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Chettri D, Verma AK, Ghosh S, Verma AK. Biogas from lignocellulosic feedstock: current status and challenges. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:1-26. [PMID: 37697197 DOI: 10.1007/s11356-023-29805-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 09/06/2023] [Indexed: 09/13/2023]
Abstract
The organic wastes and residues generated from agricultural, industrial, and domestic activities have the potential to be converted to bioenergy. One such energy is biogas, which has already been included in rural areas as an alternative cooking energy source and agricultural activities. It is produced via anaerobic digestion of a wide range of organic nutrient sources and is an essential renewable energy source. The factors influencing biogas yield, i.e., the various substrate, their characteristics, pretreatment methods involved, different microbial types, sources, and inoculum properties, are analyzed. Furthermore, the optimization of these parameters, along with fermentation media optimization, such as optimum pH, temperature, and anaerobic digestion strategies, is discussed. Novel approaches of bioaugmentation, co-digestion, phase separation, co-supplementation, nanotechnology, and biorefinery approach have also been explored for biogas production. Finally, the current challenges and prospects of the process are discussed in the review.
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Affiliation(s)
- Dixita Chettri
- Department of Microbiology, Sikkim University, Gangtok, Sikkim, India, 737102
| | - Ashwani Kumar Verma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Shilpi Ghosh
- Department of Biotechnology, University of North Bengal, Siliguri, West Bengal, India, 734104
| | - Anil Kumar Verma
- Department of Microbiology, Sikkim University, Gangtok, Sikkim, India, 737102.
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2
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Sánchez-Sánchez C, Aranda-Medina M, Rodríguez A, Hernández A, Córdoba MG, Cuadros-Blázquez F, Ruiz-Moyano S. Development of real-time PCR methods for the quantification of Methanoculleus, Methanosarcina and Methanobacterium in anaerobic digestion. J Microbiol Methods 2022; 199:106529. [PMID: 35772572 DOI: 10.1016/j.mimet.2022.106529] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/18/2022] [Accepted: 06/22/2022] [Indexed: 12/27/2022]
Abstract
Anaerobic digestion is a growing technology to manage organic waste and produce bioenergy. To promote this technology, it is essential to know, at the molecular level, the dynamics of microbial communities, specifically the methanogenic community. In the present study, three primer pairs were selected from seven primer pairs which were designed and tested with different concentrations and conditions to detect Methanosarcina, Methanoculleus and Methanobacterium by real-time PCR based on the SYBR Green System. The functionality of the developed methods was demonstrated by the high linear relationship of the standard curves, and the specificity of each primer was empirically verified by testing DNA isolated from methane-producing and non-producing strains. These assays also exhibited good repeatability and reproducibility, which indicates the robustness of the methods. The described primers were successfully used to investigate the methanogenic communities of 10 samples from an anaerobic co-digestion. The genus Methanosarcina was the dominant methanogenic group.
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Affiliation(s)
- Consolación Sánchez-Sánchez
- Departamento de Física Aplicada, Escuela de Ingenierías Agrarias, Universidad de Extremadura, Avda, de Adolfo Suárez S/n, 06007 Badajoz, Spain
| | - Mercedes Aranda-Medina
- Expresión Gráfica, Escuela de Ingenierías Industriales, Campus Universitario, Avda de Elvas sn, 06006 Badajoz, Spain
| | - Alicia Rodríguez
- Instituto Universitario de Investigación de Recursos Agrarios (INURA), Escuela de Ingenierías Agrarias, Universidad de Extremadura, Avda. Adolfo Suarez, s/n, 06071 Badajoz, Spain.
| | - Alejandro Hernández
- Instituto Universitario de Investigación de Recursos Agrarios (INURA), Escuela de Ingenierías Agrarias, Universidad de Extremadura, Avda. Adolfo Suarez, s/n, 06071 Badajoz, Spain
| | - María G Córdoba
- Instituto Universitario de Investigación de Recursos Agrarios (INURA), Escuela de Ingenierías Agrarias, Universidad de Extremadura, Avda. Adolfo Suarez, s/n, 06071 Badajoz, Spain
| | - Francisco Cuadros-Blázquez
- Departamento de Física Aplicada, Escuela de Ingenierías Agrarias, Universidad de Extremadura, Avda, de Adolfo Suárez S/n, 06007 Badajoz, Spain
| | - Santiago Ruiz-Moyano
- Instituto Universitario de Investigación de Recursos Agrarios (INURA), Escuela de Ingenierías Agrarias, Universidad de Extremadura, Avda. Adolfo Suarez, s/n, 06071 Badajoz, Spain
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Substrate Characteristics Fluctuations in Full-Scale Anaerobic Digesters Treating Food Waste at Marginal Organic Loading Rates: A Case Study. ENERGIES 2022. [DOI: 10.3390/en15093471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The design of a full-scale bioprocess is typically based on parameters derived from smaller-scale experiments from a previous study. However, disagreements often occur at up-scaling of waste-to-energy processes due to the fluctuations of the substrate characteristics, etc. Therefore, once a commercial-scale waste digester has been built and operated, it is essential to test if the performance of the process agrees with its design value; during this process, fluctuations might occur in digesters operated at marginal organic loading rates. In this study, triplicate full-scale anaerobic digesters treating food waste were monitored for five months. The digesters, operated at the design feeding ratio, showed increasing volatile fatty acid (VFA) trends (per total alkalinity) due to a 30% higher chemical oxygen demand of the influent, than the design. The organic loading rate was adjusted on a daily basis until a stable performance was observed. Significant shifts of methanogen populations from Methanobacteriales to Methanomicrobiales and Methanosarcinales were observed during the stable operation period.
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Chamkhi I, El Omari N, Balahbib A, El Menyiy N, Benali T, Ghoulam C. Is the rhizosphere a source of applicable multi-beneficial microorganisms for plant enhancement? Saudi J Biol Sci 2022; 29:1246-1259. [PMID: 35241967 PMCID: PMC8864493 DOI: 10.1016/j.sjbs.2021.09.032] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/12/2021] [Accepted: 09/13/2021] [Indexed: 01/08/2023] Open
Abstract
The plant faces different pedological and climatic challenges that influence its growth and enhancement. While, plant-microbes interactions throught the rhizosphere offer several privileges to this hotspot in the service of plant, by attracting multi-beneficial mutualistic and symbiotic microorganisms as plant growth-promoting bacteria (PGPB), archaea, mycorrhizal fungi, endophytic fungi, and others…). Currently, numerous investigations showed the beneficial effects of these microbes on growth and plant health. Indeed, rhizospheric microorganisms offer to host plants the essential assimilable nutrients, stimulate the growth and development of host plants, and induce antibiotics production. They also attributed to host plants numerous phenotypes involved in the increase the resistance to abiotic and biotic stresses. The investigations and the studies on the rhizosphere can offer a way to find a biological and sustainable solution to confront these environmental problems. Therefore, the interactions between microbes and plants may lead to interesting biotechnological applications on plant improvement and the adaptation in different climates to obtain a biological sustainable agricultures without the use of chemical fertilizers.
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Key Words
- AMF, Arbuscular Mycorrhizal Fungi
- AOA, Ammonia-Oxidizing Archaea
- BMV, Brome Mosaic Virus
- C, Carbon
- CMV, Cucumber mosaic virus
- LDH, Layered double hydroxides
- MF, Mycorrhizal fungi
- Microorganisms
- P, Phosphorus
- PAL, L-Phenylalanine Ammonia Lyase
- PCA, Phenazine-1-Carboxylic Acid
- PGPR, Plant Growth-Promoting Rhizobacteria
- POX, Peroxidase
- PPO, Polyphenol Oxidase
- Plant growth promoting microbes
- Plant-microbes interactions
- Rhizosphere
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Affiliation(s)
- Imane Chamkhi
- Geo-Biodiversity and Natural Patrimony Laboratory (GeoBio), Geophysics, Natural Patrimony Research Center (GEOPAC), Scientific Institute, Mohammed V University in Rabat, Morocco.,University Mohammed VI Polytechnic, Agrobiosciences Program, Lot 660, Hay Moulay Rachid, Benguerir, Morocco
| | - Nasreddine El Omari
- Laboratory of Histology, Embryology, and Cytogenetic, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Morocco
| | - Abdelaali Balahbib
- Laboratory of Zoology and General Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
| | - Naoual El Menyiy
- Faculty of Science, University Sidi Mohamed Ben Abdellah, Fez, Morocco
| | - Taoufiq Benali
- Environment and Health Team, Polydisciplinary Faculty of Safi, Cadi Ayyad University, Safi, Morocco
| | - Cherki Ghoulam
- University Mohammed VI Polytechnic, Agrobiosciences Program, Lot 660, Hay Moulay Rachid, Benguerir, Morocco.,Cadi Ayyad University, Faculty of Sciences and Techniques, PO Box 549, Gueliz, Marrakech,Morocco
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Yang S, Li L, Peng X, Zhang R, Song L. Methanogen Community Dynamics and Methanogenic Function Response to Solid Waste Decomposition. Front Microbiol 2021; 12:743827. [PMID: 34707594 PMCID: PMC8542853 DOI: 10.3389/fmicb.2021.743827] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 09/13/2021] [Indexed: 11/13/2022] Open
Abstract
Methane production during solid waste decomposition is a typical methanogen-mediated and enzyme-catalyzed anaerobic digestion (AD). Methanogen community dynamics and metabolic diversity during the decomposition are not known. In this study, we investigated methanogen community dynamics and methanogenic pathways during solid waste decomposition in a bioreactor using high-throughput Illumina MiSeq sequencing and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt), respectively. We also related the methanogen community differences with solid waste and leachate physiochemical parameters. Results showed that the percentage of biodegradable matter (BDM) in solid waste decreased from 55 ± 5% in aerobic phase (AP) to 30 ± 2% in anaerobic acid phase (ACP), and to 13 ± 11% in methanogenic phase (MP), resulting in 76% BDM consumption by microbes. Methanogen community structure varied in AP, ACP, and MP, showing that Methanomicrobiales and Methanosarcinales were dominant in AP and MP and archaea E2 was abundant in ACP. Each phase had abundant core methanogen orders, genera, and species with significant difference (p < 0.05). Redundancy analysis showed that biochemical oxygen demand (BOD5) and nitrate significantly influenced methanogen community composition, suggesting that methanogen community structure is nutrient-dependent. Two methanogenic pathways including acetoclastic and hydrogenotrophic pathways with associated functional genes differed at three phases. ACP had the lowest abundance of these genes, indicating that methanogenesis was inhibited in acidogenesis. Abundant hydrogenotrophic and acetoclastic methanogenesis functional genes in MP and AP are in response to the abundance of Methanomicrobiales and Methanosarcinales. The findings provide previously unidentified insight into the mechanism of methanogen community structure and function during solid waste bioconversion for methane.
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Affiliation(s)
- Shu Yang
- Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, China
| | - Lei Li
- Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, China
| | - Xuya Peng
- Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, China
| | - Rui Zhang
- Environmental Microbiology and Ecology Research Center, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - Liyan Song
- Environmental Microbiology and Ecology Research Center, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China.,School of Resources and Environmental Engineering, Anhui University, Hefei, China
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Gallardo-Altamirano MJ, Maza-Márquez P, Montemurro N, Pérez S, Rodelas B, Osorio F, Pozo C. Insights into the removal of pharmaceutically active compounds from sewage sludge by two-stage mesophilic anaerobic digestion. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 789:147869. [PMID: 34051504 DOI: 10.1016/j.scitotenv.2021.147869] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 03/22/2021] [Accepted: 05/14/2021] [Indexed: 05/23/2023]
Abstract
The removal efficiencies (REs) of twenty-seven pharmaceutically active compounds (PhACs) (eight analgesic/anti-inflammatories, six antibiotics, four β-blockers, two antihypertensives/diuretics, three lipid regulators and four psychiatric drugs) were evaluated in a pilot-scale two-stage mesophilic anaerobic digestion (MAD) system treating thickened sewage sludge from a pilot-scale A2O™ wastewater treatment plant (WWTP) which was fed with wastewater from the pre-treatment of the full-scale WWTP Murcia Este (Murcia, Spain). The MAD system was long-term operated using two different sets of sludge retention times (SRTs) for the acidogenic (AcD) and methanogenic (MD) digesters (phase I, 2 and 12 days; and phase II, 5 and 24 days, in AcD and MD, respectively). Quantitative PCR (qPCR) and Illumina MiSeq sequencing were used to estimate the absolute abundance of Bacteria, Archaea, and Fungi and investigate the structure, diversity and population dynamics of their communities in the AcD and MD effluents. The extension of the SRT from 12 (phase I) to 24 days (phase II) in the MD was significantly linked with an improved removal of carbamazepine, clarithromycin, codeine, gemfibrozil, ibuprofen, lorazepam, and propranolol. The absolute abundances of total Bacteria and Archaea were higher in the MD regardless of the phase, while the diversity of bacterial and archaeal communities was lower in phase II, in both digesters. Non-metric multidimensional scaling (MDS) plots showed strong negative correlations among phyla Proteobacteria and Firmicutes and between genera Methanosaeta and Methanosarcina throughout the full experimental period. Strong positive correlations were revealed between the relative abundances of Methanospirillum and Methanoculleus and the methanogenesis performance parameters (volatile solids removal, CH4 recovery rate and %CH4 in the biogas), which were also related to longer SRT. The REs of several PhACs (naproxen, ketoprofen, ofloxacin, fenofibrate, trimethoprim, and atenolol) correlated positively (r > 0.75) with the relative abundances of specific bacterial and archaeal groups, suggesting their participation in biodegradation/biotransformation pathways.
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Affiliation(s)
- M J Gallardo-Altamirano
- Environmental Microbiology Group, Institute of Water Research, University of Granada, Granada, Spain; Department of Civil Engineering, University of Granada, Granada, Spain
| | - P Maza-Márquez
- Environmental Microbiology Group, Institute of Water Research, University of Granada, Granada, Spain; Department of Microbiology, University of Granada, Granada, Spain
| | - N Montemurro
- Water, Environmental and Food Chemistry (ENFOCHEM), Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Barcelona, Spain
| | - S Pérez
- Water, Environmental and Food Chemistry (ENFOCHEM), Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Barcelona, Spain
| | - B Rodelas
- Environmental Microbiology Group, Institute of Water Research, University of Granada, Granada, Spain; Department of Microbiology, University of Granada, Granada, Spain.
| | - F Osorio
- Environmental Microbiology Group, Institute of Water Research, University of Granada, Granada, Spain; Department of Civil Engineering, University of Granada, Granada, Spain
| | - C Pozo
- Environmental Microbiology Group, Institute of Water Research, University of Granada, Granada, Spain; Department of Microbiology, University of Granada, Granada, Spain
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7
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Heitkamp K, Latorre-Pérez A, Nefigmann S, Gimeno-Valero H, Vilanova C, Jahmad E, Abendroth C. Monitoring of seven industrial anaerobic digesters supplied with biochar. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:185. [PMID: 34538267 PMCID: PMC8451101 DOI: 10.1186/s13068-021-02034-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 09/01/2021] [Indexed: 05/23/2023]
Abstract
BACKGROUND Recent research articles indicate that direct interspecies electron transfer (DIET) is an alternative metabolic route for methanogenic archaea that improves microbial methane productivity. It has been shown that multiple conductive materials such as biochar can be supplemented to anaerobic digesters to increase the rate of DIET. However, the industrial applicability, as well as the impact of such supplements on taxonomic profiles, has not been sufficiently assessed to date. RESULTS Seven industrial biogas plants were upgraded with a shock charge of 1.8 kg biochar per ton of reactor content and then 1.8 kg per ton were added to the substrate for one year. A joint analysis for all seven systems showed a decreasing trend for the concentration of acetic acid (p < 0.0001), propionic acid (p < 0.0001) and butyric acid (p = 0.0022), which was significant in all cases. Quantification of the cofactor F420 using fluorescence microscopy showed a reduction in methanogenic archaea by up to a power of ten. Methanogenic archaea could grow within the biochar, even if the number of cells was 4 times less than in the surrounding sludge. 16S-rRNA gene amplicon sequencing showed a higher microbial diversity in the biochar particles than in the sludge, as well as an accumulation of secondary fermenters and halotolerant bacteria. Taxonomic profiles indicate microbial electroactivity, and show the frequent occurrence of Methanoculleus, which has not been described in this context before. CONCLUSIONS Our results shed light on the interplay between biochar particles and microbial communities in anaerobic digesters. Both the microbial diversity and the absolute frequency of the microorganisms involved were significantly changed between sludge samples and biochar particles. This is particularly important against the background of microbial process monitoring. In addition, it could be shown that biochar is suitable for reducing the content of inhibitory, volatile acids on an industrial scale.
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Affiliation(s)
| | - Adriel Latorre-Pérez
- Darwin Bioprospecting Excellence, S.L. Parc Cientific Universitat de Valencia, Paterna, Valencia, Spain
| | | | - Helena Gimeno-Valero
- Darwin Bioprospecting Excellence, S.L. Parc Cientific Universitat de Valencia, Paterna, Valencia, Spain
| | - Cristina Vilanova
- Darwin Bioprospecting Excellence, S.L. Parc Cientific Universitat de Valencia, Paterna, Valencia, Spain
| | | | - Christian Abendroth
- Institute of Waste Management and Circular Economy, Technische Universität Dresden, Pirna, Germany.
- Robert Boyle Institut e.V, Jena, Germany.
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8
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Gozde Ozbayram E. Waste to energy: valorization of spent tea waste by anaerobic digestion. ENVIRONMENTAL TECHNOLOGY 2021; 42:3554-3560. [PMID: 32530785 DOI: 10.1080/09593330.2020.1782477] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 06/06/2020] [Indexed: 06/11/2023]
Abstract
The conversion of renewable resources into value-added products such as bioenergy is one of the growing concerns of bioeconomy strategy. Within this concept, assessing the proper combination of local wastes has major importance. This study set out to assess the feasibility of using spent tea waste as a single and co-substrate on anaerobic digestion and to explore the influence of the amount of microorganisms on the digester performance. For this purpose, biomethane potentials tests were conducted for seven different mixing ratios of spent tea waste and cow manure on a mass basis. The reactors operated under mesophilic conditions for 20 days with two inoculum/substrate ratios. The results revealed that using spent tea waste as a co-substrate did not reveal a significant effect on biomethane production in the reactors. Contrarily, the amount of inoculum had a remarkable effect on biomethane production, resulted in an increase in methane production between 28 and 32%. While the biomethane yields were in the range of 129-138 mLN CH4 gVS-1 for the co-digesters operated with inoculum/substrate ratio of 1, the range was 165-181 mLN CH4 gVS-1 for the co-digesters operated with inoculum/substrate ratio of 2. These findings represent the potential usage of the spent tea waste as a co-substrate within the sustainable waste management approach and are relevant to plant operators.
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Affiliation(s)
- E Gozde Ozbayram
- Department of Marine and Freshwater Resources Management, Faculty of Aquatic Sciences, Istanbul University, Istanbul, Turkey
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9
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Chettri D, Verma AK, Verma AK. Innovations in CAZyme gene diversity and its modification for biorefinery applications. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2020; 28:e00525. [PMID: 32963975 PMCID: PMC7490808 DOI: 10.1016/j.btre.2020.e00525] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/04/2020] [Accepted: 08/30/2020] [Indexed: 02/07/2023]
Abstract
For sustainable growth, concept of biorefineries as recourse to the "fossil derived" energy source is important. Here, the Carbohydrate Active enZymes (CAZymes) play decisive role in generation of biofuels and related sugar-based products utilizing lignocellulose as a carbon source. Given their industrial significance, extensive studies on the evolution of CAZymes have been carried out. Various bacterial and fungal organisms have been scrutinized for the development of CAZymes, where advance techniques for strain enhancement such as CRISPR and analysis of specific expression systems have been deployed. Specific Omic-based techniques along with protein engineering have been adopted to unearth novel CAZymes and improve applicability of existing enzymes. In-Silico computational research and functional annotation of new CAZymes to synergy experiments are being carried out to devise cocktails of enzymes for use in biorefineries. Thus, with the establishment of these technologies, increased diversity of CAZymes with broad span of functions and applications is seen.
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10
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Performance of rice straw as mono- and co-feedstock of Ulva spp. for thalassic biogas production. Heliyon 2020; 6:e05036. [PMID: 33015390 PMCID: PMC7522385 DOI: 10.1016/j.heliyon.2020.e05036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 12/17/2019] [Accepted: 09/21/2020] [Indexed: 11/23/2022] Open
Abstract
The seasonal availability of Ulva spp. (U) poses a problem for the continuous operation of thalassic (TH) biogas digesters. Hence, rice straw (RS) was tested as an alternative substrate because of its abundance in Asian countries. The anaerobic monodigestion (AMD) of RS was performed under freshwater (FW) and TH conditions to investigate the TH biogas production performance using terrestrial biomass. Biological hydrolysis (BH-P) and 3% NaOH (NaOH-P) pretreatments were employed to minimize the limitation of biomass hydrolysis in the methane fermentation process. The BH-P [FW = 62.2 ± 30.9 mLCH4 g-1VS (volatile solids); TH = 75.8 ± 5.7 mLCH4 g-1VS] of RS led to higher actual methane yield (AMY) than NaOH-P (FW = 15.8 ± 22.8 mLCH4 g-1VS; TH = 21.4 ± 4.2 mLCH4 g-1VS) under both conditions (P = 0.008), while AMY of FW BH-P was comparable (P = 0.182) to TH BH-P. Thus, TH and BH-P was applied to the anaerobic co-digestion (ACD) of U and RS of varying mixture ratios. All ACD set-ups resulted in higher AMY (25U:75RS = 107.6 ± 7.9 mLCH4 g-1VS, 50U:50RS = 130.3 ± 10.3 mLCH4 g-1VS, 75U:25RS = 121.7 ± 2.7 mLCH4 g-1VS) compared with 100% RS (75.8 ± 5.7 mLCH4 g-1VS) or 100% U (94.8 ± 6.8 mLCH4 g-1VS) alone. While the AMY of 50U:50RS was comparable to 75U:25RS (P = 0.181), it is significantly higher (P = 0.003) than its estimated methane yield (EMY; 85.3 mLCH4 g-1VS), suggesting a synergistic effect on ACD of U and RS under 50:50 ratio. The results show that RS can be used as an alternative mono-feedstock for TH biogas production, and a high AMY can be obtained when RS is used as co-feedstock with U.
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11
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Awhangbo L, Bendoula R, Roger JM, Béline F. Detection of early imbalances in semi-continuous anaerobic co-digestion process based on instantaneous biogas production rate. WATER RESEARCH 2020; 171:115444. [PMID: 31918387 DOI: 10.1016/j.watres.2019.115444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 12/22/2019] [Accepted: 12/24/2019] [Indexed: 06/10/2023]
Abstract
The aim of this study was to investigate the use of biogas production rate kinetics for the monitoring of anaerobic co-digestion. Recent extensive studies of degradation pathways showed that acetoclastic methanogenesis is not always the main pathway. Hydrogenotrophic methanogenesis and syntrophic acetate oxidation can also dominate, mostly for operating conditions with high concentrations of ammonia or volatile fatty acids … These conditions are also known to cause instability in the digester's operation especially in co-digestion due to substrate variability. Therefore, co-digestion experiments were conducted with several co-substrates using a continuously stirred 35-L tank reactor. Degradation pathways and their potential shifts were identified by monitoring variations in biogas production rate kinetics using a principal component analysis model. The shifts in the degradation pathways were used to monitor the process. These shift points were found to provide early warnings of instabilities in the anaerobic co-digestion process.
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Affiliation(s)
- L Awhangbo
- Irstea, UR OPAALE, 17 av. de Cucillé, CS 64427, F-35044, Rennes, France; Univ. Bretagne Loire, France.
| | - R Bendoula
- Irstea, UMR ITAP, 361, rue J.F. Breton, BP 5095, F-34196, Montpellier, France.
| | - J M Roger
- Irstea, UMR ITAP, 361, rue J.F. Breton, BP 5095, F-34196, Montpellier, France.
| | - F Béline
- Irstea, UR OPAALE, 17 av. de Cucillé, CS 64427, F-35044, Rennes, France.
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12
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Guo B, Zhang Y, Zhang L, Zhou Y, Liu Y. RNA-based spatial community analysis revealed intra-reactor variation and expanded collection of direct interspecies electron transfer microorganisms in anaerobic digestion. BIORESOURCE TECHNOLOGY 2020; 298:122534. [PMID: 31835200 DOI: 10.1016/j.biortech.2019.122534] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 11/27/2019] [Accepted: 11/28/2019] [Indexed: 06/10/2023]
Abstract
Granular activated carbon (GAC) has been shown to mediate direct interspecies electron transfer (DIET) in anaerobic digestion. Adding GAC to up-flow anaerobic sludge bed reactor increased the total biomass slightly from 20.0 to 26.6 gVSS/reactor, and maximum organic removal capacity remarkably from 285 to 1660 mgCOD/L/d. Since GAC occupied 7% of reactor volume (denser than suspended sludge, settled to the reactor bottom), we used a spatial sampling strategy (sludge bed top/mid/bottom layers, and tightly attached GAC-biofilm) and DNA- and RNA-based community analyses. RNA-based analysis demonstrated significant community differences between the non-GAC and GAC-amended reactors (p < 0.05) based on ANOSIM statistical analysis. In comparison, DNA-based analysis showed little community difference between these reactors (p > 0.05). RNA-based analysis revealed active enrichments in GAC-biofilm, including bacteria Geobacter, Syntrophus, Desulfovibrio and Blvii28, and archaea Methanosaeta and Methanospirillum. These are potential electro-active syntrophic microorganisms related with DIET, which expand the previously defined list of DIET microorganisms.
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Affiliation(s)
- Bing Guo
- Department of Civil and Environmental Engineering, University of Alberta, T6G 1H9 Edmonton, Canada
| | - Yingdi Zhang
- Department of Civil and Environmental Engineering, University of Alberta, T6G 1H9 Edmonton, Canada
| | - Lei Zhang
- Department of Civil and Environmental Engineering, University of Alberta, T6G 1H9 Edmonton, Canada
| | - Yun Zhou
- Department of Civil and Environmental Engineering, University of Alberta, T6G 1H9 Edmonton, Canada
| | - Yang Liu
- Department of Civil and Environmental Engineering, University of Alberta, T6G 1H9 Edmonton, Canada.
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13
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Musa MA, Idrus S, Harun MR, Tuan Mohd Marzuki TF, Abdul Wahab AM. A Comparative Study of Biogas Production from Cattle Slaughterhouse Wastewater Using Conventional and Modified Upflow Anaerobic Sludge Blanket (UASB) Reactors. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 17:E283. [PMID: 31906118 PMCID: PMC6982031 DOI: 10.3390/ijerph17010283] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 10/27/2019] [Accepted: 10/29/2019] [Indexed: 12/18/2022]
Abstract
Cattle slaughterhouses generate wastewater that is rich in organic contaminant and nutrients, which is considered as high strength wastewater with a high potential for energy recovery. Work was undertaken to evaluate the efficiency of the 12 L laboratory scale conventional and a modified upflow anaerobic sludge blanket (UASB) reactors (conventional, R1 and modified, R2), for treatment of cattle slaughterhouse wastewater (CSWW) under mesophilic condition (35 ± 1 °C). Both reactors were acclimated with synthetic wastewater for 30 days, then continuous study with real CSWW proceeds. The reactors were subjected to the same loading condition of OLR, starting from 1.75, 3, 5 10, 14, and 16 g L-1d-1, corresponding to 3.5, 6, 10, 20, 28, and 32 g COD/L at constant hydraulic retention time (HRT) of 24 h. The performance of the R1 reactor drastically dropped at OLR 10 g L-1d-1, and this significantly affected the subsequent stages. The steady-state performance of the R2 reactor under the same loading condition as the R1 reactor revealed a high COD removal efficiency of 94% and biogas and methane productions were 27 L/d and 89%. The SMP was 0.21 LCH4/gCOD added, whereas the NH3-N alkalinity ratio stood at 651 mg/L and 0.2. SEM showed that the R2 reactor was dominated by Methanosarcina bacterial species, while the R1 reactor revealed a disturb sludge with insufficient microbial biomass.
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Affiliation(s)
- Mohammed Ali Musa
- Department of Civil Engineering, Faculty of Engineering, University Putra Malaysia, Serdang 43400, Malaysia; (M.A.M.); (T.F.T.M.M.)
- Department of Civil and Water Resources Engineering, University of Maiduguri, Maiduguri P.M.B. 1069, Nigeria
| | - Syazwani Idrus
- Department of Civil Engineering, Faculty of Engineering, University Putra Malaysia, Serdang 43400, Malaysia; (M.A.M.); (T.F.T.M.M.)
| | - Mohd Razif Harun
- Department of Chemical and Environmental Engineering, Faculty of Engineering, Universiti Putra Malaysia, Serdang 43400, Malaysia;
| | - Tuan Farhana Tuan Mohd Marzuki
- Department of Civil Engineering, Faculty of Engineering, University Putra Malaysia, Serdang 43400, Malaysia; (M.A.M.); (T.F.T.M.M.)
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14
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Ozbayram EG, Kleinsteuber S, Nikolausz M. Biotechnological utilization of animal gut microbiota for valorization of lignocellulosic biomass. Appl Microbiol Biotechnol 2019; 104:489-508. [DOI: 10.1007/s00253-019-10239-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 10/25/2019] [Accepted: 11/04/2019] [Indexed: 10/25/2022]
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15
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Carabeo-Pérez A, Guerra-Rivera G, Ramos-Leal M, Jiménez-Hernández J. Metagenomic approaches: effective tools for monitoring the structure and functionality of microbiomes in anaerobic digestion systems. Appl Microbiol Biotechnol 2019; 103:9379-9390. [PMID: 31420693 DOI: 10.1007/s00253-019-10052-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 07/17/2019] [Accepted: 07/26/2019] [Indexed: 10/26/2022]
Abstract
Microbial metagenome analysis has proven its usefulness to investigate the microbiomes present in technical engineered ecosystems such as anaerobic digestion systems. The analysis of the total microbial genomic DNA allows the detailed determination of both the microbial community structure and its functionality. In addition, it enables to study the response of the microbiome to alterations in technical process parameters. Strategies of functional microbial networks to face abiotic stressors, e.g., resistance, resilience, and reorganization, can be evaluated with respect to overall process optimization. The objective of this paper is to review the main metagenomic tools used for effective studies on anaerobic digestion systems in monitoring the dynamic of the microbiomes, as well as the factors that have been identified so far as limiting the metagenomic studies in this ecosystems.
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Affiliation(s)
- Annerys Carabeo-Pérez
- Centro de Estudios de Energía y Procesos Industriales, Universidad de Sancti Spíritus "José Martí Pérez", Ave de los Mártires No. 360, CP 60100, Sancti Spíritus, Cuba
| | - Gilda Guerra-Rivera
- Facultad de Biología, Universidad de La Habana, Calle 25 e/ I y J, Vedado, CP 10400, Havana, Cuba
| | - Miguel Ramos-Leal
- Instituto de investigaciones de fruticultura tropical, Ave. 7ma No. 3005, et. 30 y 32, Playa, CP 11300, Havana, Cuba
| | - Janet Jiménez-Hernández
- Centro de Estudios de Energía y Procesos Industriales, Universidad de Sancti Spíritus "José Martí Pérez", Ave de los Mártires No. 360, CP 60100, Sancti Spíritus, Cuba.
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16
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Ye Y, Ngo HH, Guo W, Chang SW, Nguyen DD, Liu Y, Ni BJ, Zhang X. Microbial fuel cell for nutrient recovery and electricity generation from municipal wastewater under different ammonium concentrations. BIORESOURCE TECHNOLOGY 2019; 292:121992. [PMID: 31430674 DOI: 10.1016/j.biortech.2019.121992] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 08/08/2019] [Accepted: 08/09/2019] [Indexed: 06/10/2023]
Abstract
In the present study, a dual-compartment microbial fuel cell (MFC) was constructed and continuously operated under different influent concentrations of ammonium-nitrogen (5-40 mg/L). The impacts of ammonium on organics removal, energy output and nutrient recovery were investigated. Experimental results demonstrated that this MFC reactor achieved a CDO removal efficiency of greater than 85%. Moreover, excess ammonium concentration in the feed solution compromises the generation of electricity. Simultaneously, the recovery rate of phosphate achieved in the MFC was insignificantly influenced at the wider influent ammonium concentration. In contrast, a high concentration of ammonium may not be beneficial for its recovery.
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Affiliation(s)
- Yuanyao Ye
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Huu Hao Ngo
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia.
| | - Wenshan Guo
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Soon Woong Chang
- Department of Environmental Energy and Engineering, Kyonggi University, 442-760, Republic of Korea
| | - Dinh Duc Nguyen
- Department of Environmental Energy and Engineering, Kyonggi University, 442-760, Republic of Korea
| | - Yiwen Liu
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Bing-Jie Ni
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Xinbo Zhang
- Joint Research Centre for Protective Infrastructure Technology and Environmental Green Bioprocess, School of Environmental and Municipal Engineering, Tianjin Chengjian University, Tianjin 300384, China; School of Civil and Environmental Engineering, University of Technology Sydney, NSW 2007, Australia
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17
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Langer SG, Gabris C, Einfalt D, Wemheuer B, Kazda M, Bengelsdorf FR. Different response of bacteria, archaea and fungi to process parameters in nine full-scale anaerobic digesters. Microb Biotechnol 2019; 12:1210-1225. [PMID: 30995692 PMCID: PMC6801161 DOI: 10.1111/1751-7915.13409] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 02/09/2019] [Accepted: 03/29/2019] [Indexed: 01/20/2023] Open
Abstract
Biogas production is a biotechnological process realized by complex bacterial, archaeal and likely fungal communities. Their composition was assessed in nine full-scale biogas plants with distinctly differing feedstock input and process parameters. This study investigated the actually active microbial community members by using a comprehensive sequencing approach based on ribosomal 16S and 28S rRNA fragments. The prevailing taxonomical units of each respective community were subsequently linked to process parameters. Ribosomal rRNA of bacteria, archaea and fungi, respectively, showed different compositions with respect to process parameters and supplied feedstocks: (i) bacterial communities were affected by the key factors temperature and ammonium concentration; (ii) composition of archaea was mainly related to process temperature; and (iii) relative abundance of fungi was linked to feedstocks supplied to the digesters. Anaerobic digesters with a high methane yield showed remarkably similar bacterial communities regarding identified taxonomic families. Although archaeal communities differed strongly on genus level from each other, the respective digesters still showed high methane yields. Functional redundancy of the archaeal communities may explain this effect. 28S rRNA sequences of fungi in all nine full-scale anaerobic digesters were primarily classified as facultative anaerobic Ascomycota and Basidiomycota. Since the presence of ribosomal 28S rRNA indicates that fungi may be active in the biogas digesters, further research should be carried out to examine to which extent they are important players in anaerobic digestion processes.
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MESH Headings
- Anaerobiosis
- Archaea/classification
- Archaea/genetics
- Archaea/growth & development
- Bacteria, Anaerobic/classification
- Bacteria, Anaerobic/genetics
- Bacteria, Anaerobic/growth & development
- Biofuels
- Bioreactors/microbiology
- Cluster Analysis
- DNA, Archaeal/chemistry
- DNA, Archaeal/genetics
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Fungal/chemistry
- DNA, Fungal/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fungi/classification
- Fungi/genetics
- Fungi/growth & development
- Manure/microbiology
- Metagenomics
- Microbiota
- Phylogeny
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 28S/genetics
- Sequence Analysis, DNA
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Affiliation(s)
| | - Christina Gabris
- Institute of Microbiology and BiotechnologyUlm UniversityUlmGermany
- Present address:
Bühlmann Laboratories AGSchönenbuchSwitzerland
| | - Daniel Einfalt
- Institute of Systematic Botany and EcologyUlm UniversityUlmGermany
- Present address:
Institute of Food Science and BiotechnologyUniversity of HohenheimStuttgartGermany
| | - Bernd Wemheuer
- Genomic and Applied Microbiology & Göttingen Genomics LaboratoryGeorg‐August University GöttingenGöttingenGermany
| | - Marian Kazda
- Institute of Systematic Botany and EcologyUlm UniversityUlmGermany
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18
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Senés‐Guerrero C, Colón‐Contreras FA, Reynoso‐Lobo JF, Tinoco‐Pérez B, Siller‐Cepeda JH, Pacheco A. Biogas-producing microbial composition of an anaerobic digester and associated bovine residues. Microbiologyopen 2019; 8:e00854. [PMID: 31129926 PMCID: PMC6741126 DOI: 10.1002/mbo3.854] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 04/01/2019] [Accepted: 04/15/2019] [Indexed: 11/07/2022] Open
Abstract
Influenced by feedstock type and microbial inoculum, different microbial groups must precisely interact for high-quality biogas yields. As a first approach for optimization, this study aimed to identify through time the biogas-producing microbial community in a 10-ton dry anaerobic digester treating cattle manure by denaturing gradient gel electrophoresis (DGGE) and metagenomics. Moreover, the associated bovine residues or feedstocks (leachate, manure, oxidation lagoon water, rumen) were also characterized to determine their contribution. A diverse and dynamic community characterized by Bacteria (82%-88%) and a considerable amount of Archaea (8%-15%) presented profiles particular to each stage of biogas production. Eukaryotes (2.6%-3.6%), mainly fungi, were a minor but stable component. Proteobacteria represented 47% of the community at the start of the run but only 18% at the end, opposite to the Bacteroidetes/Chlorobi group (8% and 20%, respectively), while Firmicutes (12%-18%) and Actinobacteria (12%-32%) remained relatively constant. Methanogens of the order Methanomicrobiales represented by several species of Methanoculleus were abundant at the end of the run (77%) contrary to Methanosarcinales (11%) and Methanobacteriales (0.7%). Therefore, methanogenesis mainly occurred by the hydrogenotrophic pathway. Manure and oxidation lagoon water seemed to contribute key microorganisms, while rumen dominated by Methanobrevibacter (72%) did not proliferate in the digester. Manure particularly possessed Methanoculleus (24%) and uncultured methanogens identified by DGGE, whereas oxidation lagoon was exclusively abundant in Methanolinea (18%) and Methanosaeta (19%). Leachate, as the microbial inoculum from a previous run, adequately preserved the biogas-producing community. These results could lead to higher biogas yields through bioaugmentation strategies by incorporating higher proportions or an enriched inoculum from the relevant feedstocks.
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Affiliation(s)
- Carolina Senés‐Guerrero
- Tecnologico de Monterrey, Escuela de Ingenieria y CienciasCentro de Biotecnologia‐FEMSAMonterreyMexico
| | - Franco A. Colón‐Contreras
- Tecnologico de Monterrey, Escuela de Ingenieria y CienciasCentro de Biotecnologia‐FEMSAMonterreyMexico
| | | | | | | | - Adriana Pacheco
- Tecnologico de Monterrey, Escuela de Ingenieria y CienciasCentro de Biotecnologia‐FEMSAMonterreyMexico
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19
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Process Analysis of Anaerobic Fermentation Exposure to Metal Mixtures. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16142458. [PMID: 31295944 PMCID: PMC6678117 DOI: 10.3390/ijerph16142458] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/08/2019] [Accepted: 07/08/2019] [Indexed: 01/23/2023]
Abstract
Anaerobic fermentation is a cost-effective biowaste disposal approach. During fermentation, microorganisms require a trace amount of metals for optimal growth and performance. This study investigated the effects of metal mixtures on biogas properties, process stability, substrate degradation, enzyme activity, and microbial communities during anaerobic fermentation. The addition of iron (Fe), nickel (Ni), and zinc (Zn) into a copper (Cu)-stressed fermentation system resulted in higher cumulative biogas yields, ammonia nitrogen (NH4+-N) concentrations and coenzyme F420 activities. Ni and Zn addition enhanced process stability and acetate utilization. The addition of these metals also improved and brought forward the peak daily biogas yields as well as increased CH4 content to 88.94 and 86.58%, respectively. Adding Zn into the Cu-stressed system improved the abundance of Defluviitoga, Fibrobacter and Methanothermobacter, the degradation of cellulose, and the transformation of CO2 to CH4. The bacterial and archaeal communities were responsible for the degradation of lignocelluloses and CH4 production during the fermentation process. This study supports the reutilization of heavy metal-contaminated biowaste and provides references for further research on heavy metals impacted anaerobic fermentation.
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20
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Abstract
Anaerobic fermentation with biogas as an energy source is influenced by the presence of heavy metals. However, the availability of the heavy metals is dependent on the digestion temperature. In this study, the impacts of Cd on the characteristics of biogas, substrate biodegradation, and enzyme activity during anaerobic co-digestion were investigated under varying digestion temperatures. The results showed that 1 mg/L initial Cd concentration improved cumulative biogas yields by 404.96%, 16.93%, and 5.56% at 55 °C, 45 °C, and 35 °C, respectively. In contrast, at low temperatures (25 °C), the yield decreased by 0.77%. In the 55 °C group, Cd addition improved the activity of cellulase (p < 0.05) and coenzyme F420 (p < 0.01). The total chemical oxygen demand (COD) during the peak period and the transformation of hydrolytic organic components into volatile fatty acids (VFAs) influenced the CH4 and biogas yields. There were no significant differences in cellulase, dehydrogenase, and coenzyme F420 activities with or without Cd addition when the digestion temperature was 45 °C, 35 °C, and 25 °C. Therefore, thermophilic digestion is recommended for the efficient degradation of Cd-contaminated biowaste. Moreover, the impact of metals on the performance of anaerobic digestion should be considered together with temperature conditions in future research and practice.
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21
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Bonk F, Popp D, Weinrich S, Sträuber H, Becker D, Kleinsteuber S, Harms H, Centler F. Determination of Microbial Maintenance in Acetogenesis and Methanogenesis by Experimental and Modeling Techniques. Front Microbiol 2019; 10:166. [PMID: 30800108 PMCID: PMC6375858 DOI: 10.3389/fmicb.2019.00166] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 01/22/2019] [Indexed: 11/21/2022] Open
Abstract
For biogas-producing continuous stirred tank reactors, an increase in dilution rate increases the methane production rate as long as substrate input can be converted fully. However, higher dilution rates necessitate higher specific microbial growth rates, which are assumed to have a strong impact on the apparent microbial biomass yield due to cellular maintenance. To test this, we operated two reactors at 37°C in parallel at dilution rates of 0.18 and 0.07 days-1 (hydraulic retention times of 5.5 and 14 days, doubling times of 3.9 and 9.9 days in steady state) with identical inoculum and a mixture of volatile fatty acids as sole carbon sources. We evaluated the performance of the Anaerobic Digestion Model No. 1 (ADM1), a thermodynamic black box approach (TBA), and dynamic flux balance analysis (dFBA), to describe the experimental observations. All models overestimated the impact of dilution rate on the apparent microbial biomass yield when using default parameter values. Based on our analysis, a maintenance coefficient value below 0.2 kJ per carbon mole of microbial biomass per hour should be used for the TBA, corresponding to 0.12 mmol ATP per gram dry weight per hour for dFBA, which strongly deviates from the value of 9.8 kJ Cmol h-1 that has been suggested to apply to all anaerobic microorganisms at 37°C. We hypothesized that a decrease in dilution rate might select taxa with minimized maintenance expenditure. However, no major differences in the dominating taxa between the reactors were observed based on amplicon sequencing of 16S rRNA genes and terminal restriction fragment length polymorphism analysis of mcrA genes. Surprisingly, Methanosaeta dominated over Methanosarcina even at a dilution rate of 0.18 days-1, which contradicts previous model expectations. Furthermore, only 23-49% of the bacterial reads could be assigned to known syntrophic fatty acid oxidizers, indicating that unknown members of this functional group remain to be discovered. In conclusion, microbial maintenance was found to be much lower for acetogenesis and methanogenesis than previously assumed, likely due to the exceptionally low growth rates in anaerobic digestion. This finding might also be relevant for other microbial systems operating at similarly low growth rates.
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Affiliation(s)
- Fabian Bonk
- Department of Environmental Microbiology, UFZ-Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Denny Popp
- Department of Environmental Microbiology, UFZ-Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Sören Weinrich
- Biochemical Conversion Department, DBFZ-Deutsches Biomasseforschungszentrum gGmbH, Leipzig, Germany
| | - Heike Sträuber
- Department of Environmental Microbiology, UFZ-Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Daniela Becker
- Department of Environmental Microbiology, UFZ-Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Sabine Kleinsteuber
- Department of Environmental Microbiology, UFZ-Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Hauke Harms
- Department of Environmental Microbiology, UFZ-Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Florian Centler
- Department of Environmental Microbiology, UFZ-Helmholtz Centre for Environmental Research, Leipzig, Germany
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22
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Bonk F, Popp D, Weinrich S, Sträuber H, Kleinsteuber S, Harms H, Centler F. Ammonia Inhibition of Anaerobic Volatile Fatty Acid Degrading Microbial Communities. Front Microbiol 2018; 9:2921. [PMID: 30555446 PMCID: PMC6284035 DOI: 10.3389/fmicb.2018.02921] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 11/14/2018] [Indexed: 11/16/2022] Open
Abstract
Ammonia inhibition is an important reason for reactor failures and economic losses in anaerobic digestion. Its impact on acetic acid degradation is well-studied, while its effect on propionic and butyric acid degradation has received little attention and is consequently not considered in the Anaerobic Digestion Model No. 1 (ADM1). To compare ammonia inhibition of the degradation of these three volatile fatty acids (VFAs), we fed a mixture of them as sole carbon source to three continuous stirred tank reactors (CSTRs) and increased ammonium bicarbonate concentrations in the influent from 52 to 277 mM. The use of this synthetic substrate allowed for the determination of degradation efficiencies for the individual acids. While butyric acid degradation was hardly affected by the increase of ammonia concentration, propionic acid degradation turned out to be even more inhibited than acetic acid degradation with degradation efficiencies dropping to 31 and 65% for propionic and acetic acid, respectively. The inhibited reactors acclimatized and approximated pre-disturbance degradation efficiencies toward the end of the experiment, which was accompanied by strong microbial community shifts, as observed by amplicon sequencing of 16S rRNA genes and terminal restriction fragment length polymorphism (T-RFLP) of mcrA genes. The acetoclastic methanogen Methanosaeta was completely replaced by Methanosarcina. The propionic acid degrading genus Syntrophobacter was replaced by yet unknown propionic acid degraders. The butyric acid degrading genus Syntrophomonas and hydrogenotrophic Methanomicrobiaceae were hardly affected. We hypothesized that the ammonia sensitivity of the initially dominating taxa Methanosaeta and Syntrophobacter led to a stronger inhibition of the acetic and propionic acid degradation compared to butyric acid degradation and hydrogenotrophic methanogenesis, which were facilitated by the ammonia tolerant taxa Syntrophomonas and Methanomicrobiaceae. We implemented this hypothesis into a multi-taxa extension of ADM1, which was able to simulate the dynamics of both microbial community composition and VFA concentration in the experiment. It is thus plausible that the effect of ammonia on VFA degradation strongly depends on the ammonia sensitivity of the dominating taxa, for syntrophic propionate degraders as much as for acetoclastic methanogens.
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Affiliation(s)
- Fabian Bonk
- Department of Environmental Microbiology, UFZ–Helmholtz Center for Environmental Research, Leipzig, Germany
| | - Denny Popp
- Department of Environmental Microbiology, UFZ–Helmholtz Center for Environmental Research, Leipzig, Germany
| | - Sören Weinrich
- Biochemical Conversion Department, DBFZ-Deutsches Biomasseforschungszentrum gGmbH, Leipzig, Germany
| | - Heike Sträuber
- Department of Environmental Microbiology, UFZ–Helmholtz Center for Environmental Research, Leipzig, Germany
| | - Sabine Kleinsteuber
- Department of Environmental Microbiology, UFZ–Helmholtz Center for Environmental Research, Leipzig, Germany
| | - Hauke Harms
- Department of Environmental Microbiology, UFZ–Helmholtz Center for Environmental Research, Leipzig, Germany
| | - Florian Centler
- Department of Environmental Microbiology, UFZ–Helmholtz Center for Environmental Research, Leipzig, Germany
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23
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Hardegen J, Latorre-Pérez A, Vilanova C, Günther T, Porcar M, Luschnig O, Simeonov C, Abendroth C. Methanogenic community shifts during the transition from sewage mono-digestion to co-digestion of grass biomass. BIORESOURCE TECHNOLOGY 2018; 265:275-281. [PMID: 29906716 DOI: 10.1016/j.biortech.2018.06.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 05/30/2018] [Accepted: 06/04/2018] [Indexed: 06/08/2023]
Abstract
In this work, liquid and solid fractions of grass biomass were used as co-substrates for anaerobic co-digestion of sewage sludge. The input of grass biomass was increased gradually, and the underlying methanogenic microbiome was assessed by means of microscopy-based cell counting and full-length 16S rRNA gene high-throughput sequencing, proving for the first time the suitability of nanopore-based portable sequencers as a monitoring tool for anaerobic digestion systems. In both cases co-fermentation resulted in an increased number of bacteria and methanogenic archaea. Interestingly, the microbial communities were highly different between solid and liquid-fed batches. Liquid-fed batches developed a more stable microbiome, enriched in Methanosarcina spp., and resulted in higher methanogenic yield. In contrast, solid-fed batches were highly unstable at higher substrate concentrations, and kept Methanosaeta spp. - typically associated to sewage sludge - as the majoritary methanogenic archaea.
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Affiliation(s)
| | | | | | | | - Manuel Porcar
- Darwin Bioprospecting Excellence, S.L., Paterna, Valencia, Spain; Institute for Integrative Systems Biology (I2SysBio), Paterna, Valencia, Spain
| | | | | | - Christian Abendroth
- Robert Boyle Institut e.V., Jena, Germany; Institute for Integrative Systems Biology (I2SysBio), Paterna, Valencia, Spain; Technische Universität Dresden, Chair of Waste Management, Pratzschwitzer Str. 15, Pirna, Germany.
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24
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Bonk F, Popp D, Harms H, Centler F. PCR-based quantification of taxa-specific abundances in microbial communities: Quantifying and avoiding common pitfalls. J Microbiol Methods 2018; 153:139-147. [DOI: 10.1016/j.mimet.2018.09.015] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/24/2018] [Accepted: 09/25/2018] [Indexed: 11/25/2022]
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25
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Hassa J, Maus I, Off S, Pühler A, Scherer P, Klocke M, Schlüter A. Metagenome, metatranscriptome, and metaproteome approaches unraveled compositions and functional relationships of microbial communities residing in biogas plants. Appl Microbiol Biotechnol 2018; 102:5045-5063. [PMID: 29713790 PMCID: PMC5959977 DOI: 10.1007/s00253-018-8976-7] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 03/27/2018] [Accepted: 03/28/2018] [Indexed: 12/15/2022]
Abstract
The production of biogas by anaerobic digestion (AD) of agricultural residues, organic wastes, animal excrements, municipal sludge, and energy crops has a firm place in sustainable energy production and bio-economy strategies. Focusing on the microbial community involved in biomass conversion offers the opportunity to control and engineer the biogas process with the objective to optimize its efficiency. Taxonomic profiling of biogas producing communities by means of high-throughput 16S rRNA gene amplicon sequencing provided high-resolution insights into bacterial and archaeal structures of AD assemblages and their linkages to fed substrates and process parameters. Commonly, the bacterial phyla Firmicutes and Bacteroidetes appeared to dominate biogas communities in varying abundances depending on the apparent process conditions. Regarding the community of methanogenic Archaea, their diversity was mainly affected by the nature and composition of the substrates, availability of nutrients and ammonium/ammonia contents, but not by the temperature. It also appeared that a high proportion of 16S rRNA sequences can only be classified on higher taxonomic ranks indicating that many community members and their participation in AD within functional networks are still unknown. Although cultivation-based approaches to isolate microorganisms from biogas fermentation samples yielded hundreds of novel species and strains, this approach intrinsically is limited to the cultivable fraction of the community. To obtain genome sequence information of non-cultivable biogas community members, metagenome sequencing including assembly and binning strategies was highly valuable. Corresponding research has led to the compilation of hundreds of metagenome-assembled genomes (MAGs) frequently representing novel taxa whose metabolism and lifestyle could be reconstructed based on nucleotide sequence information. In contrast to metagenome analyses revealing the genetic potential of microbial communities, metatranscriptome sequencing provided insights into the metabolically active community. Taking advantage of genome sequence information, transcriptional activities were evaluated considering the microorganism's genetic background. Metaproteome studies uncovered enzyme profiles expressed by biogas community members. Enzymes involved in cellulose and hemicellulose decomposition and utilization of other complex biopolymers were identified. Future studies on biogas functional microbial networks will increasingly involve integrated multi-omics analyses evaluating metagenome, transcriptome, proteome, and metabolome datasets.
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Affiliation(s)
- Julia Hassa
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstrasse 27, 33615, Bielefeld, Germany
| | - Irena Maus
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstrasse 27, 33615, Bielefeld, Germany
| | - Sandra Off
- Dept. Biotechnologie, Hochschule für angewandte Wissenschaften (HAW) Hamburg Ulmenliet 20, 21033, Hamburg, Germany
| | - Alfred Pühler
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstrasse 27, 33615, Bielefeld, Germany
| | - Paul Scherer
- Dept. Biotechnologie, Hochschule für angewandte Wissenschaften (HAW) Hamburg Ulmenliet 20, 21033, Hamburg, Germany
| | - Michael Klocke
- Dept. Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy, Max-Eyth-Allee 100, 14469, Potsdam, Germany
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstrasse 27, 33615, Bielefeld, Germany.
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Hiegemann H, Lübken M, Schulte P, Schmelz KG, Gredigk-Hoffmann S, Wichern M. Inhibition of microbial fuel cell operation for municipal wastewater treatment by impact loads of free ammonia in bench- and 45L-scale. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 624:34-39. [PMID: 29245036 DOI: 10.1016/j.scitotenv.2017.12.072] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 11/20/2017] [Accepted: 12/06/2017] [Indexed: 06/07/2023]
Abstract
A 45-liter microbial fuel cell (MFC) system was integrated into a full-scale wastewater treatment plant (WWTP). The system was operated under practical conditions with supernatant of a pre-thickener for 50days in order to identify, whether higher power output and energy recovery is possible compared to the use of primary clarifier effluent, as used in a previous study. The higher COD (chemical oxygen demand) loading rates of supernatant neither increased power densities, nor energy recovery, but impact loads of total ammonia nitrogen (TAN) in concentrations >800mg/L (free ammonia nitrogen (FAN)>40mg/L) led to an instant collapse of power output and nutrient removal, which was reversed when ammonia concentrations decreased. Investigations in lab-scale under defined conditions verified that the inhibition of the exoelectrogenic biofilm is in fact caused by high levels of FAN. Here, COD removal, power output and energy recovery constantly decreased, when FAN-concentrations were increased above 64mg/L.
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Affiliation(s)
- Heinz Hiegemann
- Institute of Urban Water Management and Environmental Engineering, Ruhr-Universität Bochum, Universitätsstraße 150, 44801 Bochum, Germany.
| | - Manfred Lübken
- Institute of Urban Water Management and Environmental Engineering, Ruhr-Universität Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Patrick Schulte
- Emschergenossenschaft (EG), Kronprinzenstr. 24, 45128 Essen, Germany
| | | | - Sylvia Gredigk-Hoffmann
- Research Institute for Water and Waste Management at RWTH Aachen (FiW) e.V., Kackertstr. 15-17, 52072 Aachen, Germany
| | - Marc Wichern
- Institute of Urban Water Management and Environmental Engineering, Ruhr-Universität Bochum, Universitätsstraße 150, 44801 Bochum, Germany
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27
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Hassa J, Maus I, Off S, Pühler A, Scherer P, Klocke M, Schlüter A. Metagenome, metatranscriptome, and metaproteome approaches unraveled compositions and functional relationships of microbial communities residing in biogas plants. Appl Microbiol Biotechnol 2018. [PMID: 29713790 DOI: 10.1007/s00253-018-8976-7)] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The production of biogas by anaerobic digestion (AD) of agricultural residues, organic wastes, animal excrements, municipal sludge, and energy crops has a firm place in sustainable energy production and bio-economy strategies. Focusing on the microbial community involved in biomass conversion offers the opportunity to control and engineer the biogas process with the objective to optimize its efficiency. Taxonomic profiling of biogas producing communities by means of high-throughput 16S rRNA gene amplicon sequencing provided high-resolution insights into bacterial and archaeal structures of AD assemblages and their linkages to fed substrates and process parameters. Commonly, the bacterial phyla Firmicutes and Bacteroidetes appeared to dominate biogas communities in varying abundances depending on the apparent process conditions. Regarding the community of methanogenic Archaea, their diversity was mainly affected by the nature and composition of the substrates, availability of nutrients and ammonium/ammonia contents, but not by the temperature. It also appeared that a high proportion of 16S rRNA sequences can only be classified on higher taxonomic ranks indicating that many community members and their participation in AD within functional networks are still unknown. Although cultivation-based approaches to isolate microorganisms from biogas fermentation samples yielded hundreds of novel species and strains, this approach intrinsically is limited to the cultivable fraction of the community. To obtain genome sequence information of non-cultivable biogas community members, metagenome sequencing including assembly and binning strategies was highly valuable. Corresponding research has led to the compilation of hundreds of metagenome-assembled genomes (MAGs) frequently representing novel taxa whose metabolism and lifestyle could be reconstructed based on nucleotide sequence information. In contrast to metagenome analyses revealing the genetic potential of microbial communities, metatranscriptome sequencing provided insights into the metabolically active community. Taking advantage of genome sequence information, transcriptional activities were evaluated considering the microorganism's genetic background. Metaproteome studies uncovered enzyme profiles expressed by biogas community members. Enzymes involved in cellulose and hemicellulose decomposition and utilization of other complex biopolymers were identified. Future studies on biogas functional microbial networks will increasingly involve integrated multi-omics analyses evaluating metagenome, transcriptome, proteome, and metabolome datasets.
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Affiliation(s)
- Julia Hassa
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstrasse 27, 33615, Bielefeld, Germany
| | - Irena Maus
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstrasse 27, 33615, Bielefeld, Germany
| | - Sandra Off
- Dept. Biotechnologie, Hochschule für angewandte Wissenschaften (HAW) Hamburg Ulmenliet 20, 21033, Hamburg, Germany
| | - Alfred Pühler
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstrasse 27, 33615, Bielefeld, Germany
| | - Paul Scherer
- Dept. Biotechnologie, Hochschule für angewandte Wissenschaften (HAW) Hamburg Ulmenliet 20, 21033, Hamburg, Germany
| | - Michael Klocke
- Dept. Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy, Max-Eyth-Allee 100, 14469, Potsdam, Germany
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstrasse 27, 33615, Bielefeld, Germany.
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The use of extracellular DNA as a proxy for specific microbial activity. Appl Microbiol Biotechnol 2018; 102:2885-2898. [PMID: 29423636 PMCID: PMC5847193 DOI: 10.1007/s00253-018-8786-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 01/11/2018] [Accepted: 01/14/2018] [Indexed: 02/07/2023]
Abstract
The ubiquity and relevance of extracellular DNA (exDNA) are well-known and increasingly gaining importance in many fields of application such as medicine and environmental microbiology. Although sources and types of exDNA are manifold, ratios of specific DNA-molecules inside and outside of living cells can give reliable information about the activity of entire systems and of specific microbial groups or species. Here, we introduce a method to discriminate between internal (iDNA), as well as bound and free exDNA, and evaluate various DNA fractions and related ratios (ex:iDNA) regarding their applicability to be used as a fast, convenient, and reliable alternative to more tedious RNA-based activity measurements. In order to deal with microbial consortia that can be regulated regarding their activity, we tested and evaluated the proposed method in comparison to sophisticated dehydrogenase- and RNA-based activity measurements with two anaerobic microbial consortia (anaerobic fungi and syntrophic archaea and a microbial rumen consortium) and three levels of resolution (overall activity, total bacteria, methanogenic archaea). Furthermore, we introduce a 28S rRNA gene-specific primer set and qPCR protocol, targeting anaerobic fungi (Neocallimastigomycota). Our findings show that the amount of actively released free exDNA (fDNA) strongly correlates with different activity measurements and is thus suggested to serve as a proxy for microbial activity.
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29
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Maus I, Rumming M, Bergmann I, Heeg K, Pohl M, Nettmann E, Jaenicke S, Blom J, Pühler A, Schlüter A, Sczyrba A, Klocke M. Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:167. [PMID: 29951113 PMCID: PMC6010159 DOI: 10.1186/s13068-018-1162-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 06/01/2018] [Indexed: 05/13/2023]
Abstract
BACKGROUND Previous studies on the Miscellaneous Crenarchaeota Group, recently assigned to the novel archaeal phylum Bathyarchaeota, reported on the dominance of these Archaea within the anaerobic carbohydrate cycle performed by the deep marine biosphere. For the first time, members of this phylum were identified also in mesophilic and thermophilic biogas-forming biofilms and characterized in detail. RESULTS Metagenome shotgun libraries of biofilm microbiomes were sequenced using the Illumina MiSeq system. Taxonomic classification revealed that between 0.1 and 2% of all classified sequences were assigned to Bathyarchaeota. Individual metagenome assemblies followed by genome binning resulted in the reconstruction of five metagenome-assembled genomes (MAGs) of Bathyarchaeota. MAGs were estimated to be 65-92% complete, ranging in their genome sizes from 1.1 to 2.0 Mb. Phylogenetic classification based on core gene sets confirmed their placement within the phylum Bathyarchaeota clustering as a separate group diverging from most of the recently known Bathyarchaeota clusters. The genetic repertoire of these MAGs indicated an energy metabolism based on carbohydrate and amino acid fermentation featuring the potential for extracellular hydrolysis of cellulose, cellobiose as well as proteins. In addition, corresponding transporter systems were identified. Furthermore, genes encoding enzymes for the utilization of carbon monoxide and/or carbon dioxide via the Wood-Ljungdahl pathway were detected. CONCLUSIONS For the members of Bathyarchaeota detected in the biofilm microbiomes, a hydrolytic lifestyle is proposed. This is the first study indicating that Bathyarchaeota members contribute presumably to hydrolysis and subsequent fermentation of organic substrates within biotechnological biogas production processes.
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Affiliation(s)
- Irena Maus
- Dept. Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Madis Rumming
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
- Computational Metagenomics, Faculty of Technology, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Ingo Bergmann
- Dept. Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Kathrin Heeg
- Dept. Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Marcel Pohl
- Biochemical Conversion Department, Deutsches Biomasseforschungszentrum gemeinnützige GmbH, Torgauer Straße 116, 04347 Leipzig, Germany
| | - Edith Nettmann
- Urban Water Management and Environmental Engineering, Faculty of Civil and Environmental Engineering, Ruhr University Bochum, Universitätsstraße 150, 44780 Bochum, Germany
| | - Sebastian Jaenicke
- Dept. Bioinformatics and Systems Biology, Justus-Liebig University Gießen, Heinrich-Buff-Ring 58, 35392 Giessen, Germany
| | - Jochen Blom
- Dept. Bioinformatics and Systems Biology, Justus-Liebig University Gießen, Heinrich-Buff-Ring 58, 35392 Giessen, Germany
| | - Alfred Pühler
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Alexander Sczyrba
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
- Computational Metagenomics, Faculty of Technology, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Michael Klocke
- Dept. Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
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Jiang Y, Banks C, Zhang Y, Heaven S, Longhurst P. Quantifying the percentage of methane formation via acetoclastic and syntrophic acetate oxidation pathways in anaerobic digesters. WASTE MANAGEMENT (NEW YORK, N.Y.) 2018; 71:749-756. [PMID: 28396168 DOI: 10.1016/j.wasman.2017.04.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 03/28/2017] [Accepted: 04/02/2017] [Indexed: 06/07/2023]
Abstract
Ammonia concentration is one of the key factors influencing the methanogenic community composition and dominant methanogenic pathway in anaerobic digesters. This study adopted a radiolabelling technique using [2-14C] acetate to investigate the relationship between total ammonia nitrogen (TAN) and the methanogenic pathway. The radiolabelling experiments determined the ratio of 14CO2 and 14CH4 in the biogas which was used to quantitatively determine the percentage of CH4 derived from acetoclastic and syntrophic acetate oxidation routes, respectively. This technique was performed on a selection of mesophilic digesters representing samples of low to high TAN concentrations (0.2-11.1gkg-1 wet weight). In high TAN digesters, the ratio between 14CO2 and 14CH4 was in the range 2.1-3.0; indicating 68-75% of methane was produced via the hydrogenotrophic route; whereas in low ammonia samples the ratio was 0.1-0.3, indicating 9-23% of methane was produced by the hydrogenotrophic route. These findings have been confirmed further by phylogenetic studies.
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Affiliation(s)
- Ying Jiang
- Centre for Bioenergy & Resource Management, School of Water, Energy and Environment, Cranfield University, Cranfield MK43 0AL, UK.
| | - Charles Banks
- Faculty of Engineering and the Environment, University of Southampton, Southampton SO17 1BJ, UK
| | - Yue Zhang
- Faculty of Engineering and the Environment, University of Southampton, Southampton SO17 1BJ, UK
| | - Sonia Heaven
- Faculty of Engineering and the Environment, University of Southampton, Southampton SO17 1BJ, UK
| | - Philip Longhurst
- Centre for Bioenergy & Resource Management, School of Water, Energy and Environment, Cranfield University, Cranfield MK43 0AL, UK
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31
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Lambrecht J, Cichocki N, Hübschmann T, Koch C, Harms H, Müller S. Flow cytometric quantification, sorting and sequencing of methanogenic archaea based on F 420 autofluorescence. Microb Cell Fact 2017; 16:180. [PMID: 29084543 PMCID: PMC5663091 DOI: 10.1186/s12934-017-0793-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 10/24/2017] [Indexed: 02/08/2023] Open
Abstract
Background The widely established production of CH4 from renewable biomass in industrial scale anaerobic reactors may play a major role in the future energy supply. It relies on methanogenic archaea as key organisms which represent the bottleneck in the process. The quantitative analysis of these organisms can help to maximize process performance, uncover disturbances before failure, and may ultimately lead to community-based process control schemes. Existing qPCR and fluorescence microscopy-based methods are very attractive but can be cost-intensive and laborious. Results In this study we present an autofluorescence-based, flow cytometric method for the fast low-cost quantification of methanogenic archaea in complex microbial communities and crude substrates. The method was applied to a methanogenic enrichment culture (MEC) and digester samples (DS). The methanogenic archaea were quantified using the distinct fluorescence of their cofactor F420 in a range from 3.7 × 108 (± 3.3 × 106) cells mL−1 and 1.8 x 109 (± 1.1 × 108) cells mL−1. We evaluated different fixation methods and tested the sample stability. Stable abundance and fluorescence intensity were recorded up to 26 days during aerobic storage in PBS at 6 °C. The discrimination of the whole microbial community from the ubiquitous particle noise was facilitated by SYBR Green I staining and enabled calculation of relative abundances of methanogenic archaea of up to 9.64 ± 0.23% in the MEC and up to 4.43 ± 0.74% in the DS. The metaprofiling of the mcrA gene reinforced the results. Conclusions The presented method allows for fast and reliable quantification of methanogenic archaea in microbial communities under authentic digester conditions and can thus be useful for process monitoring and control in biogas digesters. Electronic supplementary material The online version of this article (10.1186/s12934-017-0793-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Johannes Lambrecht
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318, Leipzig, Germany
| | - Nicolas Cichocki
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318, Leipzig, Germany
| | - Thomas Hübschmann
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318, Leipzig, Germany
| | - Christin Koch
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318, Leipzig, Germany
| | - Hauke Harms
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318, Leipzig, Germany
| | - Susann Müller
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318, Leipzig, Germany.
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32
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Kougias PG, Campanaro S, Treu L, Zhu X, Angelidaki I. A novel archaeal species belonging to Methanoculleus genus identified via de-novo assembly and metagenomic binning process in biogas reactors. Anaerobe 2017; 46:23-32. [DOI: 10.1016/j.anaerobe.2017.02.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 01/25/2017] [Accepted: 02/12/2017] [Indexed: 10/20/2022]
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BEAP profiles as rapid test system for status analysis and early detection of process incidents in biogas plants. J Ind Microbiol Biotechnol 2017; 44:465-476. [PMID: 28064390 DOI: 10.1007/s10295-016-1894-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 12/22/2016] [Indexed: 11/26/2022]
Abstract
A method was developed to quantify the performance of microorganisms involved in different digestion levels in biogas plants. The test system was based on the addition of butyrate (BCON), ethanol (ECON), acetate (ACON) or propionate (PCON) to biogas sludge samples and the subsequent analysis of CH4 formation in comparison to control samples. The combination of the four values was referred to as BEAP profile. Determination of BEAP profiles enabled rapid testing of a biogas plant's metabolic state within 24 h and an accurate mapping of all degradation levels in a lab-scale experimental setup. Furthermore, it was possible to distinguish between specific BEAP profiles for standard biogas plants and for biogas reactors with process incidents (beginning of NH4+-N inhibition, start of acidification, insufficient hydrolysis and potential mycotoxin effects). Finally, BEAP profiles also functioned as a warning system for the early prediction of critical NH4+-N concentrations leading to a drop of CH4 formation.
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34
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Maus I, Bremges A, Stolze Y, Hahnke S, Cibis KG, Koeck DE, Kim YS, Kreubel J, Hassa J, Wibberg D, Weimann A, Off S, Stantscheff R, Zverlov VV, Schwarz WH, König H, Liebl W, Scherer P, McHardy AC, Sczyrba A, Klocke M, Pühler A, Schlüter A. Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:264. [PMID: 29158776 PMCID: PMC5684752 DOI: 10.1186/s13068-017-0947-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 11/01/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND To elucidate biogas microbial communities and processes, the application of high-throughput DNA analysis approaches is becoming increasingly important. Unfortunately, generated data can only partialy be interpreted rudimentary since databases lack reference sequences. RESULTS Novel cellulolytic, hydrolytic, and acidogenic/acetogenic Bacteria as well as methanogenic Archaea originating from different anaerobic digestion communities were analyzed on the genomic level to assess their role in biomass decomposition and biogas production. Some of the analyzed bacterial strains were recently described as new species and even genera, namely Herbinix hemicellulosilytica T3/55T, Herbinix luporum SD1DT, Clostridium bornimense M2/40T, Proteiniphilum saccharofermentans M3/6T, Fermentimonas caenicola ING2-E5BT, and Petrimonas mucosa ING2-E5AT. High-throughput genome sequencing of 22 anaerobic digestion isolates enabled functional genome interpretation, metabolic reconstruction, and prediction of microbial traits regarding their abilities to utilize complex bio-polymers and to perform specific fermentation pathways. To determine the prevalence of the isolates included in this study in different biogas systems, corresponding metagenome fragment mappings were done. Methanoculleus bourgensis was found to be abundant in three mesophilic biogas plants studied and slightly less abundant in a thermophilic biogas plant, whereas Defluviitoga tunisiensis was only prominent in the thermophilic system. Moreover, several of the analyzed species were clearly detectable in the mesophilic biogas plants, but appeared to be only moderately abundant. Among the species for which genome sequence information was publicly available prior to this study, only the species Amphibacillus xylanus, Clostridium clariflavum, and Lactobacillus acidophilus are of importance for the biogas microbiomes analyzed, but did not reach the level of abundance as determined for M. bourgensis and D. tunisiensis. CONCLUSIONS Isolation of key anaerobic digestion microorganisms and their functional interpretation was achieved by application of elaborated cultivation techniques and subsequent genome analyses. New isolates and their genome information extend the repository covering anaerobic digestion community members.
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Affiliation(s)
- Irena Maus
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Andreas Bremges
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
- Faculty of Technology, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Brunswick, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunscheig, Inhoffenstraße 7, 38124 Brunswick, Germany
| | - Yvonne Stolze
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Sarah Hahnke
- Department Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Katharina G. Cibis
- Johannes Gutenberg-University, Institute of Microbiology and Wine Research, Johann-Joachim Becherweg 15, 55128 Mainz, Germany
| | - Daniela E. Koeck
- Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - Yong S. Kim
- Faculty Life Sciences/Research Center ‘Biomass Utilization Hamburg’, University of Applied Sciences Hamburg (HAW), Ulmenliet 20, 21033 Hamburg-Bergedorf, Germany
| | - Jana Kreubel
- Johannes Gutenberg-University, Institute of Microbiology and Wine Research, Johann-Joachim Becherweg 15, 55128 Mainz, Germany
| | - Julia Hassa
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Aaron Weimann
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Brunswick, Germany
| | - Sandra Off
- Faculty Life Sciences/Research Center ‘Biomass Utilization Hamburg’, University of Applied Sciences Hamburg (HAW), Ulmenliet 20, 21033 Hamburg-Bergedorf, Germany
| | - Robbin Stantscheff
- Johannes Gutenberg-University, Institute of Microbiology and Wine Research, Johann-Joachim Becherweg 15, 55128 Mainz, Germany
- Institut für Forensische Genetik GmbH, Im Derdel 8, 48168 Münster, Germany
| | - Vladimir V. Zverlov
- Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
- Institute of Molecular Genetics, Russian Academy of Science, Kurchatov Sq. 2, Moscow, 123182 Russia
| | - Wolfgang H. Schwarz
- Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - Helmut König
- Johannes Gutenberg-University, Institute of Microbiology and Wine Research, Johann-Joachim Becherweg 15, 55128 Mainz, Germany
| | - Wolfgang Liebl
- Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - Paul Scherer
- Faculty Life Sciences/Research Center ‘Biomass Utilization Hamburg’, University of Applied Sciences Hamburg (HAW), Ulmenliet 20, 21033 Hamburg-Bergedorf, Germany
| | - Alice C. McHardy
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Brunswick, Germany
| | - Alexander Sczyrba
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
- Faculty of Technology, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Michael Klocke
- Department Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Alfred Pühler
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
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Mahajan R, Nikitina A, Nozhevnikova A, Goel G. Microbial diversity in an anaerobic digester with biogeographical proximity to geothermally active region. ENVIRONMENTAL TECHNOLOGY 2016; 37:2694-2702. [PMID: 26934210 DOI: 10.1080/09593330.2016.1159733] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 02/19/2016] [Indexed: 06/05/2023]
Abstract
Anaerobic digestion of agricultural biomass or wastes can offer renewable energy, to help meet the rise in energy demands. The performance of an anaerobic digester considerably depends upon the complex interactions between bacterial and archaeal microbiome, which is greatly influenced by environmental factors. In the present study, we evaluate a microbial community of digester located at two different geographical locations, to understand whether the biogeographical proximity of a digester to a geothermally active region has any influence on microbial composition. The comparative microbial community profiling, highlights coexistence of specific bacterial and archaeal representatives (especially, Prosthecochloris sp., Conexibacter sp., Crenarchaeota isolate (Caldivirga sp.), Metallosphaera sp., Pyrobaculum sp. and Acidianus sp.) in a digester with close proximity to geothermally active region (Site I) and their absence in a digester located far-off from geothermally active region (Site II). A Sörensen's index of similarity of 83.33% and 66.66% for bacterial and archaeal community was observed in both the reactors, respectively.
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Affiliation(s)
- Rishi Mahajan
- a Department of Biotechnology and Bioinformatics , Jaypee University of Information Technology , Waknaghat, Solan, India
| | - Anna Nikitina
- b Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences , 33,bld. 2, Leninsky ave., Moscow , Russia , 119071
| | - Alla Nozhevnikova
- b Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences , 33,bld. 2, Leninsky ave., Moscow , Russia , 119071
| | - Gunjan Goel
- a Department of Biotechnology and Bioinformatics , Jaypee University of Information Technology , Waknaghat, Solan, India
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Gehring T, Niedermayr A, Berzio S, Immenhauser A, Wichern M, Lübken M. Determination of the fractions of syntrophically oxidized acetate in a mesophilic methanogenic reactor through an (12)C and (13)C isotope-based kinetic model. WATER RESEARCH 2016; 102:362-373. [PMID: 27390036 DOI: 10.1016/j.watres.2016.06.038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 06/15/2016] [Accepted: 06/16/2016] [Indexed: 06/06/2023]
Abstract
In order to accurately describe the carbon flow in anaerobic digestion processes, this work investigates the acetate degradation pathways through the use of stable carbon isotope analysis and a mathematical model. Batch assays using labeled (13)C acetate were employed to distinguish the acetate consumption through methanogenic Archaea and acetate-oxidizing Bacteria. Suspended and sessile biomass, with over 400 days of retention time, from a mesophilic (36.5 °C) upflow anaerobic filter was used as inocula in these assays. A three-process model for acetoclastic methanogenesis and syntrophic acetate oxidation (SAO) was developed to allow for a precise quantification of the SAO contribution. The model distinguishes carbon atoms in light and heavy isotopes, (12)C and (13)C, respectively, which permitted the simulation of the isotope ratios variation in addition to gas production, gas composition and acetate concentrations. The model indicated oxidized fractions of acetate between 7 and 18%. Due to the low free ammonia inhibition potential for the acetoclastic methanogens in these assays these findings point to the biomass retention times as a driven factor for the SAO pathway. The isotope-based kinetic model developed here also describes the δ(13)C variations in unlabeled assays accurately and has the potential to determine biological (13)C fractionation factors.
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Affiliation(s)
- Tito Gehring
- Institute of Urban Water Management and Environmental Engineering, Ruhr-Universität Bochum, Germany.
| | - Andrea Niedermayr
- Institute of Geology, Mineralogy and Geophysics, Ruhr-Universität Bochum, Germany.
| | - Stephan Berzio
- Institute of Urban Water Management and Environmental Engineering, Ruhr-Universität Bochum, Germany.
| | - Adrian Immenhauser
- Institute of Geology, Mineralogy and Geophysics, Ruhr-Universität Bochum, Germany.
| | - Marc Wichern
- Institute of Urban Water Management and Environmental Engineering, Ruhr-Universität Bochum, Germany.
| | - Manfred Lübken
- Institute of Urban Water Management and Environmental Engineering, Ruhr-Universität Bochum, Germany.
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Maus I, Koeck DE, Cibis KG, Hahnke S, Kim YS, Langer T, Kreubel J, Erhard M, Bremges A, Off S, Stolze Y, Jaenicke S, Goesmann A, Sczyrba A, Scherer P, König H, Schwarz WH, Zverlov VV, Liebl W, Pühler A, Schlüter A, Klocke M. Unraveling the microbiome of a thermophilic biogas plant by metagenome and metatranscriptome analysis complemented by characterization of bacterial and archaeal isolates. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:171. [PMID: 27525040 PMCID: PMC4982221 DOI: 10.1186/s13068-016-0581-3] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 07/27/2016] [Indexed: 05/24/2023]
Abstract
BACKGROUND One of the most promising technologies to sustainably produce energy and to mitigate greenhouse gas emissions from combustion of fossil energy carriers is the anaerobic digestion and biomethanation of organic raw material and waste towards biogas by highly diverse microbial consortia. In this context, the microbial systems ecology of thermophilic industrial-scale biogas plants is poorly understood. RESULTS The microbial community structure of an exemplary thermophilic biogas plant was analyzed by a comprehensive approach comprising the analysis of the microbial metagenome and metatranscriptome complemented by the cultivation of hydrolytic and acido-/acetogenic Bacteria as well as methanogenic Archaea. Analysis of metagenome-derived 16S rRNA gene sequences revealed that the bacterial genera Defluviitoga (5.5 %), Halocella (3.5 %), Clostridium sensu stricto (1.9 %), Clostridium cluster III (1.5 %), and Tepidimicrobium (0.7 %) were most abundant. Among the Archaea, Methanoculleus (2.8 %) and Methanothermobacter (0.8 %) were predominant. As revealed by a metatranscriptomic 16S rRNA analysis, Defluviitoga (9.2 %), Clostridium cluster III (4.8 %), and Tepidanaerobacter (1.1 %) as well as Methanoculleus (5.7 %) mainly contributed to these sequence tags indicating their metabolic activity, whereas Hallocella (1.8 %), Tepidimicrobium (0.5 %), and Methanothermobacter (<0.1 %) were transcriptionally less active. By applying 11 different cultivation strategies, 52 taxonomically different microbial isolates representing the classes Clostridia, Bacilli, Thermotogae, Methanomicrobia and Methanobacteria were obtained. Genome analyses of isolates support the finding that, besides Clostridium thermocellum and Clostridium stercorarium, Defluviitoga tunisiensis participated in the hydrolysis of hemicellulose producing ethanol, acetate, and H2/CO2. The latter three metabolites are substrates for hydrogentrophic and acetoclastic archaeal methanogenesis. CONCLUSIONS Obtained results showed that high abundance of microorganisms as deduced from metagenome analysis does not necessarily indicate high transcriptional or metabolic activity, and vice versa. Additionally, it appeared that the microbiome of the investigated thermophilic biogas plant comprised a huge number of up to now unknown and insufficiently characterized species.
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Affiliation(s)
- Irena Maus
- Center for Biotechnology (CeBiTec), Institute for Genome Research and Systems Biology, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany
| | - Daniela E. Koeck
- Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - Katharina G. Cibis
- Institute of Microbiology and Wine Research, Johannes Gutenberg-University, Becherweg 15, 55128 Mainz, Germany
| | - Sarah Hahnke
- Dept. Bioengineering, Leibniz-Institut für Agrartechnik Potsdam-Bornim e.V. (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Yong S. Kim
- Faculty Life Sciences/Research Center ‚‘Biomass Utilization Hamburg’, University of Applied Sciences Hamburg (HAW), Ulmenliet 20, 21033 Hamburg-Bergedorf, Germany
| | - Thomas Langer
- Dept. Bioengineering, Leibniz-Institut für Agrartechnik Potsdam-Bornim e.V. (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Jana Kreubel
- Institute of Microbiology and Wine Research, Johannes Gutenberg-University, Becherweg 15, 55128 Mainz, Germany
| | - Marcel Erhard
- RIPAC-LABOR GmbH, Am Mühlenberg 11, 14476 Potsdam-Golm, Germany
| | - Andreas Bremges
- Center for Biotechnology (CeBiTec), Institute for Genome Research and Systems Biology, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany
- Faculty of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Sandra Off
- Faculty Life Sciences/Research Center ‚‘Biomass Utilization Hamburg’, University of Applied Sciences Hamburg (HAW), Ulmenliet 20, 21033 Hamburg-Bergedorf, Germany
| | - Yvonne Stolze
- Center for Biotechnology (CeBiTec), Institute for Genome Research and Systems Biology, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany
| | - Sebastian Jaenicke
- Department of Bioinformatics and Systems Biology, Justus-Liebig University Gießen, Heinrich-Buff-Ring 58, 35392 Giessen, Germany
| | - Alexander Goesmann
- Department of Bioinformatics and Systems Biology, Justus-Liebig University Gießen, Heinrich-Buff-Ring 58, 35392 Giessen, Germany
| | - Alexander Sczyrba
- Center for Biotechnology (CeBiTec), Institute for Genome Research and Systems Biology, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany
- Faculty of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Paul Scherer
- Faculty Life Sciences/Research Center ‚‘Biomass Utilization Hamburg’, University of Applied Sciences Hamburg (HAW), Ulmenliet 20, 21033 Hamburg-Bergedorf, Germany
| | - Helmut König
- Institute of Microbiology and Wine Research, Johannes Gutenberg-University, Becherweg 15, 55128 Mainz, Germany
| | - Wolfgang H. Schwarz
- Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - Vladimir V. Zverlov
- Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - Wolfgang Liebl
- Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - Alfred Pühler
- Center for Biotechnology (CeBiTec), Institute for Genome Research and Systems Biology, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Institute for Genome Research and Systems Biology, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany
| | - Michael Klocke
- Dept. Bioengineering, Leibniz-Institut für Agrartechnik Potsdam-Bornim e.V. (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
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Heyer R, Benndorf D, Kohrs F, De Vrieze J, Boon N, Hoffmann M, Rapp E, Schlüter A, Sczyrba A, Reichl U. Proteotyping of biogas plant microbiomes separates biogas plants according to process temperature and reactor type. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:155. [PMID: 27462366 PMCID: PMC4960849 DOI: 10.1186/s13068-016-0572-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 07/12/2016] [Indexed: 05/23/2023]
Abstract
BACKGROUND Methane yield and biogas productivity of biogas plants (BGPs) depend on microbial community structure and function, substrate supply, and general biogas process parameters. So far, however, relatively little is known about correlations between microbial community function and process parameters. To close this knowledge gap, microbial communities of 40 samples from 35 different industrial biogas plants were evaluated by a metaproteomics approach in this study. RESULTS Liquid chromatography coupled to tandem mass spectrometry (Orbitrap Elite™ Hybrid Ion Trap-Orbitrap Mass Spectrometer) of all 40 samples as triplicate enabled the identification of 3138 different metaproteins belonging to 162 biological processes and 75 different taxonomic orders. The respective database searches were performed against UniProtKB/Swiss-Prot and seven metagenome databases. Subsequent clustering and principal component analysis of these data allowed for the identification of four main clusters associated with mesophile and thermophile process conditions, the use of upflow anaerobic sludge blanket reactors and BGP feeding with sewage sludge. Observations confirm a previous phylogenetic study of the same BGP samples that was based on 16S rRNA gene sequencing by De Vrieze et al. (Water Res 75:312-323, 2015). In particular, we identified similar microbial key players of biogas processes, namely Bacillales, Enterobacteriales, Bacteriodales, Clostridiales, Rhizobiales and Thermoanaerobacteriales as well as Methanobacteriales, Methanosarcinales and Methanococcales. For the elucidation of the main biomass degradation pathways, the most abundant 1 % of metaproteins was assigned to the KEGG map 1200 representing the central carbon metabolism. Additionally, the effect of the process parameters (i) temperature, (ii) organic loading rate (OLR), (iii) total ammonia nitrogen (TAN), and (iv) sludge retention time (SRT) on these pathways was investigated. For example, high TAN correlated with hydrogenotrophic methanogens and bacterial one-carbon metabolism, indicating syntrophic acetate oxidation. CONCLUSIONS This is the first large-scale metaproteome study of BGPs. Proteotyping of BGPs reveals general correlations between the microbial community structure and its function with process parameters. The monitoring of changes on the level of microbial key functions or even of the microbial community represents a well-directed tool for the identification of process problems and disturbances.Graphical abstractCorrelation between the different orders and process parameter, as well as principle component analysis of all investigated biogas plants based on the identified metaproteins.
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Affiliation(s)
- R. Heyer
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
- Bioprocess Engineering, Otto von Guericke University Magdeburg, Universitätsplatz 2, 39106 Magdeburg, Germany
| | - D. Benndorf
- Bioprocess Engineering, Otto von Guericke University Magdeburg, Universitätsplatz 2, 39106 Magdeburg, Germany
| | - F. Kohrs
- Bioprocess Engineering, Otto von Guericke University Magdeburg, Universitätsplatz 2, 39106 Magdeburg, Germany
| | - J. De Vrieze
- Laboratory of Microbial Technology and Ecology (LabMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - N. Boon
- Laboratory of Microbial Technology and Ecology (LabMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - M. Hoffmann
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
| | - E. Rapp
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
| | - Andreas Schlüter
- Center for Biotechnology, Genome Research of Industrial Microorganisms, Universität Bielefeld, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Alexander Sczyrba
- Center for Biotechnology, Computational Metagenomics, Universität Bielefeld, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - U. Reichl
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
- Bioprocess Engineering, Otto von Guericke University Magdeburg, Universitätsplatz 2, 39106 Magdeburg, Germany
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Leite AF, Janke L, Harms H, Richnow HH, Nikolausz M. Lessons learned from the microbial ecology resulting from different inoculation strategies for biogas production from waste products of the bioethanol/sugar industry. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:144. [PMID: 27429647 PMCID: PMC4947286 DOI: 10.1186/s13068-016-0548-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 06/08/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND During strategic planning of a biogas plant, the local availability of resources for start-up and operation should be taken into consideration for a cost-efficient process. Because most bioethanol/sugar industries in Brazil are located in remote areas, the use of fresh cattle manure from local farms could be a solution for the inoculation of the biogas process. This study investigated the diversity and dynamics of bacterial and archaeal communities and the performance of biogas reactors inoculated with manure and a mixed inoculum from different biogas reactors as for a controlled start-up until steady state. RESULTS Laboratory-scale biogas reactors were fed semi-continuously with sugarcane filter cake alone (mono-digestion) or together with bagasse (co-digestion). At the initial start-up, the reactors inoculated with the mixed inoculum displayed a less diverse taxonomic composition, but with higher presence of significant abundances compared to reactors inoculated with manure. However, in the final steady state, the communities of the differently inoculated reactors were very similarly characterized by predominance of the methanogenic genera Methanosarcina and Methanobacterium, the bacterial families Bacteroidaceae, Prevotellaceae and Porphyromonadaceae (phylum Bacteroidetes) and Synergistaceae (phylum Synergistetes). In the mono-digestion reactors, the methanogenic communities varied greater than in the co-digestion reactors independently of the inoculation strategy. CONCLUSION The microbial communities involved in the biogas production from waste products of the Brazilian bioethanol/sugar industry were relatively similar and stable at the reactor's steady phase independently of the inoculum source (manure or mixed inoculum). Therefore, the locally available manure can be used as inoculum for start-up of the biogas process, since it also contains the microbial resources needed. The strong fluctuation of methanogenic communities in mono-digestion reactors indicates higher risk of process instability than in co-digestion reactors.
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Affiliation(s)
- Athaydes Francisco Leite
- />Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Leandro Janke
- />Department of Biochemical Conversion, Deutsches Biomasseforschungszentrum gemeinnützige GmbH, Torgauerstrasse 116, 04347 Leipzig, Germany
| | - Hauke Harms
- />Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Hans-Hermann Richnow
- />Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Marcell Nikolausz
- />Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
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Tian G, Li Q, Dong M, Wu Y, Yang B, Zhang L, Li Y, Yin F, Zhao X, Wang Y, Xiao W, Cui X, Zhang W. Spatiotemporal dynamics of bacterial and archaeal communities in household biogas digesters from tropical and subtropical regions of Yunnan Province, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:11137-11148. [PMID: 26916266 DOI: 10.1007/s11356-016-6265-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 02/07/2016] [Indexed: 06/05/2023]
Abstract
A combination of 16S rRNA gene PCR-based techniques and the determination of abiotic factors were used to study community composition, richness, and evenness and the correlation between biotic and abiotic factors in 19 household biogas digesters in tropical and subtropical regions of Yunnan Province, China. The results revealed that both bacterial and archaeal community composition differed between regions and archaeal community composition was more affected by season than bacterial; regardless of sampling location, the dominant bacterial phyla included Chloroflexi, Bacteroidetes, Firmicutes, and Proteobacteria, and the most dominant archaeal phylum was Euryarchaeota; in digesters from both regions, Chloroflexi as the first or second most dominant bacteria accounted for 21.50-26.10 % of bacterial library sequences, and the phylum Crenarchaeota as the second most dominant archaea accounted for 17.65-19.77 % of archaeal library sequences; the species Methanosaeta concilii as the most dominant archaeal species accounted for 67.80-72.80 % of the sequences. This study found that most of the abundant microbial communities in 19 biogas digesters are similar, and this result will provide enlightenment for finding the universal nature in rural biogas digesters at tropical and subtropical regions in China.
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Affiliation(s)
- Guangliang Tian
- Yunnan Research Center of Biogas Technology and Engineering, Yunnan Normal University, Kunming, 650500, People's Republic of China
- Engineering and Research Center of Sustainable Development and Utilization of Bioenergy, Ministry of Education, Yunnan Normal University, Kunming, 650500, People's Republic of China
- Yunnan Key Laboratory of Rural Energy Engineering, Yunnan Normal University, Kunming, 650500, People's Republic of China
| | - Qiumin Li
- Yunnan Research Center of Biogas Technology and Engineering, Yunnan Normal University, Kunming, 650500, People's Republic of China
- Engineering and Research Center of Sustainable Development and Utilization of Bioenergy, Ministry of Education, Yunnan Normal University, Kunming, 650500, People's Republic of China
- Yunnan Key Laboratory of Rural Energy Engineering, Yunnan Normal University, Kunming, 650500, People's Republic of China
| | - Minghua Dong
- Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Yan Wu
- Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Bin Yang
- Yunnan Research Center of Biogas Technology and Engineering, Yunnan Normal University, Kunming, 650500, People's Republic of China
- Engineering and Research Center of Sustainable Development and Utilization of Bioenergy, Ministry of Education, Yunnan Normal University, Kunming, 650500, People's Republic of China
- Yunnan Key Laboratory of Rural Energy Engineering, Yunnan Normal University, Kunming, 650500, People's Republic of China
| | - Lijuan Zhang
- Yunnan Research Center of Biogas Technology and Engineering, Yunnan Normal University, Kunming, 650500, People's Republic of China
- Engineering and Research Center of Sustainable Development and Utilization of Bioenergy, Ministry of Education, Yunnan Normal University, Kunming, 650500, People's Republic of China
- Yunnan Key Laboratory of Rural Energy Engineering, Yunnan Normal University, Kunming, 650500, People's Republic of China
| | - Yingjuan Li
- Yunnan Research Center of Biogas Technology and Engineering, Yunnan Normal University, Kunming, 650500, People's Republic of China
- Engineering and Research Center of Sustainable Development and Utilization of Bioenergy, Ministry of Education, Yunnan Normal University, Kunming, 650500, People's Republic of China
- Yunnan Key Laboratory of Rural Energy Engineering, Yunnan Normal University, Kunming, 650500, People's Republic of China
| | - Fang Yin
- Yunnan Research Center of Biogas Technology and Engineering, Yunnan Normal University, Kunming, 650500, People's Republic of China
- Engineering and Research Center of Sustainable Development and Utilization of Bioenergy, Ministry of Education, Yunnan Normal University, Kunming, 650500, People's Republic of China
- Yunnan Key Laboratory of Rural Energy Engineering, Yunnan Normal University, Kunming, 650500, People's Republic of China
| | - Xingling Zhao
- Yunnan Research Center of Biogas Technology and Engineering, Yunnan Normal University, Kunming, 650500, People's Republic of China
- Engineering and Research Center of Sustainable Development and Utilization of Bioenergy, Ministry of Education, Yunnan Normal University, Kunming, 650500, People's Republic of China
- Yunnan Key Laboratory of Rural Energy Engineering, Yunnan Normal University, Kunming, 650500, People's Republic of China
| | - Yongxia Wang
- Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Wei Xiao
- Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Xiaolong Cui
- Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China.
| | - Wudi Zhang
- Yunnan Research Center of Biogas Technology and Engineering, Yunnan Normal University, Kunming, 650500, People's Republic of China.
- Engineering and Research Center of Sustainable Development and Utilization of Bioenergy, Ministry of Education, Yunnan Normal University, Kunming, 650500, People's Republic of China.
- Yunnan Key Laboratory of Rural Energy Engineering, Yunnan Normal University, Kunming, 650500, People's Republic of China.
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Diversity of methane-cycling archaea in hydrothermal sediment investigated by general and group-specific PCR primers. Appl Environ Microbiol 2016; 81:1426-41. [PMID: 25527539 DOI: 10.1128/aem.03588-14] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The zonation of anaerobic methane-cycling Archaea in hydrothermal sediment of Guaymas Basin was studied by general primerpairs (mcrI, ME1/ME2, mcrIRD) targeting the alpha subunit of methyl coenzyme M reductase gene (mcrA) and by new group specific mcrA and 16S rRNA gene primer pairs. The mcrIRD primer pair outperformed the other general mcrA primer pairs indetection sensitivity and phylogenetic coverage. Methanotrophic ANME-1 Archaea were the only group detected with group specific primers only. The detection of 14 mcrA lineages surpasses the diversity previously found in this location. Most phylotypes have high sequence similarities to hydrogenotrophs, methylotrophs, and anaerobic methanotrophs previously detected at Guaymas Basin or at hydrothermal vents, cold seeps, and oil reservoirs worldwide. Additionally, five mcrA phylotypes belonging to newly defined lineages are detected. Two of these belong to deeply branching new orders, while the others are new species or genera of Methanopyraceae and Methermicoccaceae. Downcore diversity decreases from all groups detected in the upper 6 cm(2 to 40 °C, sulfate measurable to 4 cm) to only two groups below 6 cm (>40 °C). Despite the presence of hyperthermophilic genera (Methanopyrus, Methanocaldococcus) in cooler surface strata, no genes were detected below 10 cm (>60 °C). While mcrAbased and 16S rRNA gene-based community compositions are generally congruent, the deeply branching mcrA cannot be assigned to specific 16S rRNA gene lineages. Our study indicates that even among well-studied metabolic groups and in previously characterized model environments, major evolutionary branches are overlooked. Detecting these groups by improved molecular biological methods is a crucial first step toward understanding their roles in nature.
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Güllert S, Fischer MA, Turaev D, Noebauer B, Ilmberger N, Wemheuer B, Alawi M, Rattei T, Daniel R, Schmitz RA, Grundhoff A, Streit WR. Deep metagenome and metatranscriptome analyses of microbial communities affiliated with an industrial biogas fermenter, a cow rumen, and elephant feces reveal major differences in carbohydrate hydrolysis strategies. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:121. [PMID: 27279900 PMCID: PMC4897800 DOI: 10.1186/s13068-016-0534-x] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 05/26/2016] [Indexed: 05/13/2023]
Abstract
BACKGROUND The diverse microbial communities in agricultural biogas fermenters are assumed to be well adapted for the anaerobic transformation of plant biomass to methane. Compared to natural systems, biogas reactors are limited in their hydrolytic potential. The reasons for this are not understood. RESULTS In this paper, we show that a typical industrial biogas reactor fed with maize silage, cow manure, and chicken manure has relatively lower hydrolysis rates compared to feces samples from herbivores. We provide evidence that on average, 2.5 genes encoding cellulolytic GHs/Mbp were identified in the biogas fermenter compared to 3.8 in the elephant feces and 3.2 in the cow rumen data sets. The ratio of genes coding for cellulolytic GH enzymes affiliated with the Firmicutes versus the Bacteroidetes was 2.8:1 in the biogas fermenter compared to 1:1 in the elephant feces and 1.4:1 in the cow rumen sample. Furthermore, RNA-Seq data indicated that highly transcribed cellulases in the biogas fermenter were four times more often affiliated with the Firmicutes compared to the Bacteroidetes, while an equal distribution of these enzymes was observed in the elephant feces sample. CONCLUSIONS Our data indicate that a relatively lower abundance of bacteria affiliated with the phylum of Bacteroidetes and, to some extent, Fibrobacteres is associated with a decreased richness of predicted lignocellulolytic enzymes in biogas fermenters. This difference can be attributed to a partial lack of genes coding for cellulolytic GH enzymes derived from bacteria which are affiliated with the Fibrobacteres and, especially, the Bacteroidetes. The partial deficiency of these genes implies a potentially important limitation in the biogas fermenter with regard to the initial hydrolysis of biomass. Based on these findings, we speculate that increasing the members of Bacteroidetes and Fibrobacteres in biogas fermenters will most likely result in an increased hydrolytic performance.
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Affiliation(s)
- Simon Güllert
- />Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, University of Hamburg, Ohnhorststr. 18, 22609 Hamburg, Germany
| | - Martin A. Fischer
- />Institute for General Microbiology, Christian Albrecht University Kiel, Kiel, Germany
| | - Dmitrij Turaev
- />CUBE-Division for Computational Systems Biology, Dept. of Microbiology and Ecosystem Science, University of Vienna, Althanstr. 14, Vienna, Austria
| | - Britta Noebauer
- />CUBE-Division for Computational Systems Biology, Dept. of Microbiology and Ecosystem Science, University of Vienna, Althanstr. 14, Vienna, Austria
| | - Nele Ilmberger
- />Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, University of Hamburg, Ohnhorststr. 18, 22609 Hamburg, Germany
| | - Bernd Wemheuer
- />Institute of Microbiology and Genetics, Georg-August-University Göttingen, Grisebachstr. 8, Göttingen, Germany
| | - Malik Alawi
- />Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Martinistr. 52, Hamburg, Germany
- />Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistr. 52, Hamburg, Germany
| | - Thomas Rattei
- />CUBE-Division for Computational Systems Biology, Dept. of Microbiology and Ecosystem Science, University of Vienna, Althanstr. 14, Vienna, Austria
| | - Rolf Daniel
- />Institute of Microbiology and Genetics, Georg-August-University Göttingen, Grisebachstr. 8, Göttingen, Germany
| | - Ruth A. Schmitz
- />Institute for General Microbiology, Christian Albrecht University Kiel, Kiel, Germany
| | - Adam Grundhoff
- />Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistr. 52, Hamburg, Germany
| | - Wolfgang R. Streit
- />Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, University of Hamburg, Ohnhorststr. 18, 22609 Hamburg, Germany
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43
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Jiménez J, Theuerl S, Bergmann I, Klocke M, Guerra G, Romero-Romero O. Prokaryote community dynamics in anaerobic co-digestion of swine manure, rice straw and industrial clay residuals. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2016; 74:824-835. [PMID: 27533857 DOI: 10.2166/wst.2016.170] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The aim of this study was to analyze the effect of the addition of rice straw and clay residuals on the prokaryote methane-producing community structure in a semi-continuously stirred tank reactor fed with swine manure. Molecular techniques, including terminal restriction fragment length polymorphism and a comparative nucleotide sequence analyses of the prokaryotic 16S rRNA genes, were performed. The results showed a positive effect of clay addition on methane yield during the co-digestion of swine manure and rice straw. At the digestion of swine manure, the bacterial phylum Firmicutes and the archaeal family Methanosarcinaceae, particularly Methanosarcina species, were predominant. During the co-digestion of swine manure and rice straw the microbial community changed, and with the addition of clay residual, the phylum Bacteroidetes predominated. The new nutritional conditions resulted in a shift in the archaeal family Methanosarcinaceae community as acetoclastic Methanosaeta species became dominant.
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Affiliation(s)
- Janet Jiménez
- Universidad de Sancti Spíritus, Ave. de los Mártires, No. 360, Sancti Spíritus, Sancti Spíritus CP 60100, Cuba E-mail:
| | - Susanne Theuerl
- Department Bioengineering, Leibniz Institute for Agricultural Engineering Potsdam-Bornim (ATB), Max-Eyth-Allee 100, Potsdam D-14469, Germany
| | - Ingo Bergmann
- Department Bioengineering, Leibniz Institute for Agricultural Engineering Potsdam-Bornim (ATB), Max-Eyth-Allee 100, Potsdam D-14469, Germany
| | - Michael Klocke
- Department Bioengineering, Leibniz Institute for Agricultural Engineering Potsdam-Bornim (ATB), Max-Eyth-Allee 100, Potsdam D-14469, Germany
| | - Gilda Guerra
- Facultad de Biología. Universidad de La Habana, Calle 25 e/ I y J, Vedado, La Habana CP. 10400, Cuba
| | - Osvaldo Romero-Romero
- Universidad de Sancti Spíritus, Ave. de los Mártires, No. 360, Sancti Spíritus, Sancti Spíritus CP 60100, Cuba E-mail:
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44
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Polag D, May T, Müller L, König H, Jacobi F, Laukenmann S, Keppler F. Online monitoring of stable carbon isotopes of methane in anaerobic digestion as a new tool for early warning of process instability. BIORESOURCE TECHNOLOGY 2015; 197:161-70. [PMID: 26335284 DOI: 10.1016/j.biortech.2015.08.058] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Revised: 08/08/2015] [Accepted: 08/12/2015] [Indexed: 05/16/2023]
Abstract
Effective control of anaerobic digestion in biogas plants requires the monitoring of process sensitive and rapid response parameters in order to ensure efficient biogas production and to prevent potential process failure. In this study, stable carbon isotopes of methane (δ(13)CCH4) produced in a full-scale continuous stirred-tank reactor were investigated as a potential new monitoring tool for this purpose. Over a six-month period with variable organic loading rates, δ(13)CCH4-values were measured online by a portable high-precision laser absorption spectrometer. During a stress period of consecutive high organic loading, δ(13)CCH4-values early indicated process changes in contrast to traditionally monitored parameters where a change was observed some five to ten days later. Comparison of the stable isotope values with data from microbial analyses showed a distinct relationship between the quantity of potentially acetoclastic methanogens and δ(13)CCH4-values. This finding indicates an association between dominant methanogenic pathways and carbon isotope values.
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Affiliation(s)
- D Polag
- Institute of Earth Sciences, Im Neuenheimer Feld 236, D-69120 Heidelberg, Germany
| | - T May
- Institute of Microbiology and Wine Research, Johann-Joachim-Becherweg 15, D-55128 Mainz, Germany
| | - L Müller
- Deutsches Biomasseforschungszentrum, Torgauer St. 116, D-04347 Leipzig, Germany
| | - H König
- Institute of Microbiology and Wine Research, Johann-Joachim-Becherweg 15, D-55128 Mainz, Germany
| | - F Jacobi
- Deutsches Biomasseforschungszentrum, Torgauer St. 116, D-04347 Leipzig, Germany
| | - S Laukenmann
- Institute of Earth Sciences, Im Neuenheimer Feld 236, D-69120 Heidelberg, Germany
| | - F Keppler
- Institute of Earth Sciences, Im Neuenheimer Feld 236, D-69120 Heidelberg, Germany
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45
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Changing Feeding Regimes To Demonstrate Flexible Biogas Production: Effects on Process Performance, Microbial Community Structure, and Methanogenesis Pathways. Appl Environ Microbiol 2015; 82:438-49. [PMID: 26497462 DOI: 10.1128/aem.02320-15] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 10/19/2015] [Indexed: 11/20/2022] Open
Abstract
Flexible biogas production that adapts biogas output to energy demand can be regulated by changing feeding regimes. In this study, the effect of changes in feeding intervals on process performance, microbial community structure, and the methanogenesis pathway was investigated. Three different feeding regimes (once daily, every second day, and every 2 h) at the same organic loading rate were studied in continuously stirred tank reactors treating distiller's dried grains with solubles. A larger amount of biogas was produced after feeding in the reactors fed less frequently (once per day and every second day), whereas the amount remained constant in the reactor fed more frequently (every 2 h), indicating the suitability of the former for the flexible production of biogas. Compared to the conventional more frequent feeding regimes, a methane yield that was up to 14% higher and an improved stability of the process against organic overloading were achieved by employing less frequent feeding regimes. The community structures of bacteria and methanogenic archaea were monitored by terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA and mcrA genes, respectively. The results showed that the composition of the bacterial community varied under the different feeding regimes, and the observed T-RFLP patterns were best explained by the differences in the total ammonia nitrogen concentrations, H2 levels, and pH values. However, the methanogenic community remained stable under all feeding regimes, with the dominance of the Methanosarcina genus followed by that of the Methanobacterium genus. Stable isotope analysis showed that the average amount of methane produced during each feeding event by acetoclastic and hydrogenotrophic methanogenesis was not influenced by the three different feeding regimes.
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46
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Heyer R, Kohrs F, Reichl U, Benndorf D. Metaproteomics of complex microbial communities in biogas plants. Microb Biotechnol 2015; 8:749-63. [PMID: 25874383 PMCID: PMC4554464 DOI: 10.1111/1751-7915.12276] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 02/05/2015] [Accepted: 02/11/2015] [Indexed: 11/29/2022] Open
Abstract
Production of biogas from agricultural biomass or organic wastes is an important source of renewable energy. Although thousands of biogas plants (BGPs) are operating in Germany, there is still a significant potential to improve yields, e.g. from fibrous substrates. In addition, process stability should be optimized. Besides evaluating technical measures, improving our understanding of microbial communities involved into the biogas process is considered as key issue to achieve both goals. Microscopic and genetic approaches to analyse community composition provide valuable experimental data, but fail to detect presence of enzymes and overall metabolic activity of microbial communities. Therefore, metaproteomics can significantly contribute to elucidate critical steps in the conversion of biomass to methane as it delivers combined functional and phylogenetic data. Although metaproteomics analyses are challenged by sample impurities, sample complexity and redundant protein identification, and are still limited by the availability of genome sequences, recent studies have shown promising results. In the following, the workflow and potential pitfalls for metaproteomics of samples from full-scale BGP are discussed. In addition, the value of metaproteomics to contribute to the further advancement of microbial ecology is evaluated. Finally, synergistic effects expected when metaproteomics is combined with advanced imaging techniques, metagenomics, metatranscriptomics and metabolomics are addressed.
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Affiliation(s)
- Robert Heyer
- Bioprocess Engineering, Otto von Guericke University MagdeburgUniversitätsplatz 2, Magdeburg, 39106, Germany
- Max Planck Institute for Dynamics of Complex Technical SystemsSandtorstr. 1, Magdeburg, 39106, Germany
| | - Fabian Kohrs
- Bioprocess Engineering, Otto von Guericke University MagdeburgUniversitätsplatz 2, Magdeburg, 39106, Germany
- Max Planck Institute for Dynamics of Complex Technical SystemsSandtorstr. 1, Magdeburg, 39106, Germany
| | - Udo Reichl
- Bioprocess Engineering, Otto von Guericke University MagdeburgUniversitätsplatz 2, Magdeburg, 39106, Germany
- Max Planck Institute for Dynamics of Complex Technical SystemsSandtorstr. 1, Magdeburg, 39106, Germany
| | - Dirk Benndorf
- Bioprocess Engineering, Otto von Guericke University MagdeburgUniversitätsplatz 2, Magdeburg, 39106, Germany
- Max Planck Institute for Dynamics of Complex Technical SystemsSandtorstr. 1, Magdeburg, 39106, Germany
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47
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Goux X, Calusinska M, Lemaigre S, Marynowska M, Klocke M, Udelhoven T, Benizri E, Delfosse P. Microbial community dynamics in replicate anaerobic digesters exposed sequentially to increasing organic loading rate, acidosis, and process recovery. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:122. [PMID: 26288654 PMCID: PMC4539856 DOI: 10.1186/s13068-015-0309-9] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 08/07/2015] [Indexed: 05/18/2023]
Abstract
BACKGROUND Volatile fatty acid intoxication (acidosis), a common process failure recorded in anaerobic reactors, leads to drastic losses in methane production. Unfortunately, little is known about the microbial mechanisms underlining acidosis and the potential to recover the process. In this study, triplicate mesophilic anaerobic reactors of 100 L were exposed to acidosis resulting from an excessive feeding with sugar beet pulp and were compared to a steady-state reactor. RESULTS Stable operational conditions at the beginning of the experiment initially led to similar microbial populations in the four reactors, as revealed by 16S rRNA gene T-RFLP and high-throughput amplicon sequencing. Bacteroidetes and Firmicutes were the two dominant phyla, and although they were represented by a high number of operational taxonomic units, only a few were dominant. Once the environment became deterministic (selective pressure from an increased substrate feeding), microbial populations started to diverge between the overfed reactors. Interestingly, most of bacteria and archaea showed redundant functional adaptation to the changing environmental conditions. However, the dominant Bacteroidales were resistant to high volatile fatty acids content and low pH. The severe acidosis did not eradicate archaea and a clear shift in archaeal populations from acetotrophic to hydrogenotrophic methanogenesis occurred in the overfed reactors. After 11 days of severe acidosis (pH 5.2 ± 0.4), the process was quickly recovered (restoration of the biogas production with methane content above 50 %) in the overfed reactors, by adjusting the pH to around 7 using NaOH and NaHCO3. CONCLUSIONS In this study we show that once the replicate reactors are confronted with sub-optimal conditions, their microbial populations start to evolve differentially. Furthermore the alterations of commonly used microbial parameters to monitor the process, such as richness, evenness and diversity indices were unsuccessful to predict the process failure. At the same time, we tentatively propose the replacement of the dominant Methanosaeta sp. in this case by Methanoculleus sp., to be a potential warning indicator of acidosis.
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Affiliation(s)
- Xavier Goux
- />Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, 4422 Belvaux, Luxembourg
- />Laboratoire Sols et Environnement, UMR 1120, Université de Lorraine, 2 avenue de la Forêt de Haye, TSA 40602, 54518 Vandœuvre-lès-Nancy, France
- />Laboratoire Sols et Environnement, UMR 1120, INRA, 2 avenue de la Forêt de Haye, TSA 40602, 54518 Vandœuvre-lès-Nancy, France
| | - Magdalena Calusinska
- />Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, 4422 Belvaux, Luxembourg
| | - Sébastien Lemaigre
- />Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, 4422 Belvaux, Luxembourg
| | - Martyna Marynowska
- />Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, 4422 Belvaux, Luxembourg
| | - Michael Klocke
- />Department Bioengineering, Leibniz Institute for Agricultural Engineering Potsdam-Bornim, Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Thomas Udelhoven
- />Fachbereich VI- Raum- und Umweltwissenschaften, Umweltfernerkundung & Geoinformatik, Universität Trier, 54286 Trier, Germany
| | - Emile Benizri
- />Laboratoire Sols et Environnement, UMR 1120, Université de Lorraine, 2 avenue de la Forêt de Haye, TSA 40602, 54518 Vandœuvre-lès-Nancy, France
- />Laboratoire Sols et Environnement, UMR 1120, INRA, 2 avenue de la Forêt de Haye, TSA 40602, 54518 Vandœuvre-lès-Nancy, France
| | - Philippe Delfosse
- />Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, 4422 Belvaux, Luxembourg
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48
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Yadav AN, Sharma D, Gulati S, Singh S, Dey R, Pal KK, Kaushik R, Saxena AK. Haloarchaea Endowed with Phosphorus Solubilization Attribute Implicated in Phosphorus Cycle. Sci Rep 2015. [PMID: 26216440 PMCID: PMC4516986 DOI: 10.1038/srep12293] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Archaea are unique microorganisms that are present in ecological niches of high temperature, pH and salinity. A total of 157 archaea were obtained from thirteen sediment, water and rhizospheric soil samples collected from Rann of Kutch, Gujarat, India. With an aim to screen phosphate solubilizing archaea, a new medium was designed as Haloarchaea P Solubilization (HPS) medium. The medium supported the growth and P solubilization activity of archaea. Employing the HPS medium, twenty isolates showed the P-solubilization. Phosphate solubilizing archaea were identified as seventeen distinct species of eleven genera namely Haloarcula, Halobacterium, Halococcus, Haloferax, Halolamina, Halosarcina, Halostagnicola, Haloterrigena, Natrialba, Natrinema and Natronoarchaeum. Natrinema sp. strain IARI-WRAB2 was identified as the most efficient P-solubilizer (134.61 mg/L) followed by Halococcus hamelinensis strain IARI-SNS2 (112.56 mg/L). HPLC analysis detected seven different kinds of organic acids, namely: gluconic acid, citric acid, formic acid, fumaric acid succinic acid, propionic acid and tartaric acid from the cultures of these isolates. These phosphate solubilizing halophilic archaea may play a role in P nutrition to vegetation growing in these hypersaline soils. This is the first report for these haloarchaea to solubilize considerable amount of P by production of organic acids and lowering of pH.
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Affiliation(s)
- Ajar Nath Yadav
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi 110012, India
| | - Divya Sharma
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi 110012, India
| | - Sneha Gulati
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi 110012, India
| | - Surender Singh
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi 110012, India
| | - Rinku Dey
- Directorate of Groundnut Research, Junagadh 362001, India
| | | | - Rajeev Kaushik
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi 110012, India
| | - Anil Kumar Saxena
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi 110012, India
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49
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Design and application of a synthetic DNA standard for real-time PCR analysis of microbial communities in a biogas digester. Appl Microbiol Biotechnol 2015; 99:6855-63. [DOI: 10.1007/s00253-015-6721-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 05/19/2015] [Accepted: 05/23/2015] [Indexed: 11/25/2022]
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50
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Gehring T, Klang J, Niedermayr A, Berzio S, Immenhauser A, Klocke M, Wichern M, Lübken M. Determination of methanogenic pathways through carbon isotope (δ13C) analysis for the two-stage anaerobic digestion of high-solids substrates. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:4705-14. [PMID: 25741999 DOI: 10.1021/es505665z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
This study used carbon isotope (δ(13)C)-based calculations to quantify the specific methanogenic pathways in a two-stage experimental biogas plant composed of three thermophilic leach bed reactors (51-56 °C) followed by a mesophilic (36.5 °C) anaerobic filter. Despite the continuous dominance of the acetoclastic Methanosaeta in the anaerobic filter, the methane (CH4) fraction derived from carbon dioxide reduction (CO2), fmc, varied significantly over the investigation period of 200 days. At organic loading rates (OLRs) below 6.0 gCOD L(-1) d(-1), the average fmc value was 33%, whereas at higher OLRs, with a maximum level of 17.0 gCOD L(-1) d(-1), the fmc values reached 47%. The experiments allowed for a clear differentiation of the isotope fractionation related to the formation and consumption of acetate in both stages of the plant. Our data indicate constant carbon isotope fractionation for acetate formation at different OLRs within the thermophilic leach bed reactors as well as a negligible contribution of homoacetogenesis. These results present the first quantification of methanogenic pathway (fmc values) dynamics for a continually operated mesophilic bioreactor and highlight the enormous potential of δ(13)C analysis for a more comprehensive understanding of the anaerobic degradation processes in CH4-producing biogas plants.
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Affiliation(s)
- Tito Gehring
- †Institute of Urban Water Management and Environmental Engineering, Ruhr-Universität Bochum, Universitätsstrasse 150, Bochum 44801, Germany
| | - Johanna Klang
- ‡Leibniz Institute for Agricultural Engineering Potsdam-Bornim (ATB), Max-Eyth-Allee 100, Potsdam 14469, Germany
| | - Andrea Niedermayr
- §Institute of Geology, Mineralogy and Geophysics, Ruhr-Universität Bochum, Universitätsstrasse 150, Bochum 44801, Germany
| | - Stephan Berzio
- †Institute of Urban Water Management and Environmental Engineering, Ruhr-Universität Bochum, Universitätsstrasse 150, Bochum 44801, Germany
| | - Adrian Immenhauser
- §Institute of Geology, Mineralogy and Geophysics, Ruhr-Universität Bochum, Universitätsstrasse 150, Bochum 44801, Germany
| | - Michael Klocke
- ‡Leibniz Institute for Agricultural Engineering Potsdam-Bornim (ATB), Max-Eyth-Allee 100, Potsdam 14469, Germany
| | - Marc Wichern
- †Institute of Urban Water Management and Environmental Engineering, Ruhr-Universität Bochum, Universitätsstrasse 150, Bochum 44801, Germany
| | - Manfred Lübken
- †Institute of Urban Water Management and Environmental Engineering, Ruhr-Universität Bochum, Universitätsstrasse 150, Bochum 44801, Germany
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