- Center for Environmental Biotechnology, The Biodesign Institute at Arizona State University, PO Box 875701, Tempe, AZ 85287-5701, USA.
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