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Robazza A, Baleeiro FCF, Kleinsteuber S, Neumann A. Two-stage conversion of syngas and pyrolysis aqueous condensate into L-malate. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:85. [PMID: 38907325 PMCID: PMC11191387 DOI: 10.1186/s13068-024-02532-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 06/13/2024] [Indexed: 06/23/2024]
Abstract
Hybrid thermochemical-biological processes have the potential to enhance the carbon and energy recovery from organic waste. This work aimed to assess the carbon and energy recovery potential of multifunctional processes to simultaneously sequestrate syngas and detoxify pyrolysis aqueous condensate (PAC) for short-chain carboxylates production. To evaluate relevant process parameters for mixed culture co-fermentation of syngas and PAC, two identical reactors were run under mesophilic (37 °C) and thermophilic (55 °C) conditions at increasing PAC loading rates. Both the mesophilic and the thermophilic process recovered at least 50% of the energy in syngas and PAC into short-chain carboxylates. During the mesophilic syngas and PAC co-fermentation, methanogenesis was completely inhibited while acetate, ethanol and butyrate were the primary metabolites. Over 90% of the amplicon sequencing variants based on 16S rRNA were assigned to Clostridium sensu stricto 12. During the thermophilic process, on the other hand, Symbiobacteriales, Syntrophaceticus, Thermoanaerobacterium, Methanothermobacter and Methanosarcina likely played crucial roles in aromatics degradation and methanogenesis, respectively, while Moorella thermoacetica and Methanothermobacter marburgensis were the predominant carboxydotrophs in the thermophilic process. High biomass concentrations were necessary to maintain stable process operations at high PAC loads. In a second-stage reactor, Aspergillus oryzae converted acetate, propionate and butyrate from the first stage into L-malate, confirming the successful detoxification of PAC below inhibitory levels. The highest L-malate yield was 0.26 ± 2.2 molL-malate/molcarboxylates recorded for effluent from the mesophilic process at a PAC load of 4% v/v. The results highlight the potential of multifunctional reactors where anaerobic mixed cultures perform simultaneously diverse process roles, such as carbon fixation, wastewater detoxification and carboxylates intermediate production. The recovered energy in the form of intermediate carboxylates allows for their use as substrates in subsequent fermentative stages.
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Affiliation(s)
- Alberto Robazza
- Institute of Process Engineering in Life Sciences 2: Electro Biotechnology, Karlsruhe Institute of Technology - KIT, 76131, Karlsruhe, Germany
| | - Flávio C F Baleeiro
- Department of Microbial Biotechnology, Helmholtz Centre for Environmental Research - UFZ, 04318, Leipzig, Germany
| | - Sabine Kleinsteuber
- Department of Microbial Biotechnology, Helmholtz Centre for Environmental Research - UFZ, 04318, Leipzig, Germany
| | - Anke Neumann
- Institute of Process Engineering in Life Sciences 2: Electro Biotechnology, Karlsruhe Institute of Technology - KIT, 76131, Karlsruhe, Germany.
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2
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Beraud-Martínez LK, Betancourt-Lozano M, Gómez-Gil B, Asaff-Torres A, Monroy-Hermosillo OA, Franco-Nava MÁ. Methylotrophic methanogenesis induced by ammonia nitrogen in an anaerobic digestion system. Anaerobe 2024; 88:102877. [PMID: 38866129 DOI: 10.1016/j.anaerobe.2024.102877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 05/08/2024] [Accepted: 06/06/2024] [Indexed: 06/14/2024]
Abstract
OBJECTIVES This lab-scale study aimed to investigate the effect of total ammonia nitrogen (TAN) stress on the methanogenic activity and the taxonomic and functional profiles of the microbial community of anaerobic sludge (AS) from a full-scale bioreactor. METHODS The AS was subjected to a stepwise increase in TAN every 14 days at concentrations of 1, 2, 2.5, 3, 3.5, and 4 g TAN/L (Acclimated-AS or AAS). This acclimation stage was followed by an ammonia stress stage (4 g/L). A blank-AS (BAS) was maintained without TAN during the acclimation stage. In the second stress stage (ST), the BAS was divided into two new treatments: a control (BAS') and one that received a shock load of TAN of 4 g/L (SBAS'). Methane production was measured, and a metagenomic analysis was conducted to describe the microbial community. RESULTS A decrease in the relative abundance of Methanothrix soehngenii of 16 % was related to a decrease of 23 % in the methanogenic capacity of AAS when comparing with the final stage of BAS. However, recovery was observed at 3.5 g TAN/L, and a shift to methylotrophic metabolism occurred, indicated by a 4-fold increase in abundance of Methanosarcina mazei. The functional analysis of sludge metagenomes indicated that no statistical differences (p > 0.05, RM ANOVA) were found in the relative abundance of methanogenic genes that initiate acetoclastic and hydrogenotrophic pathways (acetyl-CoA synthetase, ACSS; acetate kinase, ackA; phosphate acetyltransferase, pta; and formylmethanofuran dehydrogenase subunit A, fwdA) into the BAS and AAS during the acclimation phase. The same was observed between groups of genes associated with methanogenesis from methylated compounds. In contrast, statistical differences (p < 0.05, one-way ANOVA) in the relative abundance of these genes were recorded during ST. The functional profiles of the genes involved in acetoclastic, hydrogenotrophic, and methylotrophic methanogenic pathways were brought to light for acclimatation and stress experimental stages. CONCLUSIONS TAN inhibited methanogenic activity and acetoclastic metabolism. The gradual acclimatization to TAN leads to metabolic and taxonomic changes that allow for the subsequent recovery of methanogenic functionality. The study highlights the importance of adequate management of anaerobic bioprocesses with high nitrogen loads to maintain the methanogenic functionality of the microbial community.
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Affiliation(s)
- Liov Karel Beraud-Martínez
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A. C. Unidad Mazatlán, Avenida Sábalo-Cerritos s/n, Mazatlán, Sinaloa, 82112, Mexico
| | - Miguel Betancourt-Lozano
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A. C. Unidad Mazatlán, Avenida Sábalo-Cerritos s/n, Mazatlán, Sinaloa, 82112, Mexico
| | - Bruno Gómez-Gil
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A. C. Unidad Mazatlán, Avenida Sábalo-Cerritos s/n, Mazatlán, Sinaloa, 82112, Mexico
| | - Ali Asaff-Torres
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A.C. Unidad Hermosillo, Carretera Gustavo Enrique Astiazarán Rosas, No. 46, Col. La Victoria, CP. 83304, Hermosillo, Sonora, Mexico
| | - Oscar Armando Monroy-Hermosillo
- Universidad Autónoma Metropolitana. Biotechnology Department, Av. San Rafael Atlixco 186, Col. Vicentina, 09340, Iztapalapa, Cd. México, Mexico
| | - Miguel Ángel Franco-Nava
- Tecnológico Nacional de México, Campus Mazatlán, Calle Corsario 1 No. 203 Col. Urías, A.P. 757, Mazatlán, Sinaloa, 82070, Mexico.
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3
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Qian X, Huang J, Ji X, Yan C, Cao C, Wu Y, Wang X. Modified basalt fibers boost performance of constructed wetlands: Comparison between surface coating and chemical grafting. BIORESOURCE TECHNOLOGY 2024; 397:130492. [PMID: 38408500 DOI: 10.1016/j.biortech.2024.130492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 02/22/2024] [Accepted: 02/22/2024] [Indexed: 02/28/2024]
Abstract
Modified basalt fiber (MBF) is a potential material that has been applied in wastewater treatment fields. In this study, superior performances of MBFs by calcium (Ca-MBF) and polyethyleneimine modification (PEI-MBF) were compared in constructed wetlands (CWs). Via chemical grafting, higher biofilm contents were observed on the surface of PEI-MBF, compared to Ca-MBF. Moreover, MBF increased key enzyme activities particularly in lower substrate layer, contributing to positive responses of microbial community in CWs. For instance, PEI-MBF boosted microbial richness and diversity and improved the abundances of denitrifying functional bacteria and biomarkers like Thauera, Vulcanibacillus, and Maritimimonas, probably promoting nitrate removal compared with Ca-MBF group. By contrast, Ca-MBF enriched more functional genera involved in nutrients removal, with the highest removal of ammonium (43.9 %), total nitrogen (66.2 %), and total phosphorus (37.1 %). Overall, this work provided new findings on improved performance of CWs with MBF.
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Affiliation(s)
- Xiuwen Qian
- Department of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing 211189, China
| | - Juan Huang
- Department of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing 211189, China.
| | - Xiaoyu Ji
- Shanghai Municipal Engineering Design and Research Institute (Group) Co., Ltd, Shanghai 744000, China
| | - Chunni Yan
- School of Urban Planning and Municipal Engineering, Xi'an Polytechnic University, Xi'an 710048, China
| | - Chong Cao
- Department of Municipal Engineering, College of Civil Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Yufeng Wu
- Department of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing 211189, China
| | - Xinyue Wang
- Department of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing 211189, China
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4
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Niya B, Yaakoubi K, Beraich FZ, Arouch M, Meftah Kadmiri I. Current status and future developments of assessing microbiome composition and dynamics in anaerobic digestion systems using metagenomic approaches. Heliyon 2024; 10:e28221. [PMID: 38560681 PMCID: PMC10979216 DOI: 10.1016/j.heliyon.2024.e28221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 03/12/2024] [Accepted: 03/13/2024] [Indexed: 04/04/2024] Open
Abstract
The metagenomic approach stands as a powerful technique for examining the composition of microbial communities and their involvement in various anaerobic digestion (AD) systems. Understanding the structure, function, and dynamics of microbial communities becomes pivotal for optimizing the biogas process, enhancing its stability and improving overall performance. Currently, taxonomic profiling of biogas-producing communities relies mainly on high-throughput 16S rRNA sequencing, offering insights into the bacterial and archaeal structures of AD assemblages and their correlations with fed substrates and process parameters. To delve even deeper, shotgun and genome-centric metagenomic approaches are employed to recover individual genomes from the metagenome. This provides a nuanced understanding of collective functionalities, interspecies interactions, and microbial associations with abiotic factors. The application of OMICs in AD systems holds the potential to revolutionize the field, leading to more efficient and sustainable waste management practices particularly through the implementation of precision anaerobic digestion systems. As ongoing research in this area progresses, anticipations are high for further exciting developments in the future. This review serves to explore the current landscape of metagenomic analyses, with focus on advancing our comprehension and critically evaluating biases and recommendations in the analysis of microbial communities in anaerobic digesters. Its objective is to explore how contemporary metagenomic approaches can be effectively applied to enhance our understanding and contribute to the refinement of the AD process. This marks a substantial stride towards achieving a more comprehensive understanding of anaerobic digestion systems.
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Affiliation(s)
- Btissam Niya
- Plant and Microbial Biotechnology Center, Moroccan Foundation of Advanced Science Innovation and Research MAScIR, Mohammed VI Polytechnic University (UM6P), Lot 660, Hay Moulay Rachid, 43150, Benguerir, Morocco
- Engineering, Industrial Management & Innovation Laboratory IMII, Faculty of Science and Technics (FST), Hassan 1st University of Settat, Morocco
| | - Kaoutar Yaakoubi
- Plant and Microbial Biotechnology Center, Moroccan Foundation of Advanced Science Innovation and Research MAScIR, Mohammed VI Polytechnic University (UM6P), Lot 660, Hay Moulay Rachid, 43150, Benguerir, Morocco
| | - Fatima Zahra Beraich
- Biodome.sarl, Research and Development Design Office of Biogas Technology, Casablanca, Morocco
| | - Moha Arouch
- Engineering, Industrial Management & Innovation Laboratory IMII, Faculty of Science and Technics (FST), Hassan 1st University of Settat, Morocco
| | - Issam Meftah Kadmiri
- Plant and Microbial Biotechnology Center, Moroccan Foundation of Advanced Science Innovation and Research MAScIR, Mohammed VI Polytechnic University (UM6P), Lot 660, Hay Moulay Rachid, 43150, Benguerir, Morocco
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5
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Kim D, Cha J, Lee C. Enhanced methane production with co-feeding spent coffee grounds using spare capacity of existing anaerobic food waste digesters. Sci Rep 2024; 14:4472. [PMID: 38396086 PMCID: PMC10891051 DOI: 10.1038/s41598-024-54610-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 02/14/2024] [Indexed: 02/25/2024] Open
Abstract
With increasing coffee consumption worldwide, the efficient and sustainable management of spent coffee grounds (SCG) has become increasingly challenging. This study investigated the anaerobic co-digestion of small amounts of SCG with food waste (FW) at increasing co-feeding ratios of 1:100-1:10 (volatile solids basis) to assess the possibility of SCG treatment using the spare capacity of existing anaerobic digesters. Co-feeding SCG increased methane production compared to FW mono-digestion in the tested range of co-feeding ratios without compromising process stability. Methane yield did not further increase when the SCG/FW ratio increased above 4%, and process failure occurred at a 1:10 co-feeding ratio without trace element supplementation. The enhanced methanogenic performance was attributed to increased protein removal efficiency, which was potentially related to the promotion of peptide hydrolysis. The overall results suggest that co-feeding appropriate small amounts of SCG to FW digesters can be a realistic sustainable option for SCG management.
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Affiliation(s)
- Danbee Kim
- Department of Urban and Environmental Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-Gil, Eonyang-Eup, Ulju-Gun, Ulsan, 44919, Republic of Korea
- Gwangju Clean Energy Research Center, Korea Institute of Energy Research, 25, Samso-Ro 270Beon-Gil, Buk-Gu, Gwangju, 61003, Republic of Korea
| | - Junho Cha
- Department of Urban and Environmental Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-Gil, Eonyang-Eup, Ulju-Gun, Ulsan, 44919, Republic of Korea
| | - Changsoo Lee
- Department of Urban and Environmental Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-Gil, Eonyang-Eup, Ulju-Gun, Ulsan, 44919, Republic of Korea.
- Graduate School of Carbon Neutrality, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-Gil, Eonyang-Eup, Ulju-Gun, Ulsan, 44919, Republic of Korea.
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6
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Kieft B, Finke N, McLaughlin RJ, Nallan AN, Krzywinski M, Crowe SA, Hallam SJ. Genome-resolved correlation mapping links microbial community structure to metabolic interactions driving methane production from wastewater. Nat Commun 2023; 14:5380. [PMID: 37666802 PMCID: PMC10477309 DOI: 10.1038/s41467-023-40907-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/15/2023] [Indexed: 09/06/2023] Open
Abstract
Anaerobic digestion of municipal mixed sludge produces methane that can be converted into renewable natural gas. To improve economics of this microbial mediated process, metabolic interactions catalyzing biomass conversion to energy need to be identified. Here, we present a two-year time series associating microbial metabolism and physicochemistry in a full-scale wastewater treatment plant. By creating a co-occurrence network with thousands of time-resolved microbial populations from over 100 samples spanning four operating configurations, known and novel microbial consortia with potential to drive methane production were identified. Interactions between these populations were further resolved in relation to specific process configurations by mapping metagenome assembled genomes and cognate gene expression data onto the network. Prominent interactions included transcriptionally active Methanolinea methanogens and syntrophic benzoate oxidizing Syntrophorhabdus, as well as a Methanoregulaceae population and putative syntrophic acetate oxidizing bacteria affiliated with Bateroidetes (Tenuifilaceae) expressing the glycine cleavage bypass of the Wood-Ljungdahl pathway.
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Affiliation(s)
- Brandon Kieft
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
| | - Niko Finke
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
| | - Ryan J McLaughlin
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Aditi N Nallan
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Martin Krzywinski
- Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Sean A Crowe
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
| | - Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada.
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
- Genome Science and Technology Program, University of British Columbia, 2329 West Mall, Vancouver, BC, V6T 1Z4, Canada.
- Bradshaw Research Institute for Minerals and Mining (BRIMM), University of British Columbia, Vancouver, BC, V6T1Z4, Canada.
- Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
- ECOSCOPE Training Program, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
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7
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Lin TY, Liu WT. Validation of 16S rRNA gene sequencing and metagenomics for evaluating microbial immigration in a methanogenic bioreactor. WATER RESEARCH 2023; 243:120358. [PMID: 37481999 DOI: 10.1016/j.watres.2023.120358] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 07/09/2023] [Accepted: 07/14/2023] [Indexed: 07/25/2023]
Abstract
To quantitatively evaluate the impact of microbial immigration from an upstream community on the microbial assembly of a downstream community, an ecological genomics (ecogenomics)-based mass balance (EGMB) model coupled with 16S rRNA gene sequencing was previously developed. In this study, a mock community was used to further validate the EGMB models and demonstrate the feasibility of using metagenome-based EGMB model to reveal both microbial activity and function. The mock community consisting of Aeromonas, Escherichia, and Pseudomonas was fed into a lab-scale methanogenic bioreactor together with dissolved organic substrate. Using qPCR, 16S rRNA gene, 16S rRNA gene copy number normalization (GCN), and metagenome, results showed highly comparable community profiles in the feed. In the bioreactor, Aeromonas and Pseudomonas exhibited negative growth rates throughout the experiment by all approaches. Escherichia's growth rate was negative by most biomarkers but was slightly positive by 16S rRNA gene. Still, all approaches showed a decreasing trend toward negative in the growth rate of Escherichia as reactor operation time increased. Uncultivated populations of phyla Desulfobacterota, Chloroflexi, Actinobacteriota, and Spirochaetota were observed to increase in abundance, suggesting their contribution in degrading the feed biomass. Based on metabolic reconstruction of metagenomes, these populations possessed functions of hydrolysis, fermentation, fatty acid degradation, or acetate oxidation. Overall results supported the application of both 16S rRNA gene- and metagenome-based EGMB models to measure the growth rate of microbes in the bioreactor, and the latter had advantage in providing insights into the microbial functions of uncultivated populations.
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Affiliation(s)
- Tzu-Yu Lin
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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8
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Fernández-Domínguez D, Yekta SS, Hedenström M, Patureau D, Jimenez J. Deciphering the contribution of microbial biomass to the properties of dissolved and particulate organic matter in anaerobic digestates. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 877:162882. [PMID: 36934942 DOI: 10.1016/j.scitotenv.2023.162882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/28/2023] [Accepted: 03/11/2023] [Indexed: 05/06/2023]
Abstract
The recalcitrant structures either from substrate or microbial biomass contained in digestates after anaerobic digestion (AD) highly influence digestate valorization. To properly assess the microbial biomass contribution to the digested organic matter (OM), a combination of characterization methods and the use of various substrate types in anaerobic continuous reactors was required. The use of totally biodegradable substrates allowed detecting soluble microbial products via fluorescence spectroscopy at emission wavelengths of 420 and 460 nm while the protein-like signature was enhanced by the whey protein. During reactors' operation, a transfer of complex compounds to the dissolved OM from the particulate OM was observed through fluorescence applied on biochemical fractionation. Consequently, the fluorescence complexity index of the dissolved OM increased from 0.59-0.60 to 1.06-1.07, whereas it decreased inversely for the extractable soluble from the particulate OM from 1.16-1.19 to 0.42-0.54. Accordingly, fluorescence regional integration showed differences among reactors based on visual inspection and orthogonal partial latent structures (OPLS) analysis. Similarly, the impact of the substrate type and operation time on the particulate OM was revealed by 13C nuclear magnetic resonance using OPLS, providing a good model (R2X = 0.93 and Q2 = 0.8) with a clear time-trend. A high signal resonated at ∼30 ppm attributed to CH2-groups in the aliphatic chain of lipid-like structure besides carbohydrates intensities at 60-110 ppm distinguished the reactor fed with whey protein from the other, which was mostly biomass related. Indeed, this latter displayed a higher presence of peptidoglycan (δH/C: 1.6-2.0/20-25 ppm) derived from microbial biomass by 1H-13C heteronuclear single-quantum coherence (HSQC) nuclear magnetic resonance. Interestingly, the sample distribution obtained by non-metric multidimensional scaling of bacterial communities resembled the attained using 13C NMR properties, opening new research perspectives. Overall, this study discloses the microbial biomass contribution to digestates composition to improve the OM transformation mechanism knowledge.
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Affiliation(s)
| | - Sepehr Shakeri Yekta
- Department of Thematic Studies-Environmental Change and Biogas Research Center, Linköping University, 581 83 Linköping, Sweden
| | | | - Dominique Patureau
- INRAE, Univ. Montpellier, LBE, 102 Avenue des étangs, 11100 Narbonne, France
| | - Julie Jimenez
- INRAE, Univ. Montpellier, LBE, 102 Avenue des étangs, 11100 Narbonne, France
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9
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Potential of hydrochar/pyrochar derived from sawdust of oriental plane tree for stimulating methanization by mitigating propionic acid inhibition in mesophilic anaerobic digestion of swine manure. Heliyon 2023; 9:e13984. [PMID: 36925554 PMCID: PMC10011200 DOI: 10.1016/j.heliyon.2023.e13984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 03/06/2023] Open
Abstract
VFAs accumulation in anaerobic digestion systems can lead to disturbance of the acid base balance, which has brought major challenges for methane production. Meanwhile, less research explored the potential of biochar derived from wood wastes of oriental plane tree (Platanus orientalis L.) for stimulating methanization in mesophilic anaerobic digestion. In this study, the effects of pyrochar and hydrochar derived from sawdust of oriental plane tree on mesophilic anaerobic digestion of swine manure were compared for the first time. Fourier infrared transform analysis indicated that more functional groups existed on the surface of hydrochar, whereas higher ash content and BET specific surface area were found in pyrochar. The maximum methane production rate during anaerobic digestion was observed in the pyrochar treatment, which increased by 59.5% compared with the control without biochar. Although stimulative effects on dissolved organic carbon and volatile fatty acids production were both observed in the pyrochar and hydrochar treatments, the pyrochar treatment was much easier to trigger multipath methanogenesis and direct interspecific electron transport and subdue propionic acid accumulation compared to the hydrochar treatment. Moreover, redundancy analysis indicated that the variations in acetic acid and dissolved organic carbon were mostly associated with microbial succession. These results suggest that pyrochar has better promoting effects than HC in terms of methane generation and propionic acid inhibition alleviation owing to its special porous structures, functional groups (e.g., C=O, C-O and O-H), and physicochemical properties. These excellent properties play a greater role in recruiting functional archaea and bacteria to regulate the levels of volatile fatty acids and dissolved organic carbon to enhance the methane yield of anaerobic digestion. This study provides novel and valuable information for further engineering applications of pyrochar and hydrochar derived from sawdust of oriental plane tree in energy production and environmental waste treatment.
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10
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Peltoniemi K, Velmala S, Fritze H, Jyske T, Rasi S, Pennanen T. Impacts of coniferous bark-derived organic soil amendments on microbial communities in arable soil - a microcosm study. FEMS Microbiol Ecol 2023; 99:7022313. [PMID: 36725205 PMCID: PMC10013654 DOI: 10.1093/femsec/fiad012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 01/26/2023] [Accepted: 01/27/2023] [Indexed: 02/03/2023] Open
Abstract
A decline in the carbon content of agricultural soils has been reported globally. Amendments of forest industry side-streams might counteract this. We tested the effects of industrial conifer bark and its cascade process materials on the soil microbiome under barley (Hordeum vulgare L.) in clay and silt soil microcosms for 10 months, simulating the seasonal temperature changes of the boreal region. Microbial gene copy numbers were higher in clay soils than in silt. All amendments except unextracted bark increased bacterial gene copies in both soils. In turn, all other amendments, but not unextracted bark from an anaerobic digestion process, increased fungal gene copy numbers in silt soil. In clay soil, fungal increase occurred only with unextracted bark and hot water extracted bark. Soil, amendment type and simulated season affected both the bacterial and fungal community composition. Amendments increased bacteria originating from the anaerobic digestion process, as well as dinitrogen fixers and decomposers of plant cells. In turn, unextracted and hot water extracted bark determined the fungal community composition in silt. As fungal abundance increase and community diversification are related to soil carbon acquisition, bark-based amendments to soils can thus contribute to sustainable agriculture.
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Affiliation(s)
- Krista Peltoniemi
- Corresponding author. Soil Ecosystems, Natural Resources, Natural Resources Institute Finland (Luke), Latokartanonkaari 9, FI-00790 Helsinki, Finland.E-mail:
| | - Sannakajsa Velmala
- Natural Resources, Natural Resources Institute Finland (Luke), Latokartanonkaari 9, FI-00720 Helsinki, Finland
| | - Hannu Fritze
- Natural Resources, Natural Resources Institute Finland (Luke), Latokartanonkaari 9, FI-00720 Helsinki, Finland
| | - Tuula Jyske
- Production Systems, Natural Resources Institute Finland (Luke), Viikinkaari 9, FI-00720 Helsinki, Finland
| | - Saija Rasi
- Production Systems, Natural Resources Institute Finland (Luke), Survontie 9, FI-40500 Jyväskylä, Finland
| | - Taina Pennanen
- Natural Resources, Natural Resources Institute Finland (Luke), Latokartanonkaari 9, FI-00720 Helsinki, Finland
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11
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Becker D, Popp D, Bonk F, Kleinsteuber S, Harms H, Centler F. Metagenomic Analysis of Anaerobic Microbial Communities Degrading Short-Chain Fatty Acids as Sole Carbon Sources. Microorganisms 2023; 11:microorganisms11020420. [PMID: 36838385 PMCID: PMC9959488 DOI: 10.3390/microorganisms11020420] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 02/04/2023] [Indexed: 02/11/2023] Open
Abstract
Analyzing microbial communities using metagenomes is a powerful approach to understand compositional structures and functional connections in anaerobic digestion (AD) microbiomes. Whereas short-read sequencing approaches based on the Illumina platform result in highly fragmented metagenomes, long-read sequencing leads to more contiguous assemblies. To evaluate the performance of a hybrid approach of these two sequencing approaches we compared the metagenome-assembled genomes (MAGs) resulting from five AD microbiome samples. The samples were taken from reactors fed with short-chain fatty acids at different feeding regimes (continuous and discontinuous) and organic loading rates (OLR). Methanothrix showed a high relative abundance at all feeding regimes but was strongly reduced in abundance at higher OLR, when Methanosarcina took over. The bacterial community composition differed strongly between reactors of different feeding regimes and OLRs. However, the functional potential was similar regardless of feeding regime and OLR. The hybrid sequencing approach using Nanopore long-reads and Illumina MiSeq reads improved assembly statistics, including an increase of the N50 value (on average from 32 to 1740 kbp) and an increased length of the longest contig (on average from 94 to 1898 kbp). The hybrid approach also led to a higher share of high-quality MAGs and generated five potentially circular genomes while none were generated using MiSeq-based contigs only. Finally, 27 hybrid MAGs were reconstructed of which 18 represent potentially new species-15 of them bacterial species. During pathway analysis, selected MAGs revealed similar gene patterns of butyrate degradation and might represent new butyrate-degrading bacteria. The demonstrated advantages of adding long reads to metagenomic analyses make the hybrid approach the preferable option when dealing with complex microbiomes.
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Affiliation(s)
- Daniela Becker
- UFZ—Helmholtz Centre for Environmental Research, Department of Environmental Microbiology, Permoserstr 15, 04318 Leipzig, Germany
- IAV GmbH, Kauffahrtei 23-25, 09120 Chemnitz, Germany
| | - Denny Popp
- UFZ—Helmholtz Centre for Environmental Research, Department of Environmental Microbiology, Permoserstr 15, 04318 Leipzig, Germany
- Institute of Human Genetics, University of Leipzig Medical Center, Philipp-Rosenthal-Str. 55, 04103 Leipzig, Germany
| | - Fabian Bonk
- UFZ—Helmholtz Centre for Environmental Research, Department of Environmental Microbiology, Permoserstr 15, 04318 Leipzig, Germany
- VERBIO Vereinigte Bioenergie AG, Thura Mark 18, 06780 Zörbig, Germany
| | - Sabine Kleinsteuber
- UFZ—Helmholtz Centre for Environmental Research, Department of Environmental Microbiology, Permoserstr 15, 04318 Leipzig, Germany
| | - Hauke Harms
- UFZ—Helmholtz Centre for Environmental Research, Department of Environmental Microbiology, Permoserstr 15, 04318 Leipzig, Germany
| | - Florian Centler
- UFZ—Helmholtz Centre for Environmental Research, Department of Environmental Microbiology, Permoserstr 15, 04318 Leipzig, Germany
- School of Life Sciences, University of Siegen, 57076 Siegen, Germany
- Correspondence:
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12
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A Review of Basic Bioinformatic Techniques for Microbial Community Analysis in an Anaerobic Digester. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9010062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Biogas production involves various types of intricate microbial populations in an anaerobic digester (AD). To understand the anaerobic digestion system better, a broad-based study must be conducted on the microbial population. Deep understanding of the complete metagenomics including microbial structure, functional gene form, similarity/differences, and relationships between metabolic pathways and product formation, could aid in optimization and enhancement of AD processes. With advancements in technologies for metagenomic sequencing, for example, next generation sequencing and high-throughput sequencing, have revolutionized the study of microbial dynamics in anaerobic digestion. This review includes a brief introduction to the basic process of metagenomics research and includes a detailed summary of the various bioinformatics approaches, viz., total investigation of data obtained from microbial communities using bioinformatics methods to expose metagenomics characterization. This includes (1) methods of DNA isolation and sequencing, (2) investigation of anaerobic microbial communities using bioinformatics techniques, (3) application of the analysis of anaerobic microbial community and biogas production, and (4) restriction and prediction of bioinformatics analysis on microbial metagenomics. The review has been concluded, giving a summarized insight into bioinformatic tools and also promoting the future prospects of integrating humungous data with artificial intelligence and neural network software.
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13
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Johnson LA, Hug LA. Cloacimonadota metabolisms include adaptations in engineered environments that are reflected in the evolutionary history of the phylum. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:520-529. [PMID: 35365914 DOI: 10.1111/1758-2229.13061] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 03/19/2022] [Indexed: 06/14/2023]
Abstract
Phylum Cloacimonadota (previously Cloacimonetes, WWE1) is an understudied bacterial lineage frequently associated with engineered and wastewater systems. Cloacimonadota members were abundant and diverse in metagenomic datasets from a municipal landfill, prompting an examination of phylogenetic relationships, metabolic diversity, and pangenomic dynamics across the phylum, based on the 30 publicly available genomes and 24 new metagenome-assembled genomes (MAGs) from landfill samples. We found that Cloacimonadota have distinct evolutionary histories associated with engineered versus natural environments and identified genomic features and metabolic strategies that correlate to habitat of origin. Metabolic reconstructions for MAGs predict an anaerobic, acetogenic, and mixed fermentative and flavin-bifurcation-based anaerobic respiratory lifestyle for the majority of Cloacimonadota surveyed. Genomes from engineered ecosystems encode a suite of genes not typically found in genomes from natural environments including acetate kinase, genes for cysteine degradation to pyruvate, increased diversity of carbon utilization enzymes, and different mechanisms for generating membrane potential and ATP synthesis. This phylum-level examination also clarifies the distribution of functions previously observed for members of the phylum, where propionate oxidation and reverse TCA cycles are not common components of Cloacimonadota metabolism.
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Affiliation(s)
- Lisa A Johnson
- Department of Biology, University of Waterloo, 200 University Ave W, Waterloo, ON, N2L 3G1, Canada
| | - Laura A Hug
- Department of Biology, University of Waterloo, 200 University Ave W, Waterloo, ON, N2L 3G1, Canada
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14
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Effect of Pretreatment by Freeze Vacuum Drying on Solid-State Anaerobic Digestion of Corn Straw. FERMENTATION 2022. [DOI: 10.3390/fermentation8060259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
As a common agricultural waste, corn straw (CS) has a refractory structure, which is not conducive to anaerobic digestion (AD). Appropriate pretreatment is crucial for addressing this problem. Thus, freeze vacuum drying (FVD) was proposed. In this study, fresh CS (F-CS) pretreated (5 h, −40 °C) by FVD and naturally dried CS (D-CS) were compared. Differences in substrate surface structure and nutrient composition were first investigated. Results show that a loose and porous structure, crystallinity, and broken chemical bonds, as well as higher proportions of VS, C, N, cellulose, hemicellulose, and crude proteins in F-CS show a potential for methane production. Besides, process performance and stability were also examined in both high (4, VS basis) and low (1, VS basis) S/I ratio AD. A higher degradation ratio of hemicellulose as well as richer dissolved microbial metabolites, coenzymes, tyrosine-like proteins, and hydrolysis rate of particulate organic matter in the F-CS system enhanced the efficiency of methane conversion. The cumulative methane yield increased from 169.66 (D-CS) to 209.97 (F-CS) mL/gVS in the high S/I ratio system (p = 0.02 < 0.05), and 156.97 to 171.89 mL/gVS in the low S/I ratio system. Additionally, 16S-rRNA-gene-based analysis was performed. Interestingly, the coordination of key bacteria (Clostridium_sensu_stricto_1, Bacillus, Terrisporobacter. Clostridium_sensu_stricto_7, Thermoclostrium, UCG-012, and HN-HF0106) was more active. Poorer Methanosarcina and Methanomassiliicoccus as well as richer Methanobrevibacter and Methanoculleus stimulated the co-relationship of key archaea with diverse methanogenesis pathways. This study aims to verify the positive effect of FVD pretreatment on AD of CS, so as to provide a reference for applications in waste management.
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15
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Dang H, Yu N, Mou A, Zhang L, Guo B, Liu Y. Metagenomic insights into direct interspecies electron transfer and quorum sensing in blackwater anaerobic digestion reactors supplemented with granular activated carbon. BIORESOURCE TECHNOLOGY 2022; 352:127113. [PMID: 35381332 DOI: 10.1016/j.biortech.2022.127113] [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: 02/16/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 06/14/2023]
Abstract
The addition of granular activated carbon (GAC) enhanced the performance of up-flow anaerobic sludge blanket (UASB) reactor treating blackwater at 35 °C. DNA were extracted from the sludge and biofilms attached to GAC and submitted for shotgun sequencing. In addition, the acyl-homoserine lactones (AHLs) were quantified. Diverse partners for direct interspecies electron transfer (DIET) were enriched in the sludge or biofilm (GAC-biofilm) of GAC amended UASB. Pedosphaera parvula, Syntrophus aciditrophicus and Syntrophorhabus aromaticivorans were dominant syntrophs. The analysis for type IV pilus assembly genes further suggested DIET may be functioned through GAC for GAC-biofilm, while through conductive pili for sludge aggregates. AHLs quantification and the analysis for quorum sensing (QS) related genes indicated higher QS activity at the population level was induced by GAC. Overall, the work illustrated the different DIET patterns, and suggested that QS played an important role in controlling the performance in GAC amended USAB.
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Affiliation(s)
- Hongyu Dang
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Najiaowa Yu
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Anqi Mou
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Lei Zhang
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Bing Guo
- Centre for Environmental Health and Engineering (CEHE), Department of Civil and Environmental Engineering, University of Surrey, Guildford GU2 7XH, United Kingdom.
| | - Yang Liu
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
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16
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Prolonged acetogenic phase and biological succession during anaerobic digestion using swine manure. Folia Microbiol (Praha) 2022; 67:733-745. [PMID: 35460047 DOI: 10.1007/s12223-021-00937-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 11/28/2021] [Indexed: 11/04/2022]
Abstract
In recent years, global warming and the limitation of fossil fuels have been causing the governments of different countries to think about the search for more sustainable fuel sources. Biomethane (CH4) has gained increasing attention in recent years as an alternative option for a sustainable source of energy. Biogas is generated during the anaerobic digestion of organic materials by the metabolism of complex microbial communities in the substrates that make up this digestion. The microbial community evaluation using 16S rDNA metabarcoding in a bench covered pond bioreactor using swine effluent revealed the dominant bacteria belonging to Firmicutes, Proteobacteria, and Bacteroidetes phyla. The methanogenic group was represented by the Euryarchaeota phylum. It was possible to observe that the relative frequency of the methanogenic archaea community decreased with the anaerobic digestion, indicating a biological succession stage. On the other hand, there was a predominant acetogenic diversity in this final stage. These data showed stabilization of biomethane production, although the microbial community of methanogens has drastically reduced in the late process.
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17
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Holohan BC, Duarte MS, Szabo-Corbacho MA, Cavaleiro AJ, Salvador AF, Pereira MA, Ziels RM, Frijters CTMJ, Pacheco-Ruiz S, Carballa M, Sousa DZ, Stams AJM, O'Flaherty V, van Lier JB, Alves MM. Principles, Advances, and Perspectives of Anaerobic Digestion of Lipids. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:4749-4775. [PMID: 35357187 DOI: 10.1021/acs.est.1c08722] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Several problems associated with the presence of lipids in wastewater treatment plants are usually overcome by removing them ahead of the biological treatment. However, because of their high energy content, waste lipids are interesting yet challenging pollutants in anaerobic wastewater treatment and codigestion processes. The maximal amount of waste lipids that can be sustainably accommodated, and effectively converted to methane in anaerobic reactors, is limited by several problems including adsorption, sludge flotation, washout, and inhibition. These difficulties can be circumvented by appropriate feeding, mixing, and solids separation strategies, provided by suitable reactor technology and operation. In recent years, membrane bioreactors and flotation-based bioreactors have been developed to treat lipid-rich wastewater. In parallel, the increasing knowledge on the diversity of complex microbial communities in anaerobic sludge, and on interspecies microbial interactions, contributed to extend the knowledge and to understand more precisely the limits and constraints influencing the anaerobic biodegradation of lipids in anaerobic reactors. This critical review discusses the most important principles underpinning the degradation process and recent key discoveries and outlines the current knowledge coupling fundamental and applied aspects. A critical assessment of knowledge gaps in the field is also presented by integrating sectorial perspectives of academic researchers and of prominent developers of anaerobic technology.
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Affiliation(s)
- B Conall Holohan
- Microbial Ecology Laboratory, Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland, Galway H91 TK33, Ireland
- NVP Energy Ltd., IDA Technology and Business Park, Mervue, Galway H91 TK33, Ireland
| | - M Salomé Duarte
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- LABBELS - Associate Laboratory, 4710-057 Braga, Guimarães, Portugal
| | - M Alejandra Szabo-Corbacho
- Department of Environmental Engineering and Water Technology, IHE Delft Institute for Water Education, Westvest 7, 2611 AX Delft, The Netherlands
| | - Ana J Cavaleiro
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- LABBELS - Associate Laboratory, 4710-057 Braga, Guimarães, Portugal
| | - Andreia F Salvador
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- LABBELS - Associate Laboratory, 4710-057 Braga, Guimarães, Portugal
| | - M Alcina Pereira
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- LABBELS - Associate Laboratory, 4710-057 Braga, Guimarães, Portugal
| | - Ryan M Ziels
- Department of Civil Engineering, The University of British Columbia, 6250 Applied Science Lane, Vancouver, BC V6T 1Z 4, Canada
| | | | - Santiago Pacheco-Ruiz
- Biothane, Veolia Water Technologies, Tanthofdreef 21, 2623 EW Delft, The Netherlands
| | - Marta Carballa
- CRETUS, Department of Chemical Engineering, Universidad de Santiago de Compostela, 15705 Santiago de Compostela, Spain
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE, Wageningen, The Netherlands
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE, Wageningen, The Netherlands
| | - Vincent O'Flaherty
- Microbial Ecology Laboratory, Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland, Galway H91 TK33, Ireland
| | - Jules B van Lier
- Department of Environmental Engineering and Water Technology, IHE Delft Institute for Water Education, Westvest 7, 2611 AX Delft, The Netherlands
- Section Sanitary Engineering, CEG Faculty, Delft University of Technology, 2628 CN, Delft, The Netherlands
| | - M Madalena Alves
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- LABBELS - Associate Laboratory, 4710-057 Braga, Guimarães, Portugal
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18
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Aguilar-Muñoz P, Lavergne C, Chamy R, Cabrol L. The biotechnological potential of microbial communities from Antarctic soils and sediments: application to low temperature biogenic methane production. J Biotechnol 2022; 351:38-49. [DOI: 10.1016/j.jbiotec.2022.04.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/20/2022] [Accepted: 04/26/2022] [Indexed: 11/24/2022]
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19
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Palù M, Peprah M, Tsapekos P, Kougias P, Campanaro S, Angelidaki I, Treu L. In-situ biogas upgrading assisted by bioaugmentation with hydrogenotrophic methanogens during mesophilic and thermophilic co-digestion. BIORESOURCE TECHNOLOGY 2022; 348:126754. [PMID: 35077815 DOI: 10.1016/j.biortech.2022.126754] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 06/14/2023]
Abstract
In this study, the effects of bioaugmentation of typically dominant hydrogenotrophic methanogens to CSTR co-digesting cheese whey and manure, under in-situ biomethanation operations were investigated. Reactors working at mesophilic (37 °C) and thermophilic (55 °C) conditions were independently treated and examined in terms of microbial composition and process dynamics. Addition of Methanoculleus bourgensis in the mesophilic reactor led to a stable biomethanation, and an improved microbial metabolism, resulting in 11% increase in CH4 production rate. 16S rRNA and biochemical analyses revealed an enrichment in syntrophic and acidogenic species abundance. Moreover, nearly total volatile fatty acids conversion was observed. Differently, Methanothermobacter thermautotrophicus addition in the thermophilic reactor did not promote biogas upgrading performance due to incomplete H2 conversion and inefficient community adaptation to H2 excess, ultimately favoring acetoclastic methanogenesis. Bioaugmentation constitutes a viable tool to strengthen in-situ upgrading processes and paves the way to the development of more sophisticated and robust microbial inoculants.
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Affiliation(s)
- Matteo Palù
- Department of Biology, University of Padova, Via U. Bassi 58/b, Padova 35121, Italy
| | - Maria Peprah
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Lyngby DK-2800, Denmark
| | - Panagiotis Tsapekos
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Lyngby DK-2800, Denmark
| | - Panagiotis Kougias
- Soil and Water Resources Institute, Hellenic Agricultural Organisation DIMITRA, Thermi, Thessaloniki 57001, Greece
| | - Stefano Campanaro
- Department of Biology, University of Padova, Via U. Bassi 58/b, Padova 35121, Italy; CRIBI Biotechnology Center, University of Padova, Padova 35131, Italy.
| | - Irini Angelidaki
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Lyngby DK-2800, Denmark
| | - Laura Treu
- Department of Biology, University of Padova, Via U. Bassi 58/b, Padova 35121, Italy
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20
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Willenbücher K, Wibberg D, Huang L, Conrady M, Ramm P, Gätcke J, Busche T, Brandt C, Szewzyk U, Schlüter A, Barrero Canosa J, Maus I. Phage Genome Diversity in a Biogas-Producing Microbiome Analyzed by Illumina and Nanopore GridION Sequencing. Microorganisms 2022; 10:368. [PMID: 35208823 PMCID: PMC8879888 DOI: 10.3390/microorganisms10020368] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/02/2022] [Accepted: 02/03/2022] [Indexed: 11/16/2022] Open
Abstract
The microbial biogas network is complex and intertwined, and therefore relatively stable in its overall functionality. However, if key functional groups of microorganisms are affected by biotic or abiotic factors, the entire efficacy may be impaired. Bacteriophages are hypothesized to alter the steering process of the microbial network. In this study, an enriched fraction of virus-like particles was extracted from a mesophilic biogas reactor and sequenced on the Illumina MiSeq and Nanopore GridION sequencing platforms. Metagenome data analysis resulted in identifying 375 metagenome-assembled viral genomes (MAVGs). Two-thirds of the classified sequences were only assigned to the superkingdom Viruses and the remaining third to the family Siphoviridae, followed by Myoviridae, Podoviridae, Tectiviridae, and Inoviridae. The metavirome showed a close relationship to the phage genomes that infect members of the classes Clostridia and Bacilli. Using publicly available biogas metagenomic data, a fragment recruitment approach showed the widespread distribution of the MAVGs studied in other biogas microbiomes. In particular, phage sequences from mesophilic microbiomes were highly similar to the phage sequences of this study. Accordingly, the virus particle enrichment approach and metavirome sequencing provided additional genome sequence information for novel virome members, thus expanding the current knowledge of viral genetic diversity in biogas reactors.
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Affiliation(s)
- Katharina Willenbücher
- System Microbiology, Department Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany;
- Environmental Microbiology, Faculty of Process Sciences, Institute of Environmental Technology, Technische Universität Berlin, Ernst-Reuter-Platz 1, 10587 Berlin, Germany; (U.S.); (J.B.C.)
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany; (D.W.); (T.B.); (A.S.)
| | - Liren Huang
- Faculty of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany;
| | - Marius Conrady
- Institute of Agricultural and Urban Ecological Projects, Berlin Humboldt University (IASP), Philippstr. 13, 10115 Berlin, Germany; (M.C.); (P.R.)
| | - Patrice Ramm
- Institute of Agricultural and Urban Ecological Projects, Berlin Humboldt University (IASP), Philippstr. 13, 10115 Berlin, Germany; (M.C.); (P.R.)
| | - Julia Gätcke
- Biophysics of Photosynthesis, Institute for Biology, Humboldt-Universität zu Berlin, Philippstrasse 13, 10115 Berlin, Germany;
| | - Tobias Busche
- Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany; (D.W.); (T.B.); (A.S.)
| | - Christian Brandt
- Institute for Infection Medicine and Hospital Hygiene, University Hospital Jena, Kastanienstraße 1, 07747 Jena, Germany;
| | - Ulrich Szewzyk
- Environmental Microbiology, Faculty of Process Sciences, Institute of Environmental Technology, Technische Universität Berlin, Ernst-Reuter-Platz 1, 10587 Berlin, Germany; (U.S.); (J.B.C.)
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany; (D.W.); (T.B.); (A.S.)
| | - Jimena Barrero Canosa
- Environmental Microbiology, Faculty of Process Sciences, Institute of Environmental Technology, Technische Universität Berlin, Ernst-Reuter-Platz 1, 10587 Berlin, Germany; (U.S.); (J.B.C.)
| | - Irena Maus
- Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany; (D.W.); (T.B.); (A.S.)
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21
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Mezmir Damtie M, Shin J, Lee S, Min Park C, Wang J, Mo Kim Y. Effect of type of coagulants on removal efficiency and removal mechanisms of antibiotic resistance genes in anaerobic digestion of primary sludge produced via a chemically enhanced primary treatment process. BIORESOURCE TECHNOLOGY 2022; 346:126599. [PMID: 34953986 DOI: 10.1016/j.biortech.2021.126599] [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: 11/10/2021] [Revised: 12/15/2021] [Accepted: 12/17/2021] [Indexed: 06/14/2023]
Abstract
The potential impact of the trivalent coagulant cations on the removal mechanisms, removal efficiencies and removal patterns of antibiotic resistance genes (ARGs) during anaerobic digestion (AD) of chemically enhanced primary treatment sludge (CEPTS) was investigated using polyaluminium chloride (PACl), ferric chloride (FeCl3) and mixed FeCl3-PACl. The removal efficiency of 23 ARGs and intI1 improved to 72.1% in AD of primary sludge with 100 mg/L FeCl3 and was lowest (only 54.4 %) in AD of primary sludge with 25 mg/L PACl. The removal of ARGs in AD of CEPTS with addition of single or mixed types of Al-based coagulant began to increase rapidly at the onset of batch operation. On the other hand, both the rapid increase in the removal efficiency of ARGs in AD with FeCl3 and the maximum removal efficiency were attained later than in the other ADs.
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Affiliation(s)
- Mekdimu Mezmir Damtie
- Department of Civil and Environmental Engineering, Hanyang University, Seongdong-gu, Seoul 04763, Republic of Korea
| | - Jingyeong Shin
- Department of Civil and Environmental Engineering, Hanyang University, Seongdong-gu, Seoul 04763, Republic of Korea
| | - Sungman Lee
- Department of Civil and Environmental Engineering, Hanyang University, Seongdong-gu, Seoul 04763, Republic of Korea
| | - Chang Min Park
- Department of Environmental Engineering, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
| | - Jinhua Wang
- College of Resources and Environment, Shandong Agricultural University, Tai'an 271018, China
| | - Young Mo Kim
- Department of Civil and Environmental Engineering, Hanyang University, Seongdong-gu, Seoul 04763, Republic of Korea.
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22
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Dargode PS, More PP, Gore SS, Asodekar BR, Sharma MB, Lali AM. Microbial consortia adaptation to substrate changes in anaerobic digestion. Prep Biochem Biotechnol 2021; 52:924-936. [PMID: 34895061 DOI: 10.1080/10826068.2021.2009859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Renewable natural gas (RNG) produced from anaerobic digestion (AD) of agricultural residues is emerging a serious biofuel alternative. Complex nature of lignocellulosic biomass residues coupled with complex biochemical transformations involving a large spectrum of microbial communities make anaerobic digestion of biomass difficult to understand and control. The present work aims at studying adaptation of microbial consortia in AD to substrates changes and correlating these to biogas generation. The double edged study deals with (a) using a common starting culture inoculum on different fractions of pretreated lignocellulosic biomass (LBM) fractions; and (b) using different starter inocula for gas generation from simple glucose substrate. Taxonomic analysis using 16S amplicon sequencing is shown to highlight changes in microbial community structure and predominance, majorly in hydrolytic bacterial populations. Observed variations in the rate of digestion with different starter inocula could be related to differences in microbial community structure and relative abundance. Results with different treated biomass fractions as substrates indicated that AD performance could be related to abundance of substrate-specific microbial communities. The work is a step to a deeper understanding of AD processes that may lead to better control and operation of AD for super-scale production of RNG from biomass feedstocks.
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Affiliation(s)
- Priyanka S Dargode
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology (Formerly UDCT), Mumbai, India
| | - Pooja P More
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology (Formerly UDCT), Mumbai, India
| | - Suhas S Gore
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology (Formerly UDCT), Mumbai, India
| | - Bhupal R Asodekar
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology (Formerly UDCT), Mumbai, India
| | - Manju B Sharma
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology (Formerly UDCT), Mumbai, India
| | - Arvind M Lali
- Institute of Chemical Technology (Formerly UDCT), Mumbai, India
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Wijeyekoon SLJ, Vaidya AA. Woody biomass as a potential feedstock for fermentative gaseous biofuel production. World J Microbiol Biotechnol 2021; 37:134. [PMID: 34258684 DOI: 10.1007/s11274-021-03102-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/01/2021] [Indexed: 01/22/2023]
Abstract
Biogas and biohydrogen are compatible gaseous biofuels that can be blended with natural gas for reticulated fuel supply to reduce greenhouse gas emissions. Sustainably grown woody biomass is emerging as a potential feedstock in the production of biofuels. Woody biomass is widely available, uses non-arable land for plantation, does not require synthetic fertilisers to grow and acts as a carbon sink. The cellulose and hemicellulose fractions of wood are renewable sources of sugars that can be used for fermentative production of gaseous biofuels. However, widespread use of wood as a gaseous biofuel feedstock is constrained due to the recalcitrant nature of wood to enzymatic hydrolysis. Pretreatment makes cellulose and hemicellulose accessible to microbial enzymes to produce fermentable sugars. Here we review wood composition, its structure and different pretreatment techniques in the context of their effects on deconstruction of wood to improve hydrolysis and fermentative gaseous fuel production. The anaerobic digestion of pretreated wood for biogas and dark fermentation for biohydrogen production are discussed with reference to gas yields. Key advancements in lab-scale research are described for pretreatments and for pure, co- and mixed culture fermentations. Limitations to yield improvements are identified and future perspectives and prospects of gaseous biofuel production from woody biomass are discussed, with reference to new developments in engineered biocatalysts and process integration.
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Affiliation(s)
| | - Alankar A Vaidya
- Scion, Te Papa Tipu Innovation Park, 49 Sala Street, Rotorua, 3046, New Zealand.
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Ling Z, Thakur N, El-Dalatony MM, Salama ES, Li X. Protein biomethanation: insight into the microbial nexus. Trends Microbiol 2021; 30:69-78. [PMID: 34215486 DOI: 10.1016/j.tim.2021.06.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 06/08/2021] [Accepted: 06/08/2021] [Indexed: 01/01/2023]
Abstract
Biomethanation of carbohydrates (e.g., lignocellulosic biomass) and lipids (e.g., waste oils) has been well studied. However, investigations on the biomethanation of protein-rich biowastes (PRBs) and associated microbial communities have not been reported. This review summarizes the challenges in the metabolic process of anaerobic digestion of PRBs and the microbial instability associated with it. We discuss the diversity of bacterial and archaeal communities via metagenomics under PRB mono- and codigestion. A stable community structure with enhanced metabolic activity is a core factor in PRB biomethanation. The application of strategies such as codigestion of PRBs with carbon-rich biomass and microbial stimulation/augmentation would make PRB biomethanation more feasible.
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Affiliation(s)
- Zhenmin Ling
- MOE, Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou University, Lanzhou 730000, Gansu Province, PR China
| | - Nandini Thakur
- MOE, Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou University, Lanzhou 730000, Gansu Province, PR China; Department of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou 730000, Gansu Province, PR China
| | - Marwa M El-Dalatony
- MOE, Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou University, Lanzhou 730000, Gansu Province, PR China
| | - El-Sayed Salama
- Department of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou 730000, Gansu Province, PR China.
| | - Xiangkai Li
- MOE, Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou University, Lanzhou 730000, Gansu Province, PR China.
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25
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Liu C, Xiao J, Li H, Chen Q, Sun D, Cheng X, Li P, Dang Y, Smith JA, Holmes DE. High efficiency in-situ biogas upgrading in a bioelectrochemical system with low energy input. WATER RESEARCH 2021; 197:117055. [PMID: 33789202 DOI: 10.1016/j.watres.2021.117055] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/23/2021] [Accepted: 03/14/2021] [Indexed: 06/12/2023]
Abstract
Biogas produced from anaerobic digestion usually contains 30%-50% CO2, much of which must be removed, before utilization. Bioelectrochemical biogas upgrading approaches show promise, however, they have not yet been optimized for practical applications. In this study, a bioelectrochemical system with low energy input (applied cathode potential of -0.5 V vs. standard hydrogen electrode, SHE) was used for in-situ biogas upgrading. High efficiency CO2 conversion (318.5 mol/d/m2) was achieved when the system was operated with an organic load of 1.7 kgCOD/(m3 d). Methane content in the upgraded biogas was 97.0% and CO2 concentrations stayed below 3%, which is comparable to biogas upgraded with more expensive and less sustainable physiochemical approaches. The high efficiency of this approach could likely be attributed to a significant enrichment of Methanothrix (92.7%) species on the cathode surface that were expressing genes involved in both acetogenic methanogenesis and direct electron transfer (DET). Electromethanogenesis by these organisms also increased proton consumption and created a higher pH that increased the solubility of CO2 in the bioreactor. In addition, CO2 removal from the biogas was likely further enhanced by an enrichment of Actinobacillus species known to be capable of CO2 fixation. Artificial neural network (ANN) models were also used to estimate CH4 production under different loading conditions. The ANN architecture with 10 neurons at hidden layers fit best with a mean square error of 6.06 × 10-3 and R2 of 0.99.
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Affiliation(s)
- Chuanqi Liu
- Beijing Key Laboratory for Source Control Technology of Water Pollution, Engineering Research Center for Water Pollution Source Control and Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, 35 Tsinghua East Road, Beijing, 100083, China
| | - Jiewen Xiao
- Beijing Key Laboratory for Source Control Technology of Water Pollution, Engineering Research Center for Water Pollution Source Control and Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, 35 Tsinghua East Road, Beijing, 100083, China
| | - Haoyong Li
- Beijing Key Laboratory for Source Control Technology of Water Pollution, Engineering Research Center for Water Pollution Source Control and Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, 35 Tsinghua East Road, Beijing, 100083, China
| | - Qian Chen
- Beijing Key Laboratory for Source Control Technology of Water Pollution, Engineering Research Center for Water Pollution Source Control and Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, 35 Tsinghua East Road, Beijing, 100083, China
| | - Dezhi Sun
- Beijing Key Laboratory for Source Control Technology of Water Pollution, Engineering Research Center for Water Pollution Source Control and Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, 35 Tsinghua East Road, Beijing, 100083, China
| | - Xiang Cheng
- Beijing Key Laboratory for Source Control Technology of Water Pollution, Engineering Research Center for Water Pollution Source Control and Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, 35 Tsinghua East Road, Beijing, 100083, China
| | - Pengsong Li
- Beijing Key Laboratory for Source Control Technology of Water Pollution, Engineering Research Center for Water Pollution Source Control and Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, 35 Tsinghua East Road, Beijing, 100083, China
| | - Yan Dang
- Beijing Key Laboratory for Source Control Technology of Water Pollution, Engineering Research Center for Water Pollution Source Control and Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, 35 Tsinghua East Road, Beijing, 100083, China.
| | - Jessica A Smith
- Department of Biomolecular Sciences, Central Connecticut State University, 1615 Stanley Street, New Britain, CR 06050, USA
| | - Dawn E Holmes
- Department of Physical and Biological Sciences, Western New England University, 1215 Wilbraham Rd, Springfield, MA 01119, USA
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Lv L, Feng C, Li W, Zhang G, Wang P, Ren Z. Exogenous N-acyl-homoserine lactones promote the degradation of refractory organics in oligotrophic anaerobic granular sludge. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 761:143289. [PMID: 33187711 DOI: 10.1016/j.scitotenv.2020.143289] [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: 08/16/2020] [Revised: 10/21/2020] [Accepted: 10/21/2020] [Indexed: 06/11/2023]
Abstract
For refractory industrial wastewaters, anaerobic granular sludge technology cannot be widely used because of its limited treatment capacity, so strengthening the anaerobic degradation of refractory organics should be discussed. In this paper, the feasibility of adding exogenous N-acyl-homoserine lactones (AHLs) to promote the degradation of refractory organics in oligotrophic anaerobic granular sludge was addressed. The results showed that, after easily-degradable organics were completely metabolized, exogenous AHLs strengthened the further degradation of refractory organics and improved the methanogenic activity of anaerobic granular sludge. In addition, adding AHLs could promote the secretion of more extracellular polysaccharides and proteins by anaerobic microorganisms to resist the oligotrophic environment. Microbiological analysis showed that adding AHLs significantly optimized the microbial community in oligotrophic anaerobic granular sludge. With the regulation of AHLs, the abundance proportion of hydrolytic acidifying bacteria for refractory organics in bacterial community and the abundance proportion of acetotrophic methanogens in methanogens community increased obviously. Exogenous AHLs showed concentration-related effects on the optimization of bacteria and methanogens, and AHLs of higher concentration were beneficial to the succession of community structure in a better direction. Exogenous regulation of AHLs-mediated QS provided an attractive strategy for enhancing the anaerobic degradation of refractory organics, and proposed a technical idea for the application of anaerobic granular sludge technology in refractory industrial wastewaters.
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Affiliation(s)
- Longyi Lv
- Tianjin Key Laboratory of Clean Energy and Pollution Control, School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin 300401, PR China
| | - Chendi Feng
- Tianjin Key Laboratory of Clean Energy and Pollution Control, School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin 300401, PR China
| | - Weiguang Li
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology (SKLUWRE, HIT), Harbin 150090, PR China
| | - Guangming Zhang
- Tianjin Key Laboratory of Clean Energy and Pollution Control, School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin 300401, PR China
| | - Pengfei Wang
- Tianjin Key Laboratory of Clean Energy and Pollution Control, School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin 300401, PR China
| | - Zhijun Ren
- Tianjin Key Laboratory of Clean Energy and Pollution Control, School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin 300401, PR China.
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Cabello-Yeves PJ, Callieri C, Picazo A, Mehrshad M, Haro-Moreno JM, Roda-Garcia JJ, Dzhembekova N, Slabakova V, Slabakova N, Moncheva S, Rodriguez-Valera F. The microbiome of the Black Sea water column analyzed by shotgun and genome centric metagenomics. ENVIRONMENTAL MICROBIOME 2021; 16:5. [PMID: 33902743 PMCID: PMC8067304 DOI: 10.1186/s40793-021-00374-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 02/18/2021] [Indexed: 05/03/2023]
Abstract
BACKGROUND The Black Sea is the largest brackish water body in the world, although it is connected to the Mediterranean Sea and presents an upper water layer similar to some regions of the former, albeit with lower salinity and temperature. Despite its well-known hydrology and physicochemical features, this enormous water mass remains poorly studied at the microbial genomics level. RESULTS We have sampled its different water masses and analyzed the microbiome by shotgun and genome-resolved metagenomics, generating a large number of metagenome-assembled genomes (MAGs) from them. We found various similarities with previously described Black Sea metagenomic datasets, that show remarkable stability in its microbiome. Our datasets are also comparable to other marine anoxic water columns like the Cariaco Basin. The oxic zone resembles to standard marine (e.g. Mediterranean) photic zones, with Cyanobacteria (Synechococcus but a conspicuously absent Prochlorococcus), and photoheterotrophs domination (largely again with marine relatives). The chemocline presents very different characteristics from the oxic surface with many examples of chemolithotrophic metabolism (Thioglobus) and facultatively anaerobic microbes. The euxinic anaerobic zone presents, as expected, features in common with the bottom of meromictic lakes with a massive dominance of sulfate reduction as energy-generating metabolism, a few (but detectable) methanogenesis marker genes, and a large number of "dark matter" streamlined genomes of largely unpredictable ecology. CONCLUSIONS The Black Sea oxic zone presents many similarities to the global ocean while the redoxcline and euxinic water masses have similarities to other similar aquatic environments of marine (Cariaco Basin or other Black Sea regions) or freshwater (meromictic monimolimnion strata) origin. The MAG collection represents very well the different types of metabolisms expected in this kind of environment. We are adding critical information about this unique and important ecosystem and its microbiome.
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Affiliation(s)
- Pedro J Cabello-Yeves
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel, Hernández, San Juan de Alicante, Alicante, Spain
| | - Cristiana Callieri
- National Research Council (CNR), Institute of Water Research (IRSA), Verbania, Italy
| | - Antonio Picazo
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, E-46980, Paterna, Valencia, Spain
| | - Maliheh Mehrshad
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Lennart Hjelms väg 9, 75651, Uppsala, Sweden
| | - Jose M Haro-Moreno
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel, Hernández, San Juan de Alicante, Alicante, Spain
| | - Juan J Roda-Garcia
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel, Hernández, San Juan de Alicante, Alicante, Spain
| | - Nina Dzhembekova
- Institute of Oceanology "Fridtjof Nansen" - Bulgarian Academy of Sciences, Varna, Bulgaria
| | - Violeta Slabakova
- Institute of Oceanology "Fridtjof Nansen" - Bulgarian Academy of Sciences, Varna, Bulgaria
| | - Nataliya Slabakova
- Institute of Oceanology "Fridtjof Nansen" - Bulgarian Academy of Sciences, Varna, Bulgaria
| | - Snejana Moncheva
- Institute of Oceanology "Fridtjof Nansen" - Bulgarian Academy of Sciences, Varna, Bulgaria
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel, Hernández, San Juan de Alicante, Alicante, Spain.
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia.
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Nordell E, Moestedt J, Österman J, Shakeri Yekta S, Björn A, Sun L, Schnürer A. Post-treatment of dewatered digested sewage sludge by thermophilic high-solid digestion for pasteurization with positive energy output. WASTE MANAGEMENT (NEW YORK, N.Y.) 2021; 119:11-21. [PMID: 33032154 DOI: 10.1016/j.wasman.2020.09.028] [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: 05/14/2020] [Revised: 08/12/2020] [Accepted: 09/17/2020] [Indexed: 06/11/2023]
Abstract
This study investigated the possibility to use thermophilic anaerobic high solid digestion of dewatered digested sewage sludge (DDS) at a wastewater treatment plant (WWTP) as a measure to increase total methane yield, achieve pasteurization and reduce risk for methane emissions during storage of the digestate. A pilot-scale plug-flow reactor was used to mimic thermophilic post-treatment of DDS from a WWTP in Linköping, Sweden. Process operation was evaluated with respect to biogas process performance, using both chemical and microbiological parameters. Initially, the process showed disturbance, with low methane yields and high volatile fatty acid (VFA) accumulation. However, after initiation of digestate recirculation performance improved and the specific methane production reached 46 mL CH4/g VS. Plug flow conditions were assessed with lithium chloride and the hydraulic retention time (HRT) was determined to be 19-29 days, sufficient to reach successful pasteurization. Degradation rate of raw protein was high and resulted in ammonia-nitrogen levels of up to 2.0 g/L and a 30% lower protein content in the digestate as compared to DDS. Microbial analysis suggested a shift in the methane producing pathway, with dominance of syntrophic acetate oxidation and the candidate methanogen family WSA2 by the end of the experiment. Energy balance calculations based on annual DDS production of 10000 ton/year showed that introduction of high-solid digestion as a post-treatment and pasteurization method would result in a positive energy output of 340 MWh/year. Post-digestion of DDS also decreased residual methane potential (RMP) by>96% compared with fresh DDS.
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Affiliation(s)
- E Nordell
- Tekniska verken i Linköping AB, Department of Biogas R&D, Box 1500, SE-581 15 Linköping, Sweden; Biogas Research Center, Linköping University, SE-581 83 Linköping, Sweden.
| | - J Moestedt
- Tekniska verken i Linköping AB, Department of Biogas R&D, Box 1500, SE-581 15 Linköping, Sweden; Biogas Research Center, Linköping University, SE-581 83 Linköping, Sweden; Department of Thematic Studies Environmental Change, Linköping University, SE-581 83 Linköping, Sweden
| | - J Österman
- Tekniska verken i Linköping AB, Department of Biogas R&D, Box 1500, SE-581 15 Linköping, Sweden
| | - S Shakeri Yekta
- Biogas Research Center, Linköping University, SE-581 83 Linköping, Sweden; Department of Thematic Studies Environmental Change, Linköping University, SE-581 83 Linköping, Sweden
| | - A Björn
- Biogas Research Center, Linköping University, SE-581 83 Linköping, Sweden; Department of Thematic Studies Environmental Change, Linköping University, SE-581 83 Linköping, Sweden
| | - L Sun
- Department of Molecular Sciences, Biocenter, Swedish University of Agricultural Sciences, Uppsala, Box 7015, SE-750 07 Uppsala, Sweden
| | - A Schnürer
- Biogas Research Center, Linköping University, SE-581 83 Linköping, Sweden; Department of Thematic Studies Environmental Change, Linköping University, SE-581 83 Linköping, Sweden; Department of Molecular Sciences, Biocenter, Swedish University of Agricultural Sciences, Uppsala, Box 7015, SE-750 07 Uppsala, Sweden.
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Mutschlechner M, Praeg N, Illmer P. Soil-Derived Inocula Enhance Methane Production and Counteract Common Process Failures During Anaerobic Digestion. Front Microbiol 2020; 11:572759. [PMID: 33193175 PMCID: PMC7606279 DOI: 10.3389/fmicb.2020.572759] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/14/2020] [Indexed: 02/01/2023] Open
Abstract
Although soil-borne methanogens are known to be highly diverse and adapted to extreme environments, their application as potential (anaerobic) inocula to improve anaerobic digestion has not been investigated until now. The present study aimed at evaluating if soil-derived communities can be beneficial for biogas (methane, CH4) production and endure unfavorable conditions commonly associated with digestion failure. Nine study sites were chosen and tested for suitability as inoculation sources to improve biogas production via in situ measurements (CH4 fluxes, physical and chemical soil properties, and abundance of methanogens) and during a series of anaerobic digestions with (a) combinations of both sterile or unsterile soil and diluted fermenter sludge, and (b) pH-, acetate-, propionate-, and ammonium-induced disturbance. Amplicon sequencing was performed to assess key microbial communities pivotal for successful biogas production. Four out of nine tested soil inocula exerted sufficient methanogenic activity and repeatedly allowed satisfactory CH4/biogas production even under deteriorated conditions. Remarkably, the significantly highest CH4 production was observed using unsterile soil combined with sterile sludge, which coincided with both a higher relative abundance of methanogens and predicted genes involved in CH4 metabolism in these variants. Different bacterial and archaeal community patterns depending on the soil/sludge combinations and disturbance variations were established and these patterns significantly impacted CH4 production. Methanosarcina spp. seemed to play a key role in CH4 formation and prevailed even under stressed conditions. Overall, the results provided evidence that soil-borne methanogens can be effective in enhancing digestion performance and stability and, thus, harbor vast potential for further exploitation.
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Affiliation(s)
| | - Nadine Praeg
- Department of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | - Paul Illmer
- Department of Microbiology, Universität Innsbruck, Innsbruck, Austria
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Beraud-Martínez LK, Gómez-Gil B, Franco-Nava MÁ, Almazán-Rueda P, Betancourt-Lozano M. A metagenomic assessment of microbial communities in anaerobic bioreactors and sediments: Taxonomic and functional relationships. Anaerobe 2020; 68:102296. [PMID: 33207267 DOI: 10.1016/j.anaerobe.2020.102296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 10/20/2020] [Accepted: 11/11/2020] [Indexed: 02/04/2023]
Abstract
The present study used metagenomic sequencing, metagenome assembly and physical-chemical analysis to describe taxonomically and functionally 3 anaerobic bioreactors treating manure (LI), brewery (BR) and cornmeal (CO) wastes, and an anaerobic estuarine sediment (ES). Proteobacteria, Firmicutes, Euryarchaeota and Bacteroidetes were the most abundant Phyla in all metagenomes. A bacteria/archaea ratio of 3.4 was found in the industrial full-scale anaerobic bioreactors BR and CO, while ratios greater than 10 were found for LI and ES. Canonical correspondence analysis showed that environmental variables such as chemical oxygen demand, lipid content, and ammonium nitrogen influenced the ordination of taxonomic groups. Mesotoga prima was linked to high-temperature conditions, particularly in the BR bioreactor, along with the presence of heat shock proteins genes. Likewise, the hydrogenotrophic methanogen, Methanoregula formicica, was associated with high ammonium concentration in LI bioreactor. The interactions of microbes with specific methanogenic pathways were identified using Clusters of Orthologous Groups (COG) functions, while metagenome-assembled genomes (MAGs) further confirmed relationships between taxa and functions. Our results provide valuable information to understand microbial processes in anaerobic environments.
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Affiliation(s)
- Liov Karel Beraud-Martínez
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A. C. Unit for Aquaculture, Avenida Sábalo-Cerritos SS/n, Mazatlán, Sinaloa, 82112, Mexico
| | - Bruno Gómez-Gil
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A. C. Unit for Aquaculture, Avenida Sábalo-Cerritos SS/n, Mazatlán, Sinaloa, 82112, Mexico
| | - Miguel Ángel Franco-Nava
- Tecnológico Nacional de México, Campus Mazatlán. Calle Corsario 1 No. 203 Col. Urías, A.P. 757, Mazatlán, Sinaloa, 82070, Mexico
| | - Pablo Almazán-Rueda
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A. C. Unit for Aquaculture, Avenida Sábalo-Cerritos SS/n, Mazatlán, Sinaloa, 82112, Mexico
| | - Miguel Betancourt-Lozano
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A. C. Unit for Aquaculture, Avenida Sábalo-Cerritos SS/n, Mazatlán, Sinaloa, 82112, Mexico.
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Liu T, Schnürer A, Björkmalm J, Willquist K, Kreuger E. Diversity and Abundance of Microbial Communities in UASB Reactors during Methane Production from Hydrolyzed Wheat Straw and Lucerne. Microorganisms 2020; 8:E1394. [PMID: 32932830 PMCID: PMC7565072 DOI: 10.3390/microorganisms8091394] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 09/04/2020] [Accepted: 09/09/2020] [Indexed: 01/04/2023] Open
Abstract
The use of straw for biofuel production is encouraged by the European Union. A previous study showed the feasibility of producing biomethane in upflow anaerobic sludge blanket (UASB) reactors using hydrolyzed, steam-pretreated wheat straw, before and after dark fermentation with Caldicellulosiruptor saccharolyticus, and lucerne. This study provides information on overall microbial community development in those UASB processes and changes related to acidification. The bacterial and archaeal community in granular samples was analyzed using high-throughput amplicon sequencing. Anaerobic digestion model no. 1 (ADM1) was used to predict the abundance of microbial functional groups. The sequencing results showed decreased richness and diversity in the microbial community, and decreased relative abundance of bacteria in relation to archaea, after process acidification. Canonical correspondence analysis showed significant negative correlations between the concentration of organic acids and three phyla, and positive correlations with seven phyla. Organic loading rate and total COD fed also showed significant correlations with microbial community structure, which changed over time. ADM1 predicted a decrease in acetate degraders after a decrease to pH ≤ 6.5. Acidification had a sustained effect on the microbial community and process performance.
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Affiliation(s)
- Tong Liu
- Department of Molecular Science, Swedish University of Agricultural Science, Uppsala BioCenter, 750 07 Uppsala, Sweden;
| | - Anna Schnürer
- Department of Molecular Science, Swedish University of Agricultural Science, Uppsala BioCenter, 750 07 Uppsala, Sweden;
| | - Johanna Björkmalm
- RISE, Forskningsbyn Ideon Scheelevägen 27, 223 70 Lund, Sweden; (J.B.); (K.W.)
| | - Karin Willquist
- RISE, Forskningsbyn Ideon Scheelevägen 27, 223 70 Lund, Sweden; (J.B.); (K.W.)
| | - Emma Kreuger
- Division of Biotechnology, Department of Chemistry, Lund University, P.O. Box 118, 221 00 Lund, Sweden
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32
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Savvichev AS, Kadnikov VV, Rusanov II, Beletsky AV, Krasnova ED, Voronov DA, Kallistova AY, Veslopolova EF, Zakharova EE, Kokryatskaya NM, Losyuk GN, Demidenko NA, Belyaev NA, Sigalevich PA, Mardanov AV, Ravin NV, Pimenov NV. Microbial Processes and Microbial Communities in the Water Column of the Polar Meromictic Lake Bol'shie Khruslomeny at the White Sea Coast. Front Microbiol 2020; 11:1945. [PMID: 32849486 PMCID: PMC7432294 DOI: 10.3389/fmicb.2020.01945] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 07/23/2020] [Indexed: 11/13/2022] Open
Abstract
Microbiological, molecular ecological, biogeochemical, and isotope geochemical research was carried out at the polar Lake Bol'shie Khruslomeny at the coast of the Kandalaksha Bay, White Sea in March and September 2017. The uppermost mixolimnion was oxic, with low salinity (3-5%). The lower chemocline layer was brown-green colored, with very high content of particulate organic matter (up to 11.8 mg C L-1). The lowermost monimolimnion had marine salinity (22-24%) and very high concentrations of sulfide (up to 18 mmol L-1) and CH4 (up to 1.8 mmol L-1). In the chemocline, total microbial abundance and the rate of anoxygenic photosynthesis were 8.8 × 106 cells mL-1 and 34.4 μmol C L-1 day-1, respectively. Both in March and September, sulfate reduction rate increased with depth, peaking (up to 0.6-1.1 μmol S L-1 day-1) in the lower chemocline. Methane oxidation rates in the chemocline were up to 85 and 180 nmol CH4 L-1 day-1 in March and September, respectively; stimulation of this process by light was observed in September. The percentages of cyanobacteria and methanotrophs in the layer where light-induced methane oxidation occurred were similar, ∼2.5% of the microbial community. Light did not stimulate methane oxidation in deeper layers. The carbon isotope composition of particulate organic matter (δ13C-Corg), dissolved carbonates (δ13C-DIC), and methane (δ13C- CH4) indicated high microbial activity in the chemocline. Analysis of the 16S rRNA gene sequences revealed predominance of Cyanobium cyanobacteria (order Synechococcales) in the mixolimnion. Green sulfur bacteria Chlorobium phaeovibrioides capable of anoxygenic photosynthesis constituted ∼20% of the chemocline community both in March and in September. Methyloprofundus gammaptoteobacteria (family Methylomonaceae) were present in the upper chemocline, where active methane oxidation occurred. During winter, cyanobacteria were less abundant in the chemocline, while methanotrophs occurred in higher horizons, including the under-ice layer. Chemolithotrophic gammaproteobacteria of the genus Thiomicrorhabdus, oxidizing reduced sulfur compounds at low oxygen concentrations, were revealed in the chemocline in March. Both in March and September archaea constituted up to 50% of all microorganisms in the hypolimnion. The percentage of putative methanogens in the archaeal community was low, and they occurred mainly in near-bottom horizons.
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Affiliation(s)
- Alexander S. Savvichev
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Vitaly V. Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Igor I. Rusanov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Alexey V. Beletsky
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Elena D. Krasnova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Dmitry A. Voronov
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Anna Yu. Kallistova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Elena F. Veslopolova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Elena E. Zakharova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Nataliya M. Kokryatskaya
- N. Laverov Federal Center for Integrated Arctic Research, Ural Branch, Russian Academy of Sciences, Moscow, Russia
| | - Galina N. Losyuk
- N. Laverov Federal Center for Integrated Arctic Research, Ural Branch, Russian Academy of Sciences, Moscow, Russia
| | | | - Nikolai A. Belyaev
- Shirshov Institute of Oceanology, Russian Academy of Sciences, Moscow, Russia
| | - Pavel A. Sigalevich
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Andrey V. Mardanov
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Nikolai V. Ravin
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Nikolay V. Pimenov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
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Lam TYC, Mei R, Wu Z, Lee PKH, Liu WT, Lee PH. Superior resolution characterisation of microbial diversity in anaerobic digesters using full-length 16S rRNA gene amplicon sequencing. WATER RESEARCH 2020; 178:115815. [PMID: 32380296 DOI: 10.1016/j.watres.2020.115815] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 03/18/2020] [Accepted: 04/08/2020] [Indexed: 05/24/2023]
Abstract
In the past decade, the characterisation of the microbial community in anaerobic digestion was primarily done by using high-throughput short-read amplicon sequencing. However, the short-read approach has inherent primer bias and low phylogenetic resolution. Our previous study using Illumina MiSeq suggested that the heterogeneity of AD microbiome was operation-driven. To advance our knowledge towards the complexity of the AD microbiome, we performed full-length 16S rRNA gene amplicon sequencing using PacBio Sequel for a more accurate phylogenetic identification. To this end, purified DNA samples from 19 global anaerobic digesters were sequenced. Sixteen methanogenic archaea were identified at the species level. Among them, Methanosarcina horonobensis and Methanosarcina flavescens had significant presence under specific operating conditions. Methanothrix concilii presented in all digesters sequenced. Unexpectedly, over 90% of the Smithella detected were closely related to alkane-degrading Smithella strains D17 and M82, not Smithella propionica. Using LEfSe and network analysis, the interspecies relationship between the fermentative and syntrophic bacteria was addressed. Comparison of the short- and long-read sequencing results were performed and discussed. From sample preparation to data analysis, this work characterised the digester microbiomes in a superior resolution.
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Affiliation(s)
- Theo Y C Lam
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong.
| | - Ran Mei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Zhuoying Wu
- Department of Civil and Environmental Engineering, Imperial College London, London, SW7 2AZ, UK
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Po-Heng Lee
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong; Department of Civil and Environmental Engineering, Imperial College London, London, SW7 2AZ, UK.
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Ghanbari Maman L, Palizban F, Fallah Atanaki F, Elmi Ghiasi N, Ariaeenejad S, Ghaffari MR, Hosseini Salekdeh G, Kavousi K. Co-abundance analysis reveals hidden players associated with high methane yield phenotype in sheep rumen microbiome. Sci Rep 2020; 10:4995. [PMID: 32193482 PMCID: PMC7081230 DOI: 10.1038/s41598-020-61942-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 03/05/2020] [Indexed: 12/28/2022] Open
Abstract
Rumen microbial environment hosts a variety of microorganisms that interact with each other to carry out the feed digestion and generation of several by-products especially methane, which plays an essential role in global warming as a greenhouse gas. However, due to its multi-factorial nature, the exact cause of methane production in the rumen has not yet been fully determined. The current study is an attempt to use system modeling to analyze the relationship between interacting components of rumen microbiome and its role in methane production. Metagenomic data of sheep rumen, with equal numbers of high methane yield (HMY) and low methane yield (LMY) samples, were used. As a well-known approach for the systematic comparative study of complex traits, the co-abundance networks were constructed in both operational taxonomic unit (OTU) and gene levels. A gene-catalog of 1,444 different rumen microbial strains was developed as a reference to measure gene abundances. The results from both types of co-abundance networks showed that methanogens, which are the main ruminal source for methanogenesis, need other microbial species to accomplish the task of methane production through producing the main precursor molecules like H2 and acetate for methanogenesis pathway as their byproducts. KEGG Orthology(KO) analysis of the current study shows that the metabolism and growth rate of methanogens will be increased due to the higher rate of the metabolism and carbohydrate/fiber digestion pathways in the hidden elements. This finding proposes that any ruminant methane yield alteration strategy should consider complex interactions of rumen microbiome components as one tightly integrated unit rather than several separate parts.
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Affiliation(s)
- Leila Ghanbari Maman
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Fahimeh Palizban
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Fereshteh Fallah Atanaki
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Naser Elmi Ghiasi
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Shohreh Ariaeenejad
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Mohammad Reza Ghaffari
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Ghasem Hosseini Salekdeh
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran.
| | - Kaveh Kavousi
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran.
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35
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Li Y, Liu Y, Yong X, Wu X, Jia H, Wong JWC, Wu H, Zhou J. Odor emission and microbial community succession during biogas residue composting covered with a molecular membrane. BIORESOURCE TECHNOLOGY 2020; 297:122518. [PMID: 31812915 DOI: 10.1016/j.biortech.2019.122518] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/26/2019] [Accepted: 11/27/2019] [Indexed: 06/10/2023]
Abstract
A membrane-covered composting system was used to investigate the odor emission and microbial community succession during biogas residue composting. Results showed that in comparison with the control (CK) group, the NH3 and H2S emissions outside the membrane of the membrane-covered (CT) group decreased by 58.64% and 38.13%, respectively. The nitrogen preservation rate of the CT group was increased by 17.27% in comparison with the CK group. Moreover, the ammonium nitrogen and nitrate nitrogen contents of the CT group were 37.68% and 11.77% higher than those of the CK group, respectively. Microbial analysis showed that the average abundance and co-occurrence rate of ammonification bacteria dominated by Pseudomonas and Bacillus in the CT group were lower than those in the CK group, and the abundance of anaerobic sulfate-reducing bacteria (SRB) dominated by Desulfovibrio in the CT group was higher than that in the CK group.
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Affiliation(s)
- Yinchao Li
- Bioenergy Research Institute, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu 211816, China
| | - Yongdi Liu
- Bioenergy Research Institute, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu 211816, China
| | - Xiaoyu Yong
- Bioenergy Research Institute, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu 211816, China
| | - Xiayuan Wu
- Bioenergy Research Institute, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu 211816, China
| | - Honghua Jia
- Bioenergy Research Institute, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu 211816, China
| | - Jonathan W C Wong
- Institute of Bioresource and Agriculture, Hong Kong Baptist University, Hong Kong Special Administrative Region
| | - Hao Wu
- Bioenergy Research Institute, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu 211816, China
| | - Jun Zhou
- Bioenergy Research Institute, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu 211816, China.
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36
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Bi S, Westerholm M, Qiao W, Xiong L, Mahdy A, Yin D, Song Y, Dong R. Metabolic performance of anaerobic digestion of chicken manure under wet, high solid, and dry conditions. BIORESOURCE TECHNOLOGY 2020; 296:122342. [PMID: 31711908 DOI: 10.1016/j.biortech.2019.122342] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 10/22/2019] [Accepted: 10/24/2019] [Indexed: 06/10/2023]
Abstract
The anaerobic digestion (AD) of chicken manure as a solo substrate has been challenging due to the ammonium inhibition effects when adopting a high organic loading rate (OLR). In this study, through increasing both the total solid in the feeding materials from 5% to 20%, and the OLR from 1.7 to 7.1 g-volatile solids (VS)/(L·d), the AD of chicken manure under wet, high solid, and dry conditions, with a fixed hydraulic retention time of 20 days, was investigated. The results obtained indicated that the wet AD system could achieve a methane yield of 0.28 L/g-VS and a low volatile fatty acid level. However, the process deteriorated under dry conditions, and methane formed mainly through acetate oxidation and methanogenesis. Methanosarcina and Methanoplasma were found to be more tolerant But, whether the dry AD of chicken manure can survive an ammonia-stressed environment when the OLR is lowered, still needs investigation.
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Affiliation(s)
- Shaojie Bi
- College of Engineering, China Agricultural University, Beijing 100083, China; State R & D Center for Efficient Production and Comprehensive Utilization of Biobased Gaseous Fuels, Energy Authority, National Development, and Reform Committee (BGFuels), Beijing 100083, China
| | - Maria Westerholm
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala BioCenter, Box 7025, SE-750 07 Uppsala, Sweden
| | - Wei Qiao
- College of Engineering, China Agricultural University, Beijing 100083, China; State R & D Center for Efficient Production and Comprehensive Utilization of Biobased Gaseous Fuels, Energy Authority, National Development, and Reform Committee (BGFuels), Beijing 100083, China.
| | - Linpeng Xiong
- College of Engineering, China Agricultural University, Beijing 100083, China; State R & D Center for Efficient Production and Comprehensive Utilization of Biobased Gaseous Fuels, Energy Authority, National Development, and Reform Committee (BGFuels), Beijing 100083, China
| | - Ahmed Mahdy
- Department of Agricultural Microbiology, Zagazig University, 44511 Zagazig, Egypt
| | - Dongmin Yin
- College of Engineering, China Agricultural University, Beijing 100083, China; State R & D Center for Efficient Production and Comprehensive Utilization of Biobased Gaseous Fuels, Energy Authority, National Development, and Reform Committee (BGFuels), Beijing 100083, China
| | - Yunlong Song
- College of Engineering, China Agricultural University, Beijing 100083, China; State R & D Center for Efficient Production and Comprehensive Utilization of Biobased Gaseous Fuels, Energy Authority, National Development, and Reform Committee (BGFuels), Beijing 100083, China
| | - Renjie Dong
- College of Engineering, China Agricultural University, Beijing 100083, China; State R & D Center for Efficient Production and Comprehensive Utilization of Biobased Gaseous Fuels, Energy Authority, National Development, and Reform Committee (BGFuels), Beijing 100083, China
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37
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Li K, Yun J, Zhang H, Yu Z. Full-scale anaerobic reactor samples would be more suitable than lab-scale anaerobic reactor and natural samples to inoculate the wheat straw batch anaerobic digesters. BIORESOURCE TECHNOLOGY 2019; 293:122040. [PMID: 31454734 DOI: 10.1016/j.biortech.2019.122040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/15/2019] [Accepted: 08/19/2019] [Indexed: 06/10/2023]
Abstract
This study evaluated the effects of the inocula from natural wetland, lab-scale and full-scale anaerobic reactors on wheat straw anaerobic digestion. Three replicate batch reactors were constructed for each inoculum to investigate the reactor performances and microbial communities. Reactors seeded with full-scale reactor samples were started up most rapidly, achieved the highest methane production, and were recognized as the higher efficient reactors. The dominance of acetoclastic methanogens, including Methanosaeta and Methanoscrina, was crucial for the higher efficient reactors, whereas hydrogenotrophic methanogens were dominant in other reactors. Genus Treponema, which could enhance the cellulose degradation and conduct homoacetogenesis, was first reported to be dominant in the bacterial communities of high efficient reactors. Inoculum sources and process conditions were suggested to be the deterministic factors in shaping the microbial communities in the higher efficient reactors. These findings contribute to the startup of new anaerobic reactors.
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Affiliation(s)
- Ke Li
- Water Affairs Research Institute, North China University of Water Resources and Electric Power, 36 Beihuan Road, Zhengzhou 450045, China; College of Resources and Environment, University of Chinese Academy of Sciences, 19 A Yuquan Road, Beijing 100049, China
| | - Juanli Yun
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Beijing 100101, China
| | - Hongxun Zhang
- College of Resources and Environment, University of Chinese Academy of Sciences, 19 A Yuquan Road, Beijing 100049, China
| | - Zhisheng Yu
- College of Resources and Environment, University of Chinese Academy of Sciences, 19 A Yuquan Road, Beijing 100049, China.
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38
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Saha S, Jeon BH, Kurade MB, Govindwar SP, Chatterjee PK, Oh SE, Roh HS, Lee SS. Interspecies microbial nexus facilitated methanation of polysaccharidic wastes. BIORESOURCE TECHNOLOGY 2019; 289:121638. [PMID: 31212174 DOI: 10.1016/j.biortech.2019.121638] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 06/05/2019] [Accepted: 06/10/2019] [Indexed: 06/09/2023]
Abstract
Compositional variations in organic wastes influence microbial abundancy and syntrophy during anaerobic digestion (AD), impacting the normal performance of digesters for methanation. Investigation of the microbial dynamics during AD following augmentation with polysaccharidic wastes (PW) revealed the association of effective digester performance and methane yields with the microbial nexus. Dominance of the acidogenic saccharolytic genera, Prevotella, Eubacterium, and Lachnoclostridium, enhanced the utilization of carbohydrates (54%) in PW-augmented digesters. Spearman's rs correlation showed dynamic interspecies interactions among acetogenic syntrophs, and that of iron oxidizers/reducers with acetoclastic and hydrogenotrophic methanogens. Propionate oxidizers in Chloroflexi (i.e., Bellilinea, Levilinea, and Longilinea) exhibited positive associations with acetoclastic methanogens. Increase in the population of acetoclastic methanogens (Methanosaeta, 77% and Methanosarcina, 9%) accelerated the methanogenic activity of PW-augmented digesters by 7 times during the exponential phase, increasing the methane yield (75%) compared to the control. Thus, microbial syntrophy facilitated the effective methanation of PW during AD process.
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Affiliation(s)
- Shouvik Saha
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, Republic of Korea
| | - Byong-Hun Jeon
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, Republic of Korea.
| | - Mayur B Kurade
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, Republic of Korea
| | - Sanjay P Govindwar
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, Republic of Korea
| | - Pradip K Chatterjee
- Energy Research and Technology Group, CSIR Central Mechanical Engineering Research Institute, Durgapur 713-209, India
| | - Sang-Eun Oh
- Department of Biological Environment, Kangwon National University, Chuncheon, Gangwon-do 24341, Republic of Korea
| | - Hyun-Seog Roh
- Department of Environmental Engineering, Yonsei University, Wonju, Gangwon-do 26493, Republic of Korea
| | - Sean S Lee
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, Republic of Korea
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Fischer MA, Ulbricht A, Neulinger SC, Refai S, Waßmann K, Künzel S, Schmitz RA. Immediate Effects of Ammonia Shock on Transcription and Composition of a Biogas Reactor Microbiome. Front Microbiol 2019; 10:2064. [PMID: 31555248 PMCID: PMC6742706 DOI: 10.3389/fmicb.2019.02064] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 08/21/2019] [Indexed: 12/22/2022] Open
Abstract
The biotechnological process of biogas production from organic material is carried out by a diverse microbial community under anaerobic conditions. However, the complex and sensitive microbial network present in anaerobic degradation of organic material can be disturbed by increased ammonia concentration introduced into the system by protein-rich substrates and imbalanced feeding. Here, we report on a simulated increase of ammonia concentration in a fed batch lab-scale biogas reactor experiment. Two treatment conditions were used simulating total ammonia nitrogen concentrations of 4.9 and 8.0 g/L with four replicate reactors. Each reactor was monitored concerning methane generation and microbial composition using 16S rRNA gene amplicon sequencing, while the transcriptional activity of the overall process was investigated by metatranscriptomic analysis. This allowed investigating the response of the microbial community in terms of species composition and transcriptional activity to a rapid upshift to high ammonia conditions. Clostridia and Methanomicrobiales dominated the microbial community throughout the entire experiment under both experimental conditions, while Methanosarcinales were only present in minor abundance. Transcription analysis demonstrated clostridial dominance with respect to genes encoding for enzymes of the hydrolysis step (cellulase, EC 3.2.1.4) as well as dominance of key genes for enzymes of the methanogenic pathway (methyl-CoM reductase, EC 2.8.4.1; heterodisulfide reductase, EC 1.8.98.1). Upon ammonia shock, the selected marker genes showed significant changes in transcriptional activity. Cellulose hydrolysis as well as methanogenesis were significantly reduced at high ammonia concentrations as indicated by reduced transcription levels of the corresponding genes. Based on these experiments we concluded that, apart from the methanogenic archaea, hydrolytic cellulose-degrading microorganisms are negatively affected by high ammonia concentrations. Further, Acholeplasma and Erysipelotrichia showed lower abundance under increased ammonia concentrations and thus might serve as indicator species for an earlier detection in order to counteract against ammonia crises.
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Affiliation(s)
- Martin A. Fischer
- Department of Biology, Institute of General Microbiology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Andrea Ulbricht
- Department of Biology, Institute of General Microbiology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Sven C. Neulinger
- Department of Biology, Institute of General Microbiology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Sarah Refai
- Department of Biology, Institut für Mikrobiologie und Biotechnologie, University Bonn, Bonn, Germany
| | - Kati Waßmann
- Department of Biology, Institut für Mikrobiologie und Biotechnologie, University Bonn, Bonn, Germany
| | - Sven Künzel
- Department for Evolutionary Genetics, Max-Planck-Institute for Evolutionary Biology, Plön, Germany
| | - Ruth A. Schmitz
- Department of Biology, Institute of General Microbiology, Christian-Albrechts-University Kiel, Kiel, Germany
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40
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Liébana R, Modin O, Persson F, Szabó E, Hermansson M, Wilén BM. Combined Deterministic and Stochastic Processes Control Microbial Succession in Replicate Granular Biofilm Reactors. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:4912-4921. [PMID: 30969774 DOI: 10.1021/acs.est.8b06669] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Granular sludge is an efficient and compact biofilm process for wastewater treatment. However, the ecological factors involved in microbial community assembly during the granular biofilm formation are poorly understood, and little is known about the reproducibility of the process. Here, three replicate bioreactors were used to investigate microbial succession during the formation of granular biofilms. We identified three successional phases. During the initial phase, the successional turnover was high and α-diversity decreased as a result of the selection of taxa adapted to grow on acetate and form aggregates. Despite these dynamic changes, the microbial communities in the replicate reactors were similar. The second successional phase occurred when the settling time was rapidly decreased to selectively retain granules in the reactors. The influence of stochasticity on succession increased and new niches were created as granules emerged, resulting in temporarily increased α-diversity. The third successional phase occurred when the settling time was kept stable and granules dominated the biomass. Turnover was low, and selection resulted in the same abundant taxa in the reactors, but drift, which mostly affected low-abundant community members, caused the community in one reactor to diverge from the other two. Even so, performance was stable and similar between reactors.
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Affiliation(s)
- Raquel Liébana
- Division of Water Environment Technology, Department of Architecture and Civil Engineering , Chalmers University of Technology , SE-412 96 Gothenburg , Sweden
| | - Oskar Modin
- Division of Water Environment Technology, Department of Architecture and Civil Engineering , Chalmers University of Technology , SE-412 96 Gothenburg , Sweden
| | - Frank Persson
- Division of Water Environment Technology, Department of Architecture and Civil Engineering , Chalmers University of Technology , SE-412 96 Gothenburg , Sweden
| | - Enikö Szabó
- Division of Water Environment Technology, Department of Architecture and Civil Engineering , Chalmers University of Technology , SE-412 96 Gothenburg , Sweden
| | - Malte Hermansson
- Department of Chemistry and Molecular Biology , University of Gothenburg , SE405 30 Gothenburg , Sweden
| | - Britt-Marie Wilén
- Division of Water Environment Technology, Department of Architecture and Civil Engineering , Chalmers University of Technology , SE-412 96 Gothenburg , Sweden
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Wahid R, Mulat DG, Gaby JC, Horn SJ. Effects of H 2:CO 2 ratio and H 2 supply fluctuation on methane content and microbial community composition during in-situ biological biogas upgrading. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:104. [PMID: 31164923 PMCID: PMC6489297 DOI: 10.1186/s13068-019-1443-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 04/16/2019] [Indexed: 05/30/2023]
Abstract
BACKGROUND Commercial biogas upgrading facilities are expensive and consume energy. Biological biogas upgrading may serve as a low-cost approach because it can be easily integrated with existing facilities at biogas plants. The microbial communities found in anaerobic digesters typically contain hydrogenotrophic methanogens, which can use hydrogen (H2) as a reducing agent for conversion of carbon dioxide (CO2) into methane (CH4). Thus, biological biogas upgrading through the exogenous addition of H2 into biogas digesters for the conversion of CO2 into CH4 can increase CH4 yield and lower CO2 emission. RESULTS The addition of 4 mol of H2 per mol of CO2 was optimal for batch biogas reactors and increased the CH4 content of the biogas from 67 to 94%. The CO2 content of the biogas was reduced from 33 to 3% and the average residual H2 content was 3%. At molar H2:CO2 ratios > 4:1, all CO2 was converted into CH4, but the pH increased above 8 due to depletion of CO2, which negatively influenced the process stability. Additionally, high residual H2 content in these reactors was unfavourable, causing volatile fatty acid accumulation and reduced CH4 yields. The reactor microbial communities shifted in composition over time, which corresponded to changes in the reactor variables. Numerous taxa responded to the H2 inputs, and in particular the hydrogenotrophic methanogen Methanobacterium increased in abundance with addition of H2. In addition, the apparent rapid response of hydrogenotrophic methanogens to intermittent H2 feeding indicates the suitability of biological methanation for variable H2 inputs, aligning well with fluctuations in renewable electricity production that may be used to produce H2. CONCLUSIONS Our research demonstrates that the H2:CO2 ratio has a significant effect on reactor performance during in situ biological methanation. Consequently, the H2:CO2 molar ratio should be kept at 4:1 to avoid process instability. A shift toward hydrogenotrophic methanogenesis was indicated by an increase in the abundance of the obligate hydrogenotrophic methanogen Methanobacterium.
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Affiliation(s)
- Radziah Wahid
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432 Ås, Norway
| | - Daniel Girma Mulat
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432 Ås, Norway
| | - John Christian Gaby
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432 Ås, Norway
| | - Svein Jarle Horn
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432 Ås, Norway
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42
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Fischer MA, Güllert S, Refai S, Künzel S, Deppenmeier U, Streit WR, Schmitz RA. Long-term investigation of microbial community composition and transcription patterns in a biogas plant undergoing ammonia crisis. Microb Biotechnol 2019; 12:305-323. [PMID: 30381904 PMCID: PMC6390037 DOI: 10.1111/1751-7915.13313] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 08/22/2018] [Accepted: 08/24/2018] [Indexed: 02/01/2023] Open
Abstract
Ammonia caused disturbance of biogas production is one of the most frequent incidents in regular operation of biogas reactors. This study provides a detailed insight into the microbial community of a mesophilic, full-scale biogas reactor (477 kWh h-1 ) fed with maize silage, dried poultry manure and cow manure undergoing initial process disturbance by increased ammonia concentration. Over a time period of 587 days, the microbial community of the reactor was regularly monitored on a monthly basis by high-throughput amplicon sequencing of the archaeal and bacterial 16S rRNA genes. During this sampling period, the total ammonia concentrations varied between 2.7 and 5.8 g l-1 [NH4 + -N]. To gain further inside into the active metabolic pathways, for selected time points metatranscriptomic shotgun analysis was performed allowing the quantification of marker genes for methanogenesis, hydrolysis and syntrophic interactions. The results obtained demonstrated a microbial community typical for a mesophilic biogas plant. However in response to the observed changing process conditions (e.g. increasing NH4 + levels, changing feedstock composition), the microbial community reacted highly flexible by changing and adapting the community composition. The Methanosarcina-dominated archaeal community was shifted to a Methanomicrobiales-dominated archaeal community in the presence of increased ammonia conditions. A similar trend as in the phylogenetic composition was observed in the transcription activity of genes coding for enzymes involved in acetoclastic methanogenesis and syntrophic acetate oxidations (Codh/Acs and Fthfs). In accordance, Clostridia simultaneously increased under elevated ammonia concentrations in abundance and were identified as the primary syntrophic interaction partner with the now Methanomicrobiales-dominated archaeal community. In conclusion, overall stable process performance was maintained during increased ammonia concentration in the studied reactor based on the microbial communities' ability to flexibly respond by reorganizing the community composition while remaining functionally stable.
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MESH Headings
- Ammonia/metabolism
- Archaea/classification
- Archaea/genetics
- Bacteria/classification
- Bacteria/genetics
- Biofuels/microbiology
- Bioreactors/microbiology
- Cluster Analysis
- Culture Media/chemistry
- DNA, Archaeal/chemistry
- DNA, Archaeal/genetics
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Longitudinal Studies
- Microbiota
- Phylogeny
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Transcription, Genetic
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Affiliation(s)
- Martin Alexander Fischer
- Institute of General MicrobiologyChristian‐Albrechts‐University KielAm Botanischen Garten 1‐924118KielGermany
| | - Simon Güllert
- Institute of General MicrobiologyChristian‐Albrechts‐University KielAm Botanischen Garten 1‐924118KielGermany
- Institute of Microbiology & BiotechnologyUniversity HamburgBiozentrum Klein FlottbekHamburgGermany
| | - Sarah Refai
- Institute of Microbiology & BiotechnologyUniversity BonnMeckenheimer Allee 16853115BonnGermany
| | - Sven Künzel
- Max‐Planck‐Institute of Evolutionary BiologyAugust‐Thienemann‐Str. 224306PlönGermany
| | - Uwe Deppenmeier
- Institute of Microbiology & BiotechnologyUniversity BonnMeckenheimer Allee 16853115BonnGermany
| | - Wolfgang R. Streit
- Institute of Microbiology & BiotechnologyUniversity HamburgBiozentrum Klein FlottbekHamburgGermany
| | - Ruth Anne Schmitz
- Institute of General MicrobiologyChristian‐Albrechts‐University KielAm Botanischen Garten 1‐924118KielGermany
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43
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Improved Methanogenic Communities for Biogas Production. BIOFUEL AND BIOREFINERY TECHNOLOGIES 2019. [DOI: 10.1007/978-3-030-10516-7_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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44
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Pyzik A, Ciezkowska M, Krawczyk PS, Sobczak A, Drewniak L, Dziembowski A, Lipinski L. Comparative analysis of deep sequenced methanogenic communities: identification of microorganisms responsible for methane production. Microb Cell Fact 2018; 17:197. [PMID: 30572955 PMCID: PMC6302309 DOI: 10.1186/s12934-018-1043-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 12/11/2018] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Although interactions between microorganisms involved in biogas production are largely uncharted, it is commonly accepted that methanogenic Archaea are essential for the process. Methanogens thrive in various environments, but the most extensively studied communities come from biogas plants. In this study, we employed a metagenomic analysis of deeply sequenced methanogenic communities, which allowed for comparison of taxonomic and functional diversity as well as identification of microorganisms directly involved in various stages of methanogenesis pathways. RESULTS A comprehensive metagenomic approach was used to compare seven environmental communities, originating from an agricultural biogas plant, cattle-associated samples, a lowland bog, sewage sludge from a wastewater treatment plant and sediments from an ancient gold mine. In addition to the native consortia, two laboratory communities cultivated on maize silage as the sole substrate were also analyzed. Results showed that all anaerobic communities harbored genes of all known methanogenesis pathways, but their abundance varied greatly between environments and that genes were encoded by different methanogens. Identification of microorganisms directly involved in different stages of methane production revealed that hydrogenotrophic methanogens, such as Methanoculleus, Methanobacterium, Methanobrevibacter, Methanocorpusculum or Methanoregula, predominated in most native communities, whereas acetoclastic Methanosaeta seemed to be the key methanogen in the wastewater treatment plant. Furthermore, in many environments, the methylotrophic pathway carried out by representatives of Methanomassiliicoccales, such as Candidatus Methanomethylophilus and Candidatus Methanoplasma, seemed to play an important role in methane production. In contrast, in stable laboratory reactors substrate versatile Methanosarcina predominated. CONCLUSIONS The metagenomic approach presented in this study allowed for deep exploration and comparison of nine environments in which methane production occurs. Different abundance of methanogenesis-related functions was observed and the functions were analyzed in the phylogenetic context in order to identify microbes directly involved in methane production. In addition, a comparison of two metagenomic analytical tools, MG-RAST and MetAnnotate, revealed that combination of both allows for a precise characterization of methanogenic communities.
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Affiliation(s)
- Adam Pyzik
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Martyna Ciezkowska
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Pawel S Krawczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Adam Sobczak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland.,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Lukasz Drewniak
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Andrzej Dziembowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland.,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Leszek Lipinski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland.
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Lv Z, Leite AF, Harms H, Glaser K, Liebetrau J, Kleinsteuber S, Nikolausz M. Microbial community shifts in biogas reactors upon complete or partial ammonia inhibition. Appl Microbiol Biotechnol 2018; 103:519-533. [DOI: 10.1007/s00253-018-9444-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 09/17/2018] [Accepted: 10/08/2018] [Indexed: 10/28/2022]
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46
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Grohmann A, Vainshtein Y, Euchner E, Grumaz C, Bryniok D, Rabus R, Sohn K. Genetic repertoires of anaerobic microbiomes driving generation of biogas. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:255. [PMID: 30250507 PMCID: PMC6146632 DOI: 10.1186/s13068-018-1258-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 09/11/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Biogas production is an attractive technology for a sustainable generation of renewable energy. Although the microbial community is fundamental for such production, the process control is still limited to technological and chemical parameters. Currently, most of the efforts on microbial management system (MiMaS) are focused on process-specific marker species and community dynamics, but a practical implementation is in its infancy. The high number of unknown and uncharacterized microorganisms in general is one of the reasons hindering further advancements. RESULTS A Biogas Metagenomics Hybrid Assembly (BioMETHA) database, derived from microbiomes of biogas plants, was generated using a dedicated assembly strategy for different metagenomic datasets. Long reads from nanopore sequencing (MinION) were combined with short, more accurate second-generation sequencing reads (Illumina). The hybrid assembly resulted in 231 genomic bins each representing a taxonomic unit with an average completeness of 47%. Functional annotation identified 13,190 non-redundant genes covering roughly 207 k coding sequences. Mapping rates of metagenomics DNA derived from diverse biogas plants and laboratory reactors increased up to 73%. In addition, an EC (enzyme commission) reference sequence collection (ERSC) was generated whose genes are crucial for biogas-related processes, consisting of 235 unique EC numbers organized in 52 metabolic modules. Mapping rates of metatranscriptomic data to this ERSC revealed coverages of up to 93%. Process parameters and imbalances of laboratory reactors could be reconstructed by evaluating abundance of biogas-specific metabolic modules using metatranscriptomic data derived from various fermenter systems. CONCLUSION This newly established metagenomic hybrid assembly in combination with an EC reference sequence collection might help to shed light on the microbial dark matter of biogas plants by contributing to the development of a reference for biogas plant microbiome-specific gene sequences. Considering a biogas microbiome as a complex meta-organism expressing a meta-transcriptome, the approach established here could lay the foundation for a function-based microbial management system.
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Affiliation(s)
- Anja Grohmann
- University of Stuttgart IGVP, Pfaffenwaldring 31, 70569 Stuttgart, Germany
| | | | - Ellen Euchner
- University of Applied Science Hamm-Lippstadt, Marker Allee 76–78, 59063 Hamm, Germany
| | | | - Dieter Bryniok
- University of Applied Science Hamm-Lippstadt, Marker Allee 76–78, 59063 Hamm, Germany
| | - Ralf Rabus
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Carl-von-Ossietzky-Strasse 9-11, 26111 Oldenburg, Germany
| | - Kai Sohn
- Fraunhofer IGB, Nobelstrasse 12, 70569 Stuttgart, Germany
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47
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Effect of Bioaugmentation on Biogas Yields and Kinetics in Anaerobic Digestion of Sewage Sludge. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:ijerph15081717. [PMID: 30103443 PMCID: PMC6121296 DOI: 10.3390/ijerph15081717] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 08/01/2018] [Accepted: 08/08/2018] [Indexed: 01/28/2023]
Abstract
Bioaugmentation with a mixture of microorganisms (Bacteria and Archaea) was applied to improve the anaerobic digestion of sewage sludge. The study was performed in reactors operating at a temperature of 35 °C in semi-flow mode. Three runs with different doses of bioaugmenting mixture were conducted. Bioaugmentation of sewage sludge improved fermentation and allowed satisfactory biogas/methane yields and a biodegradation efficiency of more than 46%, despite the decrease in hydraulic retention time (HRT) from 20 d to 16.7 d. Moreover, in terms of biogas production, the rate constant k increased from 0.071 h−1 to 0.087 h−1 as doses of the bioaugmenting mixture were increased, as compared to values of 0.066 h−1 and 0.069 h−1 obtained with sewage sludge alone. Next-generation sequencing revealed that Cytophaga sp. predominated among Bacteria in digesters and that the hydrogenotrophic methanogen Methanoculleus sp. was the most abundant genus among Archaea.
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48
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Lv L, Li W, Bian J, Yu Y, Li D, Zheng Z. Evaluation of phase separation in a single-stage vertical anaerobic reactor: Performance and microbial composition analysis. BIORESOURCE TECHNOLOGY 2018; 261:370-378. [PMID: 29680703 DOI: 10.1016/j.biortech.2018.04.025] [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: 02/21/2018] [Revised: 04/04/2018] [Accepted: 04/06/2018] [Indexed: 06/08/2023]
Abstract
In order to explore whether the acidogenic phase and methanogenic phase could be separated vertically into a single-stage anaerobic reactor, a controlled double circulation (CDC) anaerobic reactor was proposed for treating traditional Chinese medicine (TCM) wastewater in this study. The results showed that most of the organic pollutants and refractory were removed in the first reaction area where most of the amount of sludge existed. The organic acids were accumulated in the first reaction area, and larger specific methanogenic activity (SMA) and coenzyme F420 values were found in the second reaction area. Bacterial and archaeal community structures in the two reaction areas of the CDC reactor were analyzed by Illumina MiSeq Sequencing, which revealed that the archaeal community showed larger difference compared with the bacterial community. Differences in the performance and microbial composition of the two reaction areas confirmed that phase separation was implemented in the CDC reactor.
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Affiliation(s)
- Longyi Lv
- School of Environment, Harbin Institute of Technology, Harbin 150090, PR China
| | - Weiguang Li
- State Key Laboratory of Urban Water Resource and Environment, Harbin 150090, PR China; School of Environment, Harbin Institute of Technology, Harbin 150090, PR China.
| | - Jiyong Bian
- School of Environment, Harbin Institute of Technology, Harbin 150090, PR China
| | - Yang Yu
- School of Environment, Harbin Institute of Technology, Harbin 150090, PR China
| | - Donghui Li
- School of Environment, Harbin Institute of Technology, Harbin 150090, PR China
| | - Zejia Zheng
- School of Environment, Harbin Institute of Technology, Harbin 150090, PR China
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49
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Lv L, Li W, Zheng Z, Li D, Zhang N. Exogenous acyl-homoserine lactones adjust community structures of bacteria and methanogens to ameliorate the performance of anaerobic granular sludge. JOURNAL OF HAZARDOUS MATERIALS 2018; 354:72-80. [PMID: 29729601 DOI: 10.1016/j.jhazmat.2018.04.075] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 04/26/2018] [Accepted: 04/28/2018] [Indexed: 06/08/2023]
Abstract
Quorum sensing (QS) signalling has been extensively studied in single species populations, activated sludge, biofilm and aerobic granular sludge. However, ecological roles of QS in anaerobic granular sludge, particularly in the content of the relationship between QS signalling and microbial community composition and function, have been rarely reported. Herein, five acyl-homoserine lactones (AHLs) molecules were added in the anaerobic granular sludge system for treating traditional Chinese medicine (TCM) wastewater respectively. The results indicated that the introduction of specific AHLs could enhance the abilities of organic matters removal and methanation in anaerobic granular sludge, and meanwhile, exogenous AHLs played an important role to regulate the concentration of EPS. Sequencing analysis indicated that microbial community structures of bacteria and methanogens changed to varying degrees by adding AHLs. This study suggested that exogenous AHLs could play a role in mediating microbial community structure, thereby enhancing the performance of anaerobic granular sludge. The regulatory mechanism of AHLs on community structure was discussed, and a speculative action model was established. Exogenous regulation by selective enhancement of AHLs-mediated QS in anaerobic granular sludge provided an innovative and attractive strategy for strengthening wastewater treatments.
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Affiliation(s)
- Longyi Lv
- School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin, 150090, PR China
| | - Weiguang Li
- State Key Laboratory of Urban Water Resource and Environment, Harbin, 150090, PR China; School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin, 150090, PR China.
| | - Zejia Zheng
- School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin, 150090, PR China
| | - Donghui Li
- School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin, 150090, PR China
| | - Ning Zhang
- School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin, 150090, PR China
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50
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Greses S, Zamorano-López N, Borrás L, Ferrer J, Seco A, Aguado D. Effect of long residence time and high temperature over anaerobic biodegradation of Scenedesmus microalgae grown in wastewater. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2018; 218:425-434. [PMID: 29709811 DOI: 10.1016/j.jenvman.2018.04.086] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 04/11/2018] [Accepted: 04/20/2018] [Indexed: 06/08/2023]
Abstract
Anaerobic digestion of indigenous Scenedesmus spp. microalgae was studied in continuous lab-scale anaerobic reactors at different temperatures (35 °C and 55 °C), and sludge retention time - SRT (50 and 70 days). Mesophilic digestion was performed in a continuous stirred-tank reactor (CSTR) and in an anaerobic membrane bioreactor (AnMBR). Mesophilic CSTR operated at 50 days SRT only achieved 11.9% of anaerobic biodegradability whereas in the AnMBR at 70 days SRT and 50 days HRT reached 39.5%, which is even higher than the biodegradability achieved in the thermophilic CSTR at 50 days SRT (30.4%). Microbial analysis revealed a high abundance of cellulose-degraders in both reactors, AnMBR (mainly composed of 9.4% Bacteroidetes, 10.1% Chloroflexi, 8.0% Firmicutes and 13.2% Thermotogae) and thermophilic CSTR (dominated by 23.8% Chloroflexi and 12.9% Firmicutes). However, higher microbial diversity was found in the AnMBR compared to the thermophilic CSTR which is related to the SRT. since high SRT promoted low growth-rate microorganisms, increasing the hydrolytic potential of the system. These results present the membrane technology as a promising approach to revalue microalgal biomass, suggesting that microalgae biodegradability and consequently the methane production could be improved operating at higher SRT.
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Affiliation(s)
- S Greses
- CALAGUA - Unidad Mixta UV-UPV, Departament d'Enginyeria Química, Universitat de València, Av. de la Universitat s/n, 46100, Burjassot, Valencia, Spain.
| | - N Zamorano-López
- CALAGUA - Unidad Mixta UV-UPV, Departament d'Enginyeria Química, Universitat de València, Av. de la Universitat s/n, 46100, Burjassot, Valencia, Spain.
| | - L Borrás
- CALAGUA - Unidad Mixta UV-UPV, Departament d'Enginyeria Química, Universitat de València, Av. de la Universitat s/n, 46100, Burjassot, Valencia, Spain.
| | - J Ferrer
- CALAGUA - Unidad Mixta UV-UPV, Institut Universitari d'Investigació d'Enginyeria de l'Aigua i Medi Ambient - IIAMA, Universitat Politècnica de Valencia, Camí de Vera s/n, 46022, Valencia, Spain.
| | - A Seco
- CALAGUA - Unidad Mixta UV-UPV, Departament d'Enginyeria Química, Universitat de València, Av. de la Universitat s/n, 46100, Burjassot, Valencia, Spain.
| | - D Aguado
- CALAGUA - Unidad Mixta UV-UPV, Institut Universitari d'Investigació d'Enginyeria de l'Aigua i Medi Ambient - IIAMA, Universitat Politècnica de Valencia, Camí de Vera s/n, 46022, Valencia, Spain.
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