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Metagenomic Analysis of Bacterial Community Structure and Dynamics of a Digestate and a More Stabilized Digestate-Derived Compost from Agricultural Waste. Processes (Basel) 2022. [DOI: 10.3390/pr10020379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Recycling of different products and waste materials plays a crucial role in circular economy, where the anaerobic digestion (AD) constitutes an important pillar since it reuses nutrients in the form of organic fertilizers. Knowledge about the digestate and compost microbial community structure and its variations over time is important. The aim of the current study was to investigate the microbiome of a slurry cow digestate produced on a farm (ADG) and of a more stabilized digestate-derived compost (DdC) in order to ascertain their potential uses as organic amendments in agriculture. The results from this study, based on a partial fragment of 16S bacterial rRNA NGS sequencing, showed that there is a greater microbial diversity in the DdC originated from agricultural waste compared to the ADG. Overall, the existence of a higher microbial diversity in the DdC was confirmed by an elevated number (1115) of OTUs identified, compared with the ADG (494 OTUs identified). In the DdC, 74 bacterial orders and 125 families were identified, whereas 27 bacterial orders and 54 families were identified in the ADG. Shannon diversity and Chao1 richness indexes were higher in DdC samples compared to ADG ones (Shannon: 3.014 and 1.573, Chao1: 68 and 24.75; p < 0.001 in both cases). A possible association between the microbiome composition at different stages of composting process and the role that these microorganisms may have on the quality of the compost-like substrate and its future uses is also discussed.
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Hashemi S, Hashemi SE, Lien KM, Lamb JJ. Molecular Microbial Community Analysis as an Analysis Tool for Optimal Biogas Production. Microorganisms 2021; 9:microorganisms9061162. [PMID: 34071282 PMCID: PMC8226781 DOI: 10.3390/microorganisms9061162] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/17/2021] [Accepted: 05/26/2021] [Indexed: 11/16/2022] Open
Abstract
The microbial diversity in anaerobic digestion (AD) is important because it affects process robustness. High-throughput sequencing offers high-resolution data regarding the microbial diversity and robustness of biological systems including AD; however, to understand the dynamics of microbial processes, knowing the microbial diversity is not adequate alone. Advanced meta-omic techniques have been established to determine the activity and interactions among organisms in biological processes like AD. Results of these methods can be used to identify biomarkers for AD states. This can aid a better understanding of system dynamics and be applied to producing comprehensive models for AD. The paper provides valuable knowledge regarding the possibility of integration of molecular methods in AD. Although meta-genomic methods are not suitable for on-line use due to long operating time and high costs, they provide extensive insight into the microbial phylogeny in AD. Meta-proteomics can also be explored in the demonstration projects for failure prediction. However, for these methods to be fully realised in AD, a biomarker database needs to be developed.
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Affiliation(s)
- Seyedbehnam Hashemi
- Department of Energy and Process Engineering & Enersense, Norwegian University of Science and Technology (NTNU), 7034 Trondheim, Norway; (S.H.); (S.E.H.); (K.M.L.)
| | - Sayed Ebrahim Hashemi
- Department of Energy and Process Engineering & Enersense, Norwegian University of Science and Technology (NTNU), 7034 Trondheim, Norway; (S.H.); (S.E.H.); (K.M.L.)
| | - Kristian M. Lien
- Department of Energy and Process Engineering & Enersense, Norwegian University of Science and Technology (NTNU), 7034 Trondheim, Norway; (S.H.); (S.E.H.); (K.M.L.)
| | - Jacob J. Lamb
- Department of Energy and Process Engineering & Enersense, Norwegian University of Science and Technology (NTNU), 7034 Trondheim, Norway; (S.H.); (S.E.H.); (K.M.L.)
- Department of Electronic Systems, Norwegian University of Science and Technology (NTNU), 7034 Trondheim, Norway
- Correspondence:
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Vendruscolo ECG, Mesa D, Rissi DV, Meyer BH, de Oliveira Pedrosa F, de Souza EM, Cruz LM. Microbial communities network analysis of anaerobic reactors fed with bovine and swine slurry. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 742:140314. [PMID: 33167293 DOI: 10.1016/j.scitotenv.2020.140314] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 05/18/2020] [Accepted: 06/15/2020] [Indexed: 05/28/2023]
Abstract
Anaerobic digestion can produce biogas as an eco-friendly energy source, driven by a microbial community-dependent process and, as such, suffer influences from many biotic and abiotic factors. Understanding the players and how they interact, the mechanisms involved, what the factors are, and how they influence the biogas process and production is an important way to better control it and make it more efficient. Metagenomic approach is a powerful tool to assess microbial diversity and further, allow correlating changes in microbial communities with multiple factors in virtually all environments. In the present study, we used metagenomic approach to assess microbial community structure changes in two biodigesters, differing in their biogas production capacity, architecture, and feed. A total of 1,440,096 reads of the 16S rRNA gene V4 region were obtained and analyzed. The main bacterial phyla were Firmicutes and Bacteroidetes in both biodigesters, but the biodiversity was greater in the Upflow Anaerobic Sludge Blanket (UASB) reactor fed with bovine manure than in the Continuous Stirred Tank Reactor (CSTR) fed with swine manure, which also correlated with an increase in biogas or methane production. Microbial community structure associated with biodigesters changed seasonally and depended on animal growth stage. Random forest algorithm analysis revealed key microbial taxa for each biodigester. Candidatus Cloacomonas, Methanospirillum, and Methanosphaera were the marker taxa for UASB and the archaea groups Methanobrevibacter and Candidatus Methanoplasma were the marker taxa for CSTR. A high abundance of Candidatus Methanoplasma and Marinimicrobia SAR406 clade suggested lower increments in methane production. Network analysis pointed to negative and positive associations and specific key groups, essential in maintaining the anaerobic digestion (AD) process, as being uncultured Parcubacteria bacteria, Candidatus Cloacomonas, and Candidatus Methanoplasma groups, whose functions in AD require investigation.
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Affiliation(s)
| | - Dany Mesa
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Av. Coronel Francisco H. dos Santos,100, CP 19031, Centro Politécnico, Curitiba, PR, 81531-980, Brazil
| | - Daniel Vasconcelos Rissi
- Sector of Professional and Technological Education, Federal University of Paraná, R. Dr. Alcides Vieira Arcoverde, 1225 - Jardim das Américas, Curitiba, PR, 81520-260, Brazil
| | - Bruno Henrique Meyer
- Department of Informatics, Federal University of Paraná, R. Evaristo F. Ferreira da Costa, 383-391 - Jardim das Américas, Curitiba, PR, 82590-300, Brazil
| | - Fábio de Oliveira Pedrosa
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Av. Coronel Francisco H. dos Santos,100, CP 19031, Centro Politécnico, Curitiba, PR, 81531-980, Brazil
| | - Emanuel Maltempi de Souza
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Av. Coronel Francisco H. dos Santos,100, CP 19031, Centro Politécnico, Curitiba, PR, 81531-980, Brazil
| | - Leonardo Magalhães Cruz
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Av. Coronel Francisco H. dos Santos,100, CP 19031, Centro Politécnico, Curitiba, PR, 81531-980, Brazil; Department of Informatics, Federal University of Paraná, R. Evaristo F. Ferreira da Costa, 383-391 - Jardim das Américas, Curitiba, PR, 82590-300, Brazil
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Impact of the inoculum composition on the structure of the total and active community and its performance in identically operated anaerobic reactors. Appl Microbiol Biotechnol 2019; 103:9191-9203. [DOI: 10.1007/s00253-019-10041-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 05/16/2019] [Accepted: 07/23/2019] [Indexed: 10/26/2022]
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5
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Akyol Ç, Ince O, Bozan M, Ozbayram EG, Ince B. Fungal bioaugmentation of anaerobic digesters fed with lignocellulosic biomass: What to expect from anaerobic fungus Orpinomyces sp. BIORESOURCE TECHNOLOGY 2019; 277:1-10. [PMID: 30654102 DOI: 10.1016/j.biortech.2019.01.024] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 01/06/2019] [Accepted: 01/07/2019] [Indexed: 06/09/2023]
Abstract
Energy-efficient biogas reactors are often designed and operated mimicking natural microbial ecosystems such as the digestive tracts of ruminants. Anaerobic fungi play a crucial role in the degradation of lignocellulose-rich fiber thanks to their high cellulolytic activity. Fungal bioaugmentation is therefore at the heart of our understanding of enhancing anaerobic digestion (AD). The efficiency of bioaugmentation with anaerobic fungus Orpinomyces sp. was evaluated in lignocellulose-based AD configurations. Fungal bioaugmentation increased the methane yield by 15-33% during anaerobic co-digestion of cow manure and selected cereal crops/straws. Harvesting stage of the crops was a decisive parameter to influence methane production together with fungal bioaugmentation. A more efficient fermentation process in the bioaugmented digesters was distinguished by relatively-higher abundance of Synergistetes, which was mainly represented by the genus Anaerobaculum. On the contrary, the composition of the methanogenic archaea did not change, and the majority of methanogens was assigned to Methanosarcina.
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Affiliation(s)
- Çağrı Akyol
- Institute of Environmental Sciences, Boğaziçi University, Bebek, 34342 Istanbul, Turkey
| | - Orhan Ince
- Department of Environmental Engineering, Istanbul Technical University, Maslak, 34469 Istanbul, Turkey.
| | - Mahir Bozan
- Institute of Environmental Sciences, Boğaziçi University, Bebek, 34342 Istanbul, Turkey
| | - E Gozde Ozbayram
- Department of Environmental Engineering, Istanbul Technical University, Maslak, 34469 Istanbul, Turkey
| | - Bahar Ince
- Institute of Environmental Sciences, Boğaziçi University, Bebek, 34342 Istanbul, Turkey
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Process Disturbances in Agricultural Biogas Production—Causes, Mechanisms and Effects on the Biogas Microbiome: A Review. ENERGIES 2019. [DOI: 10.3390/en12030365] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Disturbances of the anaerobic digestion process reduce the economic and environmental performance of biogas systems. A better understanding of the highly complex process is of crucial importance in order to avoid disturbances. This review defines process disturbances as significant changes in the functionality within the microbial community leading to unacceptable and severe decreases in biogas production and requiring an active counteraction to be overcome. The main types of process disturbances in agricultural biogas production are classified as unfavorable process temperatures, fluctuations in the availability of macro- and micronutrients (feedstock variability), overload of the microbial degradation potential, process-related accumulation of inhibiting metabolites such as hydrogen (H2), ammonium/ammonia (NH4+/NH3) or hydrogen sulphide (H2S) and inhibition by other organic and inorganic toxicants. Causes, mechanisms and effects on the biogas microbiome are discussed. The need for a knowledge-based microbiome management to ensure a stable and efficient production of biogas with low susceptibility to disturbances is derived and an outlook on potential future process monitoring and control by means of microbial indicators is provided.
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Wirth R, Kádár G, Kakuk B, Maróti G, Bagi Z, Szilágyi Á, Rákhely G, Horváth J, Kovács KL. The Planktonic Core Microbiome and Core Functions in the Cattle Rumen by Next Generation Sequencing. Front Microbiol 2018; 9:2285. [PMID: 30319585 PMCID: PMC6165872 DOI: 10.3389/fmicb.2018.02285] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 09/07/2018] [Indexed: 12/31/2022] Open
Abstract
The cow rumen harbors a great variety of diverse microbes, which form a complex, organized community. Understanding the behavior of this multifarious network is crucial in improving ruminant nutrient use efficiency. The aim of this study was to expand our knowledge by examining 10 Holstein dairy cow rumen fluid fraction whole metagenome and transcriptome datasets. DNA and mRNA sequence data, generated by Ion Torrent, was subjected to quality control and filtering before analysis for core elements. The taxonomic core microbiome consisted of 48 genera belonging to Bacteria (47) and Archaea (1). The genus Prevotella predominated the planktonic core community. Core functional groups were identified using co-occurrence analysis and resulted in 587 genes, from which 62 could be assigned to metabolic functions. Although this was a minimal functional core, it revealed key enzymes participating in various metabolic processes. A diverse and rich collection of enzymes involved in carbohydrate metabolism and other functions were identified. Transcripts coding for enzymes active in methanogenesis made up 1% of the core functions. The genera associated with the core enzyme functions were also identified. Linking genera to functions showed that the main metabolic pathways are primarily provided by Bacteria and several genera may serve as a “back-up” team for the central functions. The key actors in most essential metabolic routes belong to the genus Prevotella. Confirming earlier studies, the genus Methanobrevibacter carries out the overwhelming majority of rumen methanogenesis and therefore methane emission mitigation seems conceivable via targeting the hydrogenotrophic methanogenesis.
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Affiliation(s)
- Roland Wirth
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | | | - Balázs Kakuk
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary
| | - Zoltán Bagi
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Árpád Szilágyi
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Gábor Rákhely
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Biophysics, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary
| | - József Horváth
- Faculty of Agriculture, University of Szeged, Hódmezövásárhely, Hungary
| | - Kornél L Kovács
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Biophysics, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary.,Department of Oral Biology and Experimental Dental Research, University of Szeged, Szeged, Hungary
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Gomes TG, Hadi SIIA, Costa Alves GS, Mendonça S, De Siqueira FG, Miller RNG. Current Strategies for the Detoxification of Jatropha curcas Seed Cake: A Review. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:2510-2522. [PMID: 29498277 DOI: 10.1021/acs.jafc.7b05691] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Jatropha curcas is an important oilseed plant, with considerable potential in the development of biodiesel. Although Jatropha seed cake, the byproduct of oil extraction, is a residue rich in nitrogen, phosphorus, potassium, and carbon, with high protein content suitable for application in animal feed, the presence of toxic phorbol esters limits its application in feed supplements and fertilizers. This review summarizes the current methods available for detoxification of this residue, based upon chemical, physical, biological, or combined processes. The advantages and disadvantages of each process are discussed, and future directions involving genomic and proteomic approaches for advancing our understanding of biodegradation processes involving microorganisms are highlighted.
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Affiliation(s)
- Taisa G Gomes
- Instituto de Ciências Biológicas, Departamento de Biologia Celular , Universidade de Brasília , Campus Universitário Darcy Ribeiro, Asa Norte , 70910-900 , Brasília , DF , Brazil
| | - Sámed I I A Hadi
- Universidade Federal de Minas Gerais , Instituto de Ciências Biológicas - ICB , Av. Pres. Antônio Carlos, 6627 , 31270-010 , Belo Horizonte , MG , Brazil
| | - Gabriel S Costa Alves
- Instituto de Ciências Biológicas, Departamento de Biologia Celular , Universidade de Brasília , Campus Universitário Darcy Ribeiro, Asa Norte , 70910-900 , Brasília , DF , Brazil
| | - Simone Mendonça
- Embrapa Agroenergia, STN-70297-400 , 70297-400 , Brasília , DF , Brazil
| | | | - Robert N G Miller
- Instituto de Ciências Biológicas, Departamento de Biologia Celular , Universidade de Brasília , Campus Universitário Darcy Ribeiro, Asa Norte , 70910-900 , Brasília , DF , Brazil
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9
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Ecem Öner B, Akyol Ç, Bozan M, Ince O, Aydin S, Ince B. Bioaugmentation with Clostridium thermocellum to enhance the anaerobic biodegradation of lignocellulosic agricultural residues. BIORESOURCE TECHNOLOGY 2018; 249:620-625. [PMID: 29091846 DOI: 10.1016/j.biortech.2017.10.040] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 10/06/2017] [Accepted: 10/08/2017] [Indexed: 06/07/2023]
Abstract
This study aimed to improve biomethane production from lignocellulosic biomass by assessing the impact of bioaugmentation with Clostridium thermocellum on the performance of anaerobic digesters at different inoculation ratios. The outputs of the digestion experiments revealed that bioaugmentation strategies with C. thermocellum increased the methane yield up to 39%. The sequencing analysis indicated that the indigenous microbial community was modified by the bioaugmentation. During the process of bioaugmentation, in the digester that was inoculated at the ratio of 20% (v:v), an increase in the abundance of Ruminococcaceae family led to a decrease in the Bacteroidaceae and Synergistaceae families. Furthermore, the metabolic products of the bioaugmented strains greatly influenced the diversity of the archaeal community and an increase in the abundance of Methanomicrobiales was observed.
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Affiliation(s)
- Büşra Ecem Öner
- Institute of Environmental Sciences, Boğaziçi University, Bebek, 34342 Istanbul, Turkey
| | - Çağrı Akyol
- Institute of Environmental Sciences, Boğaziçi University, Bebek, 34342 Istanbul, Turkey
| | - Mahir Bozan
- Institute of Environmental Sciences, Boğaziçi University, Bebek, 34342 Istanbul, Turkey
| | - Orhan Ince
- Department of Environmental Engineering, Istanbul Technical University, Maslak, 34469 Istanbul, Turkey
| | - Sevcan Aydin
- Department of Genetics and Bioengineering, Nişantaşı University, Maslak, 34398 Istanbul, Turkey.
| | - Bahar Ince
- Institute of Environmental Sciences, Boğaziçi University, Bebek, 34342 Istanbul, Turkey
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