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Turner KE, Belesky DP, Zobel RW, Fortuna AM. Initial effects of supplemental forages and feedstuffs on bovine rumen ecology in vitro as determined by DNA-based molecular procedures. JOURNAL OF APPLIED ANIMAL RESEARCH 2020. [DOI: 10.1080/09712119.2020.1781648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Kenneth E. Turner
- Research Animal Scientist, USDA, ARS, Grazinglands Research Laboratory, El Reno, OK, USA
| | - David P. Belesky
- Agronomist, Clinical Associate Professor and Director of WVU Farms, West Virginia University, Morgantown, WV, USA
| | - Richard W. Zobel
- Research Plant Physiologist (Retired), USDA, ARS, Plant Science Research Unit, Raleigh, NC, USA
| | - Ann-Marie Fortuna
- Research Soil Microbiologist, USDA, ARS, Grazinglands Research Laboratory, El Reno, OK, USA
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Lebuhn M, Weiß S, Munk B, Guebitz GM. Microbiology and Molecular Biology Tools for Biogas Process Analysis, Diagnosis and Control. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2015; 151:1-40. [PMID: 26337842 DOI: 10.1007/978-3-319-21993-6_1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Many biotechnological processes such as biogas production or defined biotransformations are carried out by microorganisms or tightly cooperating microbial communities. Process breakdown is the maximum credible accident for the operator. Any time savings that can be provided by suitable early-warning systems and allow for specific countermeasures are of great value. Process disturbance, frequently due to nutritional shortcomings, malfunction or operational deficits, is evidenced conventionally by process chemistry parameters. However, knowledge on systems microbiology and its function has essentially increased in the last two decades, and molecular biology tools, most of which are directed against nucleic acids, have been developed to analyze and diagnose the process. Some of these systems have been shown to indicate changes of the process status considerably earlier than the conventionally applied process chemistry parameters. This is reasonable because the triggering catalyst is determined, activity changes of the microbes that perform the reaction. These molecular biology tools have thus the potential to add to and improve the established process diagnosis system. This chapter is dealing with the actual state of the art of biogas process analysis in practice, and introduces molecular biology tools that have been shown to be of particular value in complementing the current systems of process monitoring and diagnosis, with emphasis on nucleic acid targeted molecular biology systems.
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Affiliation(s)
- Michael Lebuhn
- Department for Quality Assurance and Analytics, Bavarian State Research Center for Agriculture (LfL), Lange Point 6, 85354, Freising, Germany
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Alvarado A, Montañez-Hernández LE, Palacio-Molina SL, Oropeza-Navarro R, Luévanos-Escareño MP, Balagurusamy N. Microbial trophic interactions and mcrA gene expression in monitoring of anaerobic digesters. Front Microbiol 2014; 5:597. [PMID: 25429286 PMCID: PMC4228917 DOI: 10.3389/fmicb.2014.00597] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Accepted: 10/22/2014] [Indexed: 11/13/2022] Open
Abstract
Anaerobic digestion (AD) is a biological process where different trophic groups of microorganisms break down biodegradable organic materials in the absence of oxygen. A wide range of AD technologies is being used to convert livestock manure, municipal and industrial wastewaters, and solid organic wastes into biogas. AD gains importance not only because of its relevance in waste treatment but also because of the recovery of carbon in the form of methane, which is a renewable energy and is used to generate electricity and heat. Despite the advances on the engineering and design of new bioreactors for AD, the microbiology component always poses challenges. Microbiology of AD processes is complicated as the efficiency of the process depends on the interactions of various trophic groups involved. Due to the complex interdependence of microbial activities for the functionality of the anaerobic bioreactors, the genetic expression of mcrA, which encodes a key enzyme in methane formation, is proposed as a parameter to monitor the process performance in real time. This review evaluates the current knowledge on microbial groups, their interactions, and their relationship to the performance of anaerobic biodigesters with a focus on using mcrA gene expression as a tool to monitor the process.
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Affiliation(s)
- Alejandra Alvarado
- Laboratorio de Biorremediación, Escuela de Ciencias Biológicas, Universidad Autónoma de Coahuila, TorreónMéxico
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, MarburgGermany
| | - Lilia E. Montañez-Hernández
- Laboratorio de Biorremediación, Escuela de Ciencias Biológicas, Universidad Autónoma de Coahuila, TorreónMéxico
| | - Sandra L. Palacio-Molina
- Laboratorio de Biorremediación, Escuela de Ciencias Biológicas, Universidad Autónoma de Coahuila, TorreónMéxico
| | | | - Miriam P. Luévanos-Escareño
- Laboratorio de Biorremediación, Escuela de Ciencias Biológicas, Universidad Autónoma de Coahuila, TorreónMéxico
| | - Nagamani Balagurusamy
- Laboratorio de Biorremediación, Escuela de Ciencias Biológicas, Universidad Autónoma de Coahuila, TorreónMéxico
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Dynamics of microbial communities in untreated and autoclaved food waste anaerobic digesters. Anaerobe 2014; 29:3-9. [PMID: 24791674 DOI: 10.1016/j.anaerobe.2014.04.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 04/17/2014] [Accepted: 04/18/2014] [Indexed: 02/07/2023]
Abstract
This study describes the microbial community richness and dynamics of two semi-continuously stirred biogas reactors during a time-course study of 120 days. The reactors were fed with untreated and autoclaved (160 °C, 6.2 bar) food waste. The microbial community was analysed using a bacteria- and archaea-targeting 16S rRNA gene-based Terminal-Restriction Fragment Length Polymorphism (T-RFLP) approach. Compared with the archaeal community, the structures and functions of the bacterial community were found to be more complex and diverse. With the principal coordinates analysis it was possible to separate both microbial communities with 75 and 50% difference for bacteria and archaea, respectively, in the two reactors fed with the same waste but with different pretreatment. Despite the use of the same feeding material, anaerobic reactors showed a distinct community profile which could explain the differences in methane yield (2-17%). The community composition was highly dynamic for bacteria and archaea during the entire studied period. This study illustrates that microbial communities are dependent on feeding material and that correlations among specific bacterial and archaeal T-RFs can be established.
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Manyi-Loh CE, Mamphweli SN, Meyer EL, Okoh AI, Makaka G, Simon M. Microbial anaerobic digestion (bio-digesters) as an approach to the decontamination of animal wastes in pollution control and the generation of renewable energy. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2013; 10:4390-417. [PMID: 24048207 PMCID: PMC3799523 DOI: 10.3390/ijerph10094390] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 09/09/2013] [Accepted: 09/10/2013] [Indexed: 11/16/2022]
Abstract
With an ever increasing population rate; a vast array of biomass wastes rich in organic and inorganic nutrients as well as pathogenic microorganisms will result from the diversified human, industrial and agricultural activities. Anaerobic digestion is applauded as one of the best ways to properly handle and manage these wastes. Animal wastes have been recognized as suitable substrates for anaerobic digestion process, a natural biological process in which complex organic materials are broken down into simpler molecules in the absence of oxygen by the concerted activities of four sets of metabolically linked microorganisms. This process occurs in an airtight chamber (biodigester) via four stages represented by hydrolytic, acidogenic, acetogenic and methanogenic microorganisms. The microbial population and structure can be identified by the combined use of culture-based, microscopic and molecular techniques. Overall, the process is affected by bio-digester design, operational factors and manure characteristics. The purpose of anaerobic digestion is the production of a renewable energy source (biogas) and an odor free nutrient-rich fertilizer. Conversely, if animal wastes are accidentally found in the environment, it can cause a drastic chain of environmental and public health complications.
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Affiliation(s)
- Christy E. Manyi-Loh
- Fort Hare Institute of Technology, University of Fort Hare, Alice Campus, Alice 5700, Eastern Cape Province, South Africa; E-Mails: (S.N.M.); (E.L.M.); (M.S.)
- Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, Alice Campus, Alice 5700, Eastern Cape Province, South Africa; E-Mail:
| | - Sampson N. Mamphweli
- Fort Hare Institute of Technology, University of Fort Hare, Alice Campus, Alice 5700, Eastern Cape Province, South Africa; E-Mails: (S.N.M.); (E.L.M.); (M.S.)
| | - Edson L. Meyer
- Fort Hare Institute of Technology, University of Fort Hare, Alice Campus, Alice 5700, Eastern Cape Province, South Africa; E-Mails: (S.N.M.); (E.L.M.); (M.S.)
| | - Anthony I. Okoh
- Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, Alice Campus, Alice 5700, Eastern Cape Province, South Africa; E-Mail:
| | - Golden Makaka
- Department of Physics, University of Fort Hare, Alice Campus, Alice 5700, Eastern Cape Province, South Africa; E-Mail:
| | - Michael Simon
- Fort Hare Institute of Technology, University of Fort Hare, Alice Campus, Alice 5700, Eastern Cape Province, South Africa; E-Mails: (S.N.M.); (E.L.M.); (M.S.)
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Steinberg LM, Regan JM. Response of lab-scale methanogenic reactors inoculated from different sources to organic loading rate shocks. BIORESOURCE TECHNOLOGY 2011; 102:8790-8798. [PMID: 21824765 DOI: 10.1016/j.biortech.2011.07.017] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Revised: 07/05/2011] [Accepted: 07/09/2011] [Indexed: 05/31/2023]
Abstract
Anaerobic digester failure due to a pH drop may be overcome with the use of an acidotolerant methanogenic community. To test this, lab-scale reactors were inoculated from acidic bog sediments, a municipal sludge digester, or a combination of these inocula and challenged with glucose pulses without pH control. Only the bog reactor survived the first glucose shock, and the methanogen community was dominated by members of the acidic Fen Cluster. After restarting the digester and hybrid reactors, two subsequent glucose shocks were applied. Methanogenic communities converged in all reactors and were dominated by Methanosarcina and Methanobacteriaceae. The Fen Cluster was eventually nondetectable in bog and hybrid reactors, presumably due to periods of circumneutral pH with only intermittent periods of low pH following glucose shocks. Although the resultant communities required base addition, an increase in Methanosarcina numbers after glucose pulses resulted in decreased acetate and increased reactor pH and methane production.
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Affiliation(s)
- Lisa M Steinberg
- Department of Civil and Environmental Engineering, The Pennsylvania State University, University Park, PA 16802, USA
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Belila A, Snoussi M, Hassan A. Rapid qualitative characterization of bacterial community in eutrophicated wastewater stabilization plant by T-RFLP method based on 16S rRNA genes. World J Microbiol Biotechnol 2011; 28:135-43. [DOI: 10.1007/s11274-011-0802-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Accepted: 05/20/2011] [Indexed: 11/29/2022]
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Feng XM, Karlsson A, Svensson BH, Bertilsson S. Impact of trace element addition on biogas production from food industrial waste - linking process to microbial communities. FEMS Microbiol Ecol 2010; 74:226-40. [DOI: 10.1111/j.1574-6941.2010.00932.x] [Citation(s) in RCA: 144] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
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McKeown RM, Scully C, Mahony T, Collins G, O'Flaherty V. Long-term (1,243 days), low-temperature (4-15 degrees C), anaerobic biotreatment of acidified wastewaters: bioprocess performance and physiological characteristics. WATER RESEARCH 2009; 43:1611-20. [PMID: 19217137 DOI: 10.1016/j.watres.2009.01.015] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2008] [Revised: 01/07/2009] [Accepted: 01/14/2009] [Indexed: 05/15/2023]
Abstract
The feasibility of long-term (>3 years), low-temperature (4-15 degrees C) and anaerobic bioreactor operation, for the treatment of acidified wastewater, was investigated. A hybrid, expanded granular sludge bed-anaerobic filter bioreactor was seeded with a mesophilic inoculum and employed for the mineralization of moderate-strength (3.75-10 kg chemical oxygen demand (COD)m(-3)) volatile fatty acid-based wastewaters at 4-15 degrees C. Bioprocess performance was assessed in terms of COD removal efficiency (CODRE), methane biogas concentration, and yield, and biomass retention. Batch specific methanogenic activity assays were performed to physiologically characterise reactor biomass. Despite transient disimprovements, CODRE and methane biogas concentrations exceeded 80% and 65%, respectively, at an applied organic loading rate (OLR) of 10 kgCODm(-3)d(-1) between 9.5 and 15 degrees C (sludge loading rate (SLR), 0.6 kgCOD kg[VSS](-1)d(-1)). Over 50% of the granular sludge bed was lost to disintegration during operation at 9.5 degrees C, warranting a reduction in the applied OLR to 3.75-5 kgCODm(-3)d(-1) (SLR, c. 0.4-0.5kgCOD kg[VSS](-1)d(-1)). From that point forward, remarkably stable and efficient performance was observed during operation at 4-10 degrees C, with respect to CODRE (>or=82%), methane biogas concentration (>70%) and methane yields (>4l(Methane)d(-1)), suggesting the adaptation of our mesophilic inoculum to psychrophilic operating conditions. Physiological activity assays indicated the development of psychroactive syntrophic and methanogenic populations, including the emergence of putatively psychrophilic propionate-oxidising and hydrogenotrophic methanogenic activity. The data suggest that mesophilic inocula can physiologically adapt to sub-optimal operational temperatures: treatment efficiencies and sludge loading rates at 4 degrees C (day, 1243) were comparable to those achieved at 15 degrees C (day 0). Furthermore, long-term, low-temperature bioreactor operation may act as a selective enrichment for psychrophilic methanogenic activity from mesophilic inocula. The observed efficient and stable bioprocess performance highlights the potential for long-term, low-temperature bioreactor operation.
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Affiliation(s)
- Rory M McKeown
- Microbial Ecology Laboratory, Department of Microbiology, Environmental Change Institute, National University of Ireland, Galway (NUI, Galway), University Road, Galway, Ireland
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Unusual bacterial populations observed in a full-scale municipal sludge digester affected by intermittent seawater inputs. J Ind Microbiol Biotechnol 2009; 36:769-73. [DOI: 10.1007/s10295-009-0557-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2009] [Accepted: 03/06/2009] [Indexed: 11/25/2022]
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Effect of seed sludge and operation conditions on performance and archaeal community structure of low-temperature anaerobic solvent-degrading bioreactors. Syst Appl Microbiol 2009; 32:65-79. [DOI: 10.1016/j.syapm.2008.10.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2008] [Revised: 10/25/2008] [Accepted: 10/31/2008] [Indexed: 11/20/2022]
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Lee C, Kim J, Shin SG, Hwang S. Monitoring bacterial and archaeal community shifts in a mesophilic anaerobic batch reactor treating a high-strength organic wastewater. FEMS Microbiol Ecol 2008; 65:544-54. [DOI: 10.1111/j.1574-6941.2008.00530.x] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Talbot G, Topp E, Palin MF, Massé DI. Evaluation of molecular methods used for establishing the interactions and functions of microorganisms in anaerobic bioreactors. WATER RESEARCH 2008; 42:513-37. [PMID: 17719078 DOI: 10.1016/j.watres.2007.08.003] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2006] [Revised: 07/31/2007] [Accepted: 08/01/2007] [Indexed: 05/16/2023]
Abstract
Molecular techniques have unveiled the complexity of the microbial consortium in anaerobic bioreactors and revealed the presence of several uncultivated species. This paper presents a review of the panoply of classical and recent molecular approaches and multivariate analyses that have been, or might be used to establish the interactions and functions of these anaerobic microorganisms. Most of the molecular approaches used so far are based on the analysis of small subunit ribosomal RNA but recent studies also use quantification of functional gene expressions. There are now several studies that have developed quantitative real-time PCR assays to investigate methanogens. With a view to improving the stability and performance of bioreactors, monitoring with molecular methods is also discussed. Advances in metagenomics and proteomics will lead to the development of promising lab-on chip technologies for cost-effective monitoring.
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Affiliation(s)
- G Talbot
- Dairy and Swine Research and Development Centre, Agriculture and Agri-Food Canada, 2000 College Street, Sherbrooke, Quebec, Canada J1M 0C8.
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