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Hasanan K, Badr OA, El-Meihy R, Nasr M, Tawfik A. Biochar-enhanced anaerobic mixed culture for biodegradation of 1,2-dichloroethane: Microbial community, mechanisms, and techno-economics. CHEMOSPHERE 2024; 354:141666. [PMID: 38494001 DOI: 10.1016/j.chemosphere.2024.141666] [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: 11/24/2023] [Revised: 02/05/2024] [Accepted: 03/06/2024] [Indexed: 03/19/2024]
Abstract
While anaerobic digestion (AD) has been employed for the degradation of chlorinated aliphatic hydrocarbons, the associated digester performance might suffer from volatile fatty acids accumulation, insufficient substrate-microbes interaction, and lower biogas yields. To overcome these limitations, this study is the first to augment the hydrocarbon-degrading microbial capacities by adding agricultural waste-based biochar to the digestion medium. 1,2-dichloroethane (1,2-DCA) was selected as the target pollutant because it is discharged in large quantities from oil refining, petrochemical, and chemical industries, causing serious environmental and human health concerns. A multi-chamber anaerobic reactor (MAR) was operated at a 1,2-DCA loading rate of 1.13 g/L/d, glucose dosage (as an electron donor) range of 200-700 mg/L, and hydraulic retention time of 11.2 h, giving dechlorination = 32.2 ± 6.9% and biogas yield = 210 ± 30 mL/g CODremoved. These values increased after biochar supplementation (100 mg/g volatile solids, VS, as an inoculum carrier) up to 60.2 ± 11.5% and 290 ± 40 mL/g CODremoved, respectively, owing to the enhancement of dehydrogenase enzyme activities. Burkholderiales (15.3%), Clostridiales (2.3%), Bacteroidales (3.5%), Xanthomonadales (3.3%), and Rhodobacterales (6.1%) involved in 1,2-DCA degradation were dominant in the reactor supplemented with biochar. It's suggested that biochar played a major role in facilitating the direct interspecies electron transfer (DIET) between syntrophic bacteria and methanogens, where chloride, ethylene glycol, and acetate derived from 1,2-DCA dechlorination could be further used to promote methanogenesis and methane production. The synergetic effect of adsorption and dechlorination towards 1,2-DCA removal was validated at various biochar dosages (50-120 mg/g) and 1,2-DCA concentrations (50-1000 mg/L). The techno-economic results showed that the cost of treating 1,2-DCA-laden discharge (100 m3/d) by the MAR module could be 0.83 USD/m3 with a payback period of 6.24 years (NPV = 2840 USD and IRR = 10%), retrieving profits from pollution reduction (9542 USD/yr), biogas selling (10418 USD/yr), and carbon credit (10294 USD/yr).
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Affiliation(s)
- Khaled Hasanan
- Agricultural Microbiology Department, Faculty of Agriculture, Benha University, Moshtohor, Qalyubia, 13736, Egypt
| | - Omnia A Badr
- Department of Genetics and Genetic Engineering, Faculty of Agriculture, Benha University, Qalyubia, Egypt
| | - Rasha El-Meihy
- Agricultural Microbiology Department, Faculty of Agriculture, Benha University, Moshtohor, Qalyubia, 13736, Egypt
| | - Mahmoud Nasr
- Sanitary Engineering Department, Faculty of Engineering, Alexandria University, Alexandria, 21544, Egypt
| | - Ahmed Tawfik
- Department of Environmental Sciences, College of Life Sciences, Kuwait University, P.O. Box 5969, Safat, 13060, Kuwait.
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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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Heyer R, Hellwig P, Maus I, Walke D, Schlüter A, Hassa J, Sczyrba A, Tubbesing T, Klocke M, Mächtig T, Schallert K, Seick I, Reichl U, Benndorf D. Breakdown of hardly degradable carbohydrates (lignocellulose) in a two-stage anaerobic digestion plant is favored in the main fermenter. WATER RESEARCH 2024; 250:121020. [PMID: 38128305 DOI: 10.1016/j.watres.2023.121020] [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: 06/23/2023] [Revised: 12/05/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023]
Abstract
The yield and productivity of biogas plants depend on the degradation performance of their microbiomes. The spatial separation of the anaerobic digestion (AD) process into a separate hydrolysis and a main fermenter should improve cultivation conditions of the microorganisms involved in the degradation of complex substrates like lignocellulosic biomass (LCB) and, thus, the performance of anaerobic digesters. However, relatively little is known about such two-stage processes. Here, we investigated the process performance of a two-stage agricultural AD over one year, focusing on chemical and technical process parameters and metagenome-centric metaproteomics. Technical and chemical parameters indicated stable operation of the main fermenter but varying conditions for the open hydrolysis fermenter. Matching this, the microbiome in the hydrolysis fermenter has a higher dynamic than in the main fermenter. Metaproteomics-based microbiome analysis revealed a partial separation between early and common steps in carbohydrate degradation and primary fermentation in the hydrolysis fermenter but complex carbohydrate degradation, secondary fermentation, and methanogenesis in the main fermenter. Detailed metagenomics and metaproteomics characterization of the single metagenome-assembled genomes showed that the species focus on specific substrate niches and do not utilize their full genetic potential to degrade, for example, LCB. Overall, it seems that a separation of AD in a hydrolysis and a main fermenter does not improve the cleavage of complex substrates but significantly improves the overall process performance. In contrast, the remaining methanogenic activity in the hydrolysis fermenter may cause methane losses.
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Affiliation(s)
- Robert Heyer
- Otto von Guericke University, Bioprocess Engineering, Universitätsplatz 2, 39106 Magdeburg, Germany; Multidimensional Omics Analyses Group, Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Bunsen-Kirchhoff-Straße 11, 44139 Dortmund, Germany; Multidimensional Omics Analyses Group, Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany.
| | - Patrick Hellwig
- Otto von Guericke University, Bioprocess Engineering, Universitätsplatz 2, 39106 Magdeburg, Germany; Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany.
| | - Irena Maus
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany; Research Center Jülich GmbH, Institute of Bio- and Geosciences (IBG), IBG-5: Computational Metagenomics, Leo-Brandt-Str., 52428 Jülich, Germany.
| | - Daniel Walke
- Otto von Guericke University, Bioprocess Engineering, Universitätsplatz 2, 39106 Magdeburg, Germany; Otto von Guericke University, Database and Software Engineering, Universitätsplatz 2, 39106 Magdeburg, Germany.
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany.
| | - Julia Hassa
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany.
| | - Alexander Sczyrba
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany; Research Center Jülich GmbH, Institute of Bio- and Geosciences (IBG), IBG-5: Computational Metagenomics, Leo-Brandt-Str., 52428 Jülich, Germany; Faculty of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany.
| | - Tom Tubbesing
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany; Faculty of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany.
| | - Michael Klocke
- Institute of Agricultural and Urban Ecological Projects affiliated to Berlin Humboldt University (IASP), Philippstraße 13, 10115 Berlin, Germany.
| | - Torsten Mächtig
- Christian-Albrechts-Universität Kiel, Institute of Agricultural Engineering, Olshausenstr. 40, 24098 Kiel, Germany.
| | - Kay Schallert
- Multidimensional Omics Analyses Group, Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Bunsen-Kirchhoff-Straße 11, 44139 Dortmund, Germany.
| | - Ingolf Seick
- Urban Water Management/Wastewater, Hochschule Magdeburg-Stendal, Breitscheidstrasse 2, 39114 Magdeburg, Germany.
| | - Udo Reichl
- Otto von Guericke University, Bioprocess Engineering, Universitätsplatz 2, 39106 Magdeburg, Germany; Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany.
| | - Dirk Benndorf
- Otto von Guericke University, Bioprocess Engineering, Universitätsplatz 2, 39106 Magdeburg, Germany; Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany; Applied Biosciences and Process Engineering, Anhalt University of Applied Sciences, Microbiology, Bernburger Straße 55, 06354 Köthen, Germany.
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Korsa G, Konwarh R, Masi C, Ayele A, Haile S. Microbial cellulase production and its potential application for textile industries. ANN MICROBIOL 2023; 73:13. [DOI: 10.1186/s13213-023-01715-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 03/22/2023] [Indexed: 09/03/2023] Open
Abstract
Abstract
Purpose
The textile industry’s previous chemical use resulted in thousands of practical particulate emissions, such as machine component damage and drainage system blockage, both of which have practical implications. Enzyme-based textile processing is cost-effective, environmentally friendly, non-hazardous, and water-saving. The purpose of this review is to give evidence on the potential activity of microbial cellulase in the textile industry, which is mostly confined to the realm of research.
Methods
This review was progressive by considering peer-reviewed papers linked to microbial cellulase production, and its prospective application for textile industries was appraised and produced to develop this assessment. Articles were divided into two categories based on the results of trustworthy educational journals: methods used to produce the diversity of microorganisms through fermentation processes and such approaches used to produce the diversity of microbes through microbial fermentation. Submerged fermentation (SMF) and solid-state fermentation (SSF) techniques are currently being used to meet industrial demand for microbial cellulase production in the bio textile industry.
Results
Microbial cellulase is vital for increasing day to day due to its no side effect on the environment and human health becoming increasingly important. In conventional textile processing, the gray cloth was subjected to a series of chemical treatments that involved breaking the dye molecule’s amino group with Cl − , which started and accelerated dye(-resistant) bond cracking. A cellulase enzyme is primarily derived from a variety of microbial species found in various ecological settings as a biotextile/bio-based product technology for future needs in industrial applications.
Conclusion
Cellulase has been produced for its advantages in cellulose-based textiles, as well as for quality enhancement and fabric maintenance over traditional approaches. Cellulase’s role in the industry was microbial fermentation processes in textile processing which was chosen as an appropriate and environmentally sound solution for a long and healthy lifestyle.
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Tang T, Liu M, Du Y, Chen Y. Mechanism of action of single and mixed antibiotics during anaerobic digestion of swine wastewater: Microbial functional diversity and gene expression analysis. ENVIRONMENTAL RESEARCH 2023; 219:115119. [PMID: 36549483 DOI: 10.1016/j.envres.2022.115119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/04/2022] [Accepted: 12/18/2022] [Indexed: 06/17/2023]
Abstract
The mechanism by which antibiotics in swine wastewater affect anaerobic digestion (AD) remains unclear. Herein, we investigated how single and mixed antibiotics affect AD in swine wastewater. Both single and mixed antibiotics stimulated methane production at actual concentrations of 0.5-2 mg/L. Low-dose antibiotics (0.5 mg/L) exerted the most significant stimulatory effect on methane production, which increased by 211.63% (single) and 60.93% (mixed), respectively. However, an increased dose decreased the stimulatory effect on methane production. Overall, single antibiotics were more beneficial for methane production than mixed antibiotics since single antibiotics could promote the conversion of propionic and butyric acid, while mixed antibiotics inhibited the process. Microbial community analysis showed that single and mixed antibiotics could also lead to large changes in functional acidogens, ultimately leading to changes in methanogenic pathways.
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Affiliation(s)
- Taotao Tang
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, PR China
| | - Min Liu
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, PR China
| | - Ye Du
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, PR China
| | - Ying Chen
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, PR China.
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Yu X, Chen H, Liu Y, Yu L, Wang K, Xue G. Iron scraps packing rapidly enhances nitrogen removal in an aerobic sludge system and the mechanism. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:159081. [PMID: 36179843 DOI: 10.1016/j.scitotenv.2022.159081] [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: 06/02/2022] [Revised: 09/18/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
Simultaneous nitrification and denitrification (SND) has the advantage of energy saving and carbon demand reduction. Here, readily available low-cost iron scraps packing was added to an aerobic sludge system. This successfully enhanced the efficiency of total nitrogen removal from 37.7 ± 13.2 % to 62.7 ± 7.9 % over 2 days. While electrons from iron biocorrosion did not contribute to nitrate reduction, iron promoted heterotrophic denitrification. The iron scraps changed the spatial distribution of the microbial community, where more denitrification bacteria accumulated around the packing and higher denitrification capacity was noted. Metagenomic analysis of the sludge cultured in the presence of iron scraps for 2 days revealed that, with the exception of the enriched amoA/B/C gene expression, the abundance of other key nitrogen removal genes showed little variation. Furthermore, the structure of the microbial community was unchanged probably due to the relatively short culturing period. However, metatranscriptomic analysis indicated that iron increased the abundance of nitrifying bacteria (i.e. unclassified Nitrosomonas, Nitrosomonas sp. Is79A3 and Nitrospira defluvii) and promoted higher expression of nitrification genes. Notably, iron scraps packing decreased the abundance of the key denitrification bacteria Thauera sp. MZ1T from 52.92 to 7.58 %. The expression of napA/B also decreased, while expression of narG/H/I increased by 9 to 23 fold and a 2 to 3 fold over expression was noted for nirS, norB/C and nosZ in the presence of iron scraps. This suggested that aerobic denitrification was inhibited and anaerobic denitrification was promoted. This study has provided in-depth understanding of the influence of iron on SND to improve the application of iron-supported biological processes.
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Affiliation(s)
- Xin Yu
- College of Environmental Science and Engineering, Donghua University, 2999 North Renmin Road, Shanghai 201620, China
| | - Hong Chen
- College of Environmental Science and Engineering, Donghua University, 2999 North Renmin Road, Shanghai 201620, China.
| | - Yunfan Liu
- College of Environmental Science and Engineering, Donghua University, 2999 North Renmin Road, Shanghai 201620, China
| | - Luying Yu
- College of Environmental Science and Engineering, Donghua University, 2999 North Renmin Road, Shanghai 201620, China
| | - Kai Wang
- College of Environmental Science and Engineering, Donghua University, 2999 North Renmin Road, Shanghai 201620, China
| | - Gang Xue
- College of Environmental Science and Engineering, Donghua University, 2999 North Renmin Road, Shanghai 201620, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
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Jiang F, Li Q, Wang S, Shen T, Wang H, Wang A, Xu D, Yuan L, Lei L, Chen R, Yang B, Deng Y, Fan W. Recovery of metagenome-assembled microbial genomes from a full-scale biogas plant of food waste by pacific biosciences high-fidelity sequencing. Front Microbiol 2023; 13:1095497. [PMID: 36699587 PMCID: PMC9869026 DOI: 10.3389/fmicb.2022.1095497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 12/20/2022] [Indexed: 01/12/2023] Open
Abstract
Background Anaerobic digestion (AD) is important in treating of food waste, and thousands of metagenome-assembled genomes (MAGs) have been constructed for the microbiome in AD. However, due to the limitations of the short-read sequencing and assembly technologies, most of these MAGs are grouped from hundreds of short contigs by binning algorithms, and the errors are easily introduced. Results In this study, we constructed a total of 60 non-redundant microbial genomes from 64.5 Gb of PacBio high-fidelity (HiFi) long reads, generated from the digestate samples of a full-scale biogas plant fed with food waste. Of the 60 microbial genomes, all genomes have at least one copy of rRNA operons (16S, 23S, and 5S rRNA), 54 have ≥18 types of standard tRNA genes, and 39 are circular complete genomes. In comparison with the published short-read derived MAGs for AD, we found 23 genomes with average nucleotide identity less than 95% to any known MAGs. Besides, our HiFi-derived genomes have much higher average contig N50 size, slightly higher average genome size and lower contamination. GTDB-Tk classification of these genomes revealed two genomes belonging to novel genus and four genomes belonging to novel species, since their 16S rRNA genes have identities lower than 95 and 97% to any known 16S rRNA genes, respectively. Microbial community analysis based on the these assembled genomes reveals the most predominant phylum was Thermotogae (70.5%), followed by Euryarchaeota (6.1%), and Bacteroidetes (4.7%), and the most predominant bacterial and archaeal genera were Defluviitoga (69.1%) and Methanothrix (5.4%), respectively. Analysis of the full-length 16S rRNA genes identified from the HiFi reads gave similar microbial compositions to that derived from the 60 assembled genomes. Conclusion High-fidelity sequencing not only generated microbial genomes with obviously improved quality but also recovered a substantial portion of novel genomes missed in previous short-read based studies, and the novel genomes will deepen our understanding of the microbial composition in AD of food waste.
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Affiliation(s)
- Fan Jiang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Qiang Li
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, Sichuan, China,Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture and Rural Affairs, Chengdu, Sichuan, China
| | - Sen Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Ting Shen
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, Sichuan, China,Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture and Rural Affairs, Chengdu, Sichuan, China
| | - Hengchao Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Anqi Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Dong Xu
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Lihua Yuan
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Lihong Lei
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Rong Chen
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Boyuan Yang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Yu Deng
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, Sichuan, China,Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture and Rural Affairs, Chengdu, Sichuan, China,*Correspondence: Yu Deng, ; Wei Fan,
| | - Wei Fan
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China,*Correspondence: Yu Deng, ; Wei Fan,
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Chen J, Cai Y, Deng W, Xing S, Liao X. Transmission of tetracycline resistance genes and microbiomes from manure-borne black soldier fly larvae frass to rhizosphere soil and pakchoi endophytes. Front Microbiol 2022; 13:1014910. [DOI: 10.3389/fmicb.2022.1014910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 10/17/2022] [Indexed: 11/13/2022] Open
Abstract
Manure treatment with black soldier fly larvae (BSFL) and BSFL frass application in crop land is a sustainable strategy; however, whether residual antibiotic resistance genes (ARGs) and their transmission risk are related to the manure BSFL treatment process is still unknown. In this paper, the effect of BSFL addition density on residual tetracycline resistance genes (TRGs) and transmission from frass to pakchoi was determined. The results showed that BSFL frass can provide sufficient nutrients for growth, improve the economic value of pakchoi, and reduce the risk of transmission of TRGs in chicken manure regardless of BSFL density. The potential hosts of the TRGs we detected were found in BSFL frass (Oblitimonas and Tissierella), rhizosphere soil (Mortierella and Fermentimonas), and pakchoi endophytes (Roseomonas). The present study concluded that BSFL frass produced by adding 100 BSFL per 100 g of chicken manure has the advantages of high value and low risk. These findings will provide important strategic guidance for animal manure disposal and theoretical support for preventing the transmission of TRGs in BSFL applications.
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Van Camp PJ, Porollo A. SEQ2MGS: an effective tool for generating realistic artificial metagenomes from the existing sequencing data. NAR Genom Bioinform 2022; 4:lqac050. [PMID: 35899079 PMCID: PMC9310082 DOI: 10.1093/nargab/lqac050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 05/02/2022] [Accepted: 06/23/2022] [Indexed: 11/18/2022] Open
Abstract
Assessment of bioinformatics tools for the metagenomics analysis from the whole genome sequencing data requires realistic benchmark sets. We developed an effective and simple generator of artificial metagenomes from real sequencing experiments. The tool (SEQ2MGS) analyzes the input FASTQ files, precomputes genomic content, and blends shotgun reads from different sequenced isolates, or spike isolate(s) in real metagenome, in desired proportions. SEQ2MGS eliminates the need for simulation of sequencing platform variations, reads distributions, presence of plasmids, viruses, and contamination. The tool is especially useful for a quick generation of multiple complex samples that include new or understudied organisms, even without assembled genomes. For illustration, we first demonstrated the ease of SEQ2MGS use for the simulation of altered Schaedler flora (ASF) in comparison with de novo metagenomics generators Grinder and CAMISIM. Next, we emulated the emergence of a pathogen in the human gut microbiome and observed that Kraken, Centrifuge, and MetaPhlAn, while correctly identified Klebsiella pneumoniae, produced inconsistent results for the rest of real metagenome. Finally, using the MG-RAST platform, we affirmed that SEQ2MGS properly transfers genomic information from an isolate into the simulated metagenome by the correct identification of antimicrobial resistance genes anticipated to appear compared to the original metagenome.
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Affiliation(s)
- Pieter-Jan Van Camp
- Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Aleksey Porollo
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
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Wang D, Huang K, He X, Zhang XX, Meng Y. Varied interspecies interactions between anammox and denitrifying bacteria enhanced nitrogen removal in a single-stage simultaneous anammox and denitrification system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 813:152519. [PMID: 34968587 DOI: 10.1016/j.scitotenv.2021.152519] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/08/2021] [Accepted: 12/14/2021] [Indexed: 05/05/2023]
Abstract
The simultaneous anammox and denitrification (SAD) system has received growing interest for the enhanced nitrogen removal, while the ecological traits of microbial community including spatial distribution characteristics, assembly processes and interspecies interactions have not been fully unraveled. The present study applied metagenomics and ecological analysis methods to gain the ecological traits of microbial communities in the SAD system across different organic substrate loadings. Results showed that organic matter significantly affected the bioreactor performance, and the optimal total nitrogen removal efficiency reached 93.4 ± 0.7% under the COD concentrations of 180 ± 18.2 mg/L. Functional organisms including Candidatus Brocadia (3.9%), Denitratisoma (1.6%), Dokdonella (4.4%) and Thauera (4.6%) obviously enriched under the optimal organic loading conditions. Moreover, microbial communities were significantly governed by deterministic process under high organic concentrations, and the denitrifying organisms displayed important ecological roles in the communities. Although anammox bacteria obviously enriched at the middle of bioreactor, it possessed the highest expression activities at both bottom and middle sites. Denitrifying bacteria that enriched at the bottom sites strongly achieved nitrate reduction and provided nitrite for anammox bacteria, while these organisms trended to compete nitrite with anammox bacteria at the middle site. These findings highlight the importance of microbial ecology in the SAD systems, which may expand our understanding of the synergistic patterns between anammox and denitrifying bacteria.
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Affiliation(s)
- Depeng Wang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Kailong Huang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China; Nanjing Jiangdao Institute of Environmental Research Co., Ltd., Nanjing 210019, China
| | - Xiwei He
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Xu-Xiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Yabing Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China.
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11
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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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12
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Braga Nan L, Trably E, Santa-Catalina G, Bernet N, Delgenes JP, Escudie R. Microbial community redundance in biomethanation systems lead to faster recovery of methane production rates after starvation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 804:150073. [PMID: 34517312 DOI: 10.1016/j.scitotenv.2021.150073] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 08/11/2021] [Accepted: 08/28/2021] [Indexed: 06/13/2023]
Abstract
The Power-to-Gas concept corresponds to the use of the electric energy surplus to produce H2 by water electrolysis, that can be further converted to methane by biomethanation. However, the fluctuant production of renewable energy sources can lead to discontinuous H2 injections into the reactors, that may interfere with the adaptation of the microbial community to high H2 partial pressures. In this study, the response of the microbial community to H2 and organic feed starvation was evaluated in in-situ and ex-situ biomethanation. The fed-batch reactors were fed with acetate or glucose and H2, and one or four weeks of starvation periods were investigated. Methane productivity was mostly affected by the four-week starvation period. However, both in-situ and ex-situ biomethanation reactors recovered their methane production rate after starvation within approximately one-week of normal operation, while the anaerobic digestion (AD) reactors did not recover their performances even after 3 weeks of normal operation. The recovery failure of the AD reactors was probably related to a slow growth of the syntrophic and methanogen microorganisms, that led to a VFA accumulation. On the contrary, the faster recovery of both biomethanation reactors was related to the replacement of Methanoculleus sp. by Methanobacterium sp., restoring the methane production in the in-situ and ex-situ biomethanation reactors. This study has shown that biomethanation processes can respond favourably to the intermittent H2 addition without compromising their CH4 production performance.
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Affiliation(s)
- L Braga Nan
- INRAE, Univ. Montpellier, LBE, 102 AV. des Etangs, 11100 Narbonne, France
| | - E Trably
- INRAE, Univ. Montpellier, LBE, 102 AV. des Etangs, 11100 Narbonne, France
| | - G Santa-Catalina
- INRAE, Univ. Montpellier, LBE, 102 AV. des Etangs, 11100 Narbonne, France
| | - N Bernet
- INRAE, Univ. Montpellier, LBE, 102 AV. des Etangs, 11100 Narbonne, France
| | - J-P Delgenes
- INRAE, Univ. Montpellier, LBE, 102 AV. des Etangs, 11100 Narbonne, France
| | - R Escudie
- INRAE, Univ. Montpellier, LBE, 102 AV. des Etangs, 11100 Narbonne, France.
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13
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Arthur R, Antonczyk S, Off S, Scherer PA. Mesophilic and Thermophilic Anaerobic Digestion of Wheat Straw in a CSTR System with 'Synthetic Manure': Impact of Nickel and Tungsten on Methane Yields, Cell Count, and Microbiome. Bioengineering (Basel) 2022; 9:bioengineering9010013. [PMID: 35049722 PMCID: PMC8772805 DOI: 10.3390/bioengineering9010013] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/23/2021] [Accepted: 12/28/2021] [Indexed: 11/16/2022] Open
Abstract
Lignocellulosic residues, such as straw, are currently considered as candidates for biogas production. Therefore, straw fermentations were performed to quantitatively estimate methane yields and cell counts, as well as to qualitatively determine the microbiome. Six fully automated, continuously stirred biogas reactors were used: three mesophilic (41 °C) and three thermophilic (58 °C). They were fed every 8 h with milled wheat straw suspension in a defined, buffered salt solution, called 'synthetic manure'. Total reflection X-ray fluorescence spectrometry analyses showed nickel and tungsten deficiency in the straw suspension. Supplementation of nickel and subsequently tungsten, or with an increasing combined dosage of both elements, resulted in a final concentration of approximately 0.1 mg/L active, dissolved tungsten ions, which caused an increase of the specific methane production, up to 63% under mesophilic and 31% under thermophilic conditions. That is the same optimal range for pure cultures of methanogens or bacteria found in literature. A simultaneous decrease of volatile fatty acids occurred. The Ni/W effect occurred with all three organic loading rates, being 4.5, 7.5, and 9.0 g volatile solids per litre and day, with a concomitant hydraulic retention time of 18, 10, or 8 days, respectively. A maximum specific methane production of 0.254 m3 CH4, under standard temperature and pressure per kg volatile solids (almost 90% degradation), was obtained. After the final supplementation of tungsten, the cell counts of methanogens increased by 300%, while the total microbial cell counts increased by only 3-62%. The mesophilic methanogenic microflora was shifted from the acetotrophic Methanosaeta to the hydrogenotrophic Methanoculleus (85%) by tungsten, whereas the H2-CO2-converter, Methanothermobacter, always dominated in the thermophilic fermenters.
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Affiliation(s)
- Richard Arthur
- Energy Systems Engineering Department, Koforidua Technical University, Koforidua P.O. Box KF 981, Ghana;
| | - Sebastian Antonczyk
- Research Center for Biomass Utilization, Faculty Life Sciences, Hamburg University of Applied Sciences (HAW), 20099 Hamburg, Germany; (S.A.); (S.O.)
| | - Sandra Off
- Research Center for Biomass Utilization, Faculty Life Sciences, Hamburg University of Applied Sciences (HAW), 20099 Hamburg, Germany; (S.A.); (S.O.)
| | - Paul A. Scherer
- Research Center for Biomass Utilization, Faculty Life Sciences, Hamburg University of Applied Sciences (HAW), 20099 Hamburg, Germany; (S.A.); (S.O.)
- Correspondence:
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14
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Sun L, Long M, Li J, Wu R, Ma L, Tang D, Lu Y, Wang Z. Different Effects of Thermophilic Microbiological Inoculation With and Without Biochar on Physicochemical Characteristics and Bacterial Communities in Pig Manure Composting. Front Microbiol 2021; 12:746718. [PMID: 34899633 PMCID: PMC8660119 DOI: 10.3389/fmicb.2021.746718] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 10/04/2021] [Indexed: 11/13/2022] Open
Abstract
This study evaluated the effects of thermophilic microbiological inoculation alone (TA) and integrated with biochar (TB) on the physicochemical characteristics and bacterial communities in pig manure (PM) composting with wheat straw. Both TA and TB accelerated the rate of temperature increase during the PM composting. TA significantly reduced total nitrogen loss by 18.03% as opposed to TB which significantly accelerated total organic carbon degradation by 12.21% compared with the control. Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria were the major phyla in composting. Variation of the relative abundance of genera depended on the composting period and treatment. The genera Lactobacillus (26.88-46.71%) and Clostridium_sensu_stricto (9.03-31.69%) occupied a superior position in the temperature rise stage, and Bacillus (30.90-36.19%) was outstanding in the cooling stage. Temperature, total nitrogen (TN), and ammonium nitrogen significantly influenced the bacterial phyla composition. TN, water content, and nitrite nitrogen were the main drivers of the bacterial community genera. Furthermore, our results demonstrated that microbiological consortia were resistant to high temperatures and could fix nitrogen for enriched Pseudomonas; however, when interacted with biochar, total organic carbon (TOC) degradation was accelerated for higher bacterial richness and diversity as well as overrepresented Corynebacterium.
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Affiliation(s)
- Likun Sun
- College of Animal Science, Gansu Agricultural University, Lanzhou, China.,Gansu Provincial Engineering Research Center for Animal Waste Utilization, Gansu Agricultural University, Lanzhou, China
| | - Min Long
- College of Animal Science, Gansu Agricultural University, Lanzhou, China.,College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
| | - Jianshu Li
- College of Animal Science, Gansu Agricultural University, Lanzhou, China
| | - Renfei Wu
- College of Animal Science, Gansu Agricultural University, Lanzhou, China
| | - Lin Ma
- College of Animal Science, Gansu Agricultural University, Lanzhou, China.,Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Defu Tang
- College of Animal Science, Gansu Agricultural University, Lanzhou, China
| | - Yongli Lu
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou, China
| | - Ziyu Wang
- College of Animal Science, Gansu Agricultural University, Lanzhou, China
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15
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Contreras-Dávila CA, Esveld J, Buisman CJN, Strik DPBTB. nZVI Impacts Substrate Conversion and Microbiome Composition in Chain Elongation From D- and L-Lactate Substrates. Front Bioeng Biotechnol 2021; 9:666582. [PMID: 34211964 PMCID: PMC8239352 DOI: 10.3389/fbioe.2021.666582] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 05/25/2021] [Indexed: 12/12/2022] Open
Abstract
Medium-chain carboxylates (MCC) derived from biomass biorefining are attractive biochemicals to uncouple the production of a wide array of products from the use of non-renewable sources. Biological conversion of biomass-derived lactate during secondary fermentation can be steered to produce a variety of MCC through chain elongation. We explored the effects of zero-valent iron nanoparticles (nZVI) and lactate enantiomers on substrate consumption, product formation and microbiome composition in batch lactate-based chain elongation. In abiotic tests, nZVI supported chemical hydrolysis of lactate oligomers present in concentrated lactic acid. In fermentation experiments, nZVI created favorable conditions for either chain-elongating or propionate-producing microbiomes in a dose-dependent manner. Improved lactate conversion rates and n-caproate production were promoted at 0.5-2 g nZVI⋅L-1 while propionate formation became relevant at ≥ 3.5 g nZVI⋅L-1. Even-chain carboxylates (n-butyrate) were produced when using enantiopure and racemic lactate with lactate conversion rates increased in nZVI presence (1 g⋅L-1). Consumption of hydrogen and carbon dioxide was observed late in the incubations and correlated with acetate formation or substrate conversion to elongated products in the presence of nZVI. Lactate racemization was observed during chain elongation while isomerization to D-lactate was detected during propionate formation. Clostridium luticellarii, Caproiciproducens, and Ruminococcaceae related species were associated with n-valerate and n-caproate production while propionate was likely produced through the acrylate pathway by Clostridium novyi. The enrichment of different potential n-butyrate producers (Clostridium tyrobutyricum, Lachnospiraceae, Oscillibacter, Sedimentibacter) was affected by nZVI presence and concentrations. Possible theories and mechanisms underlying the effects of nZVI on substrate conversion and microbiome composition are discussed. An outlook is provided to integrate (bio)electrochemical systems to recycle (n)ZVI and provide an alternative reducing power agent as durable control method.
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Affiliation(s)
| | - Johan Esveld
- Environmental Technology, Wageningen University & Research, Wageningen, Netherlands
| | - Cees J N Buisman
- Environmental Technology, Wageningen University & Research, Wageningen, Netherlands
| | - David P B T B Strik
- Environmental Technology, Wageningen University & Research, Wageningen, Netherlands
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16
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Maus I, Tubbesing T, Wibberg D, Heyer R, Hassa J, Tomazetto G, Huang L, Bunk B, Spröer C, Benndorf D, Zverlov V, Pühler A, Klocke M, Sczyrba A, Schlüter A. The Role of Petrimonas mucosa ING2-E5A T in Mesophilic Biogas Reactor Systems as Deduced from Multiomics Analyses. Microorganisms 2020; 8:E2024. [PMID: 33348776 PMCID: PMC7768429 DOI: 10.3390/microorganisms8122024] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 12/17/2022] Open
Abstract
Members of the genera Proteiniphilum and Petrimonas were speculated to represent indicators reflecting process instability within anaerobic digestion (AD) microbiomes. Therefore, Petrimonas mucosa ING2-E5AT was isolated from a biogas reactor sample and sequenced on the PacBio RSII and Illumina MiSeq sequencers. Phylogenetic classification positioned the strain ING2-E5AT in close proximity to Fermentimonas and Proteiniphilum species (family Dysgonomonadaceae). ING2-E5AT encodes a number of genes for glycosyl-hydrolyses (GH) which are organized in Polysaccharide Utilization Loci (PUL) comprising tandem susCD-like genes for a TonB-dependent outer-membrane transporter and a cell surface glycan-binding protein. Different GHs encoded in PUL are involved in pectin degradation, reflecting a pronounced specialization of the ING2-E5AT PUL systems regarding the decomposition of this polysaccharide. Genes encoding enzymes participating in amino acids fermentation were also identified. Fragment recruitments with the ING2-E5AT genome as a template and publicly available metagenomes of AD microbiomes revealed that Petrimonas species are present in 146 out of 257 datasets supporting their importance in AD microbiomes. Metatranscriptome analyses of AD microbiomes uncovered active sugar and amino acid fermentation pathways for Petrimonas species. Likewise, screening of metaproteome datasets demonstrated expression of the Petrimonas PUL-specific component SusC providing further evidence that PUL play a central role for the lifestyle of Petrimonas species.
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Affiliation(s)
- Irena Maus
- Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany; (I.M.); (D.W.); (J.H.); (A.P.)
| | - Tom Tubbesing
- Faculty of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany; (T.T.); (L.H.); (A.S.)
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany; (I.M.); (D.W.); (J.H.); (A.P.)
| | - Robert Heyer
- Bioprocess Engineering, Otto von Guericke University Magdeburg, Universitätspl. 2, 39106 Magdeburg, Germany; (R.H.); (D.B.)
- Database and Software Engineering Group, Department of Computer Science, Institute for Technical and Business Information Systems, Otto von Guericke University Magdeburg, Universitätspl. 2, 39106 Magdeburg, Germany
| | - Julia Hassa
- Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany; (I.M.); (D.W.); (J.H.); (A.P.)
- Department of Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy, Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Geizecler Tomazetto
- Biological and Chemical Engineering Section (BCE), Department of Engineering, Aarhus University, 8000 Aarhus, Denmark;
| | - Liren Huang
- Faculty of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany; (T.T.); (L.H.); (A.S.)
| | - Boyke Bunk
- Department Bioinformatics and Databases, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstraße 7B, 38124 Braunschweig, Germany; (B.B.); (C.S.)
| | - Cathrin Spröer
- Department Bioinformatics and Databases, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstraße 7B, 38124 Braunschweig, Germany; (B.B.); (C.S.)
| | - Dirk Benndorf
- Bioprocess Engineering, Otto von Guericke University Magdeburg, Universitätspl. 2, 39106 Magdeburg, Germany; (R.H.); (D.B.)
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, 39106 Magdeburg, Germany
- Microbiology, Anhalt University of Applied Sciences, Bernburger Straße 55, 06354 Köthen, Germany
| | - Vladimir Zverlov
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany;
- Institute of Molecular Genetics, National Research Centre «Kurchatov Institute», Kurchatov Sq. 2, 123128 Moscow, Russia
| | - Alfred Pühler
- Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany; (I.M.); (D.W.); (J.H.); (A.P.)
| | - Michael Klocke
- Institute of Agricultural and Urban Ecological Projects Affiliated to Berlin Humboldt University (IASP), Philippstraße 13, 10115 Berlin, Germany;
| | - Alexander Sczyrba
- Faculty of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany; (T.T.); (L.H.); (A.S.)
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany; (I.M.); (D.W.); (J.H.); (A.P.)
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17
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Li J, Liang Y, Miao Y, Wang D, Jia S, Liu CH. Metagenomic insights into aniline effects on microbial community and biological sulfate reduction pathways during anaerobic treatment of high-sulfate wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 742:140537. [PMID: 32623173 DOI: 10.1016/j.scitotenv.2020.140537] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/10/2020] [Accepted: 06/24/2020] [Indexed: 06/11/2023]
Abstract
For comprehensive insights into the change of sulfate reduction pathway responding to the toxic stress and the shift of microbial community and performance of sulfate reduction, we built a laboratory-scale expanded granular sludge bed reactor (EGSB) treating high-sulfate wastewater with elevated aniline concentrations from 0 to 480 mg/L. High-throughput sequencing and metagenomic approaches were applied to decipher the molecular mechanisms of sulfate reduction under aniline stress through taxonomic and functional profiles. The increasing aniline in the anaerobic system induced the accumulation of volatile fatty acids (VFA), further turned the bioreactor into acidification, which was the principal reason for the deterioration of system performance and finally resulted in the accumulation of toxic free sulfide. Moreover, aniline triggered the change of bacterial community and genes relating to sulfate reduction pathways. The increase of aniline from 0 to 320 mg/L enriched total sulfate-reducing bacteria (SRB), and the most abundant genus was Desulfomicrobium, accounting for 66.85-91.25% of total SRB. The assimilatory sulfate reduction pathway was obviously inhibited when aniline was over 160 mg/L, while genes associated with dissimilatory sulfate reduction pathways all exhibited an upward tendency with the increasing aniline content. The enrichment of aniline-resistant SRB (e.g. Desulfomicrobium) carrying genes associated with the dissimilatory sulfate reduction pathway also confirmed the underlying mechanism that sulfate reduction turned into dissimilation under high aniline condition. Taken together, these results comprehensively provided solid evidence for the effects of aniline on the biological sulfate reduction processes treating high-sulfate wastewater and the underlying molecular mechanisms which may highlight the important roles of SRB and related sulfate reduction genes during treatment.
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Affiliation(s)
- Jun Li
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Ying Liang
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Yu Miao
- Department of Civil and Environmental Engineering, University of California, Los Angeles, CA 90095, United States
| | - Depeng Wang
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Shuyu Jia
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China.
| | - Chang-Hong Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
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18
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Methanothermobacter thermautotrophicus strain ΔH as a potential microorganism for bioconversion of CO2 to methane. J CO2 UTIL 2020. [DOI: 10.1016/j.jcou.2020.101210] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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19
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Rettenmaier R, Lo YK, Schmidt L, Munk B, Lagkouvardos I, Neuhaus K, Schwarz W, Liebl W, Zverlov V. A Novel Primer Mixture for GH48 Genes: Quantification and Identification of Truly Cellulolytic Bacteria in Biogas Fermenters. Microorganisms 2020; 8:E1297. [PMID: 32854333 PMCID: PMC7565076 DOI: 10.3390/microorganisms8091297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/21/2020] [Accepted: 08/23/2020] [Indexed: 12/22/2022] Open
Abstract
Genomic studies revealed the glycoside hydrolases of family 48 (GH48) as a powerful marker for the identification of truly cellulolytic bacteria. Here we report an improved method for detecting cellulolytic bacteria in lab-scale biogas fermenters by using GH48 genes as a molecular marker in DNA and RNA samples. We developed a mixture of primers for the specific amplification of a GH48 gene region in a broad range of bacteria. Additionally, we built a manually curated reference database containing GH48 gene sequences directly linked to the corresponding taxonomic information. Phylogenetic correlation analysis of GH48 to 16S rRNA gene sequences revealed that GH48 gene sequences with 94% identity belong with high confidence to the same genus. Applying this analysis, GH48 amplicon reads revealed that at mesophilic fermenter conditions, 50-99% of the OTUs appear to belong to novel taxa. In contrast, at thermophilic conditions, GH48 gene sequences from the genus Hungateiclostridium dominated with 60-91% relative abundance. The novel primer combinations enabled detection and relative quantification of a wide spectrum of GH48 genes in cellulolytic microbial communities. Deep phylogenetic correlation analysis and a simplified taxonomic identification with the novel database facilitate identification of cellulolytic organisms, including the detection of novel taxa in biogas fermenters.
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Affiliation(s)
- Regina Rettenmaier
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany; (R.R.); (Y.K.L.); (L.S.); (W.L.)
| | - Yat Kei Lo
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany; (R.R.); (Y.K.L.); (L.S.); (W.L.)
| | - Larissa Schmidt
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany; (R.R.); (Y.K.L.); (L.S.); (W.L.)
| | - Bernhard Munk
- Bavarian State Research Center for Agriculture, Central Department for Quality Assurance and Analytics, Lange Point 6, 85354 Freising, Germany;
| | - Ilias Lagkouvardos
- ZIEL—Core Facility Microbiome, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany; (I.L.); (K.N.)
| | - Klaus Neuhaus
- ZIEL—Core Facility Microbiome, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany; (I.L.); (K.N.)
| | - Wolfgang Schwarz
- Aspratis GmbH. Munich, Germany, Hübnerstr. 11, 80637 Munich, Germany;
| | - Wolfgang Liebl
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany; (R.R.); (Y.K.L.); (L.S.); (W.L.)
| | - Vladimir Zverlov
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany; (R.R.); (Y.K.L.); (L.S.); (W.L.)
- Institute of Molecular Genetics of National Research Centre (Kurchatov Institute), Kurchatov Sq. 2, 123182 Moscow, Russia
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Rettenmaier R, Schneider M, Munk B, Lebuhn M, Jünemann S, Sczyrba A, Maus I, Zverlov V, Liebl W. Importance of Defluviitalea raffinosedens for Hydrolytic Biomass Degradation in Co-Culture with Hungateiclostridium thermocellum. Microorganisms 2020; 8:E915. [PMID: 32560349 PMCID: PMC7355431 DOI: 10.3390/microorganisms8060915] [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: 05/19/2020] [Revised: 06/06/2020] [Accepted: 06/11/2020] [Indexed: 01/02/2023] Open
Abstract
Bacterial hydrolysis of polysaccharides is an important step for the production of sustainable energy, for example during the conversion of plant biomass to methane-rich biogas. Previously, Hungateiclostridium thermocellum was identified as cellulolytic key player in thermophilic biogas microbiomes with a great frequency as an accompanying organism. The aim of this study was to physiologically characterize a recently isolated co-culture of H. thermocellum and the saccharolytic bacterium Defluviitalea raffinosedens from a laboratory-scale biogas fermenter. The characterization focused on cellulose breakdown by applying the measurement of cellulose hydrolysis, production of metabolites, and the activity of secreted enzymes. Substrate degradation and the production of volatile metabolites was considerably enhanced when both organisms acted synergistically. The metabolic properties of H. thermocellum have been studied well in the past. To predict the role of D. raffinosedens in this bacterial duet, the genome of D. raffinosedens was sequenced for the first time. Concomitantly, to deduce the prevalence of D. raffinosedens in anaerobic digestion, taxonomic composition and transcriptional activity of different biogas microbiomes were analyzed in detail. Defluviitalea was abundant and metabolically active in reactor operating at highly efficient process conditions, supporting the importance of this organism for the hydrolysis of the raw substrate.
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Affiliation(s)
- Regina Rettenmaier
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany; (R.R.); (M.S.); (W.L.)
| | - Martina Schneider
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany; (R.R.); (M.S.); (W.L.)
| | - Bernhard Munk
- Department for Quality Assurance and Analytics, Bavarian State Research Center for Agriculture, Lange Point 6, 85354 Freising, Germany; (B.M.); (M.L.)
| | - Michael Lebuhn
- Department for Quality Assurance and Analytics, Bavarian State Research Center for Agriculture, Lange Point 6, 85354 Freising, Germany; (B.M.); (M.L.)
| | - Sebastian Jünemann
- Center for Biotechnology (CeBiTec), Universitätsstr. 27, 33615 Bielefeld, Germany;
- Faculty of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany;
| | - Alexander Sczyrba
- Faculty of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany;
| | - Irena Maus
- Center for Biotechnology (CeBiTec), Universitätsstr. 27, 33615 Bielefeld, Germany;
| | - Vladimir Zverlov
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany; (R.R.); (M.S.); (W.L.)
- Institute of Molecular Genetics, RAS, Kurchatov Sq. 2, 123182 Moscow, Russia
| | - Wolfgang Liebl
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany; (R.R.); (M.S.); (W.L.)
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Prathiviraj R, Chellapandi P. Comparative genomic analysis reveals starvation survival systems in Methanothermobacter thermautotrophicus ΔH. Anaerobe 2020; 64:102216. [PMID: 32504807 DOI: 10.1016/j.anaerobe.2020.102216] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 05/07/2020] [Accepted: 05/18/2020] [Indexed: 12/26/2022]
Abstract
Methanothermobacter thermautotrophicus ΔH (MTH) is a thermophilic hydrogenotrophic methanogenic archaeon capable of reducing CO2 with H2 to produce methane gas. It is the potential candidate in the biomethanation of CO2 and CO in anaerobic reactors and biogas upgrading process. However, systematic studies addressing its genome conservation and function remain scant in this genome. In this study, we have evaluated its evolutionary resemblance and metabolic discrepancy, particularly in starvation survival systems by comparing the genomic contexts with Methanothermobacter marburgensis str. Marburg (MMG) and Methanobacterium formicicum DSM 1535 (MFO). The phylogenomic analysis of this study indicated that there was a strong phylogenomic signal among MTH, MMG, and MFO in the whole-genome tree. DNA replication machinery was conserved in the MTH genome and might have evolved at different evolution rates. Genome synteny analysis observed collinearity of either gene orders or gene families has to be maintained with syntenic blocks located in the syntenic out-paralogs. A genome-wide metabolic analysis identified some unique putative metabolic subsystems in MTH, which are proposed to determine its growth characteristics in diverse environments. MTH genome comprised of 93 unique genes-coding for starvation survival and stress-response proteins. These proteins confer its adaptation to nutritional deprivation and other abiotic stresses. MTH has a typical system to withstand its growth and cell viability during stable operation and recovery after prolonged starvation. Thus, the present work will provide an insight to improve the genome refinement and metabolic reconstruction in parallel to other closely related species.
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Affiliation(s)
- R Prathiviraj
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, 620024, Tamil Nadu, India
| | - P Chellapandi
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, 620024, Tamil Nadu, India.
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22
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Maus I, Klocke M, Derenkó J, Stolze Y, Beckstette M, Jost C, Wibberg D, Blom J, Henke C, Willenbücher K, Rumming M, Rademacher A, Pühler A, Sczyrba A, Schlüter A. Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics. ENVIRONMENTAL MICROBIOME 2020; 15:7. [PMID: 33902713 PMCID: PMC8067321 DOI: 10.1186/s40793-020-00354-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 02/14/2020] [Indexed: 05/16/2023]
Abstract
BACKGROUND Anaerobic digestion (AD) of protein-rich grass silage was performed in experimental two-stage two-phase biogas reactor systems at low vs. increased organic loading rates (OLRs) under mesophilic (37 °C) and thermophilic (55 °C) temperatures. To follow the adaptive response of the biomass-attached cellulolytic/hydrolytic biofilms at increasing ammonium/ammonia contents, genome-centered metagenomics and transcriptional profiling based on metagenome assembled genomes (MAGs) were conducted. RESULTS In total, 78 bacterial and archaeal MAGs representing the most abundant members of the communities, and featuring defined quality criteria were selected and characterized in detail. Determination of MAG abundances under the tested conditions by mapping of the obtained metagenome sequence reads to the MAGs revealed that MAG abundance profiles were mainly shaped by the temperature but also by the OLR. However, the OLR effect was more pronounced for the mesophilic systems as compared to the thermophilic ones. In contrast, metatranscriptome mapping to MAGs subsequently normalized to MAG abundances showed that under thermophilic conditions, MAGs respond to increased OLRs by shifting their transcriptional activities mainly without adjusting their proliferation rates. This is a clear difference compared to the behavior of the microbiome under mesophilic conditions. Here, the response to increased OLRs involved adjusting of proliferation rates and corresponding transcriptional activities. The analysis led to the identification of MAGs positively responding to increased OLRs. The most outstanding MAGs in this regard, obviously well adapted to higher OLRs and/or associated conditions, were assigned to the order Clostridiales (Acetivibrio sp.) for the mesophilic biofilm and the orders Bacteroidales (Prevotella sp. and an unknown species), Lachnospirales (Herbinix sp. and Kineothrix sp.) and Clostridiales (Clostridium sp.) for the thermophilic biofilm. Genome-based metabolic reconstruction and transcriptional profiling revealed that positively responding MAGs mainly are involved in hydrolysis of grass silage, acidogenesis and / or acetogenesis. CONCLUSIONS An integrated -omics approach enabled the identification of new AD biofilm keystone species featuring outstanding performance under stress conditions such as increased OLRs. Genome-based knowledge on the metabolic potential and transcriptional activity of responsive microbiome members will contribute to the development of improved microbiological AD management strategies for biomethanation of renewable biomass.
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Affiliation(s)
- Irena Maus
- Bielefeld University, Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Universitätsstr. 27, 33615 Bielefeld, Germany
| | - Michael Klocke
- Department Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Jaqueline Derenkó
- Department Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Yvonne Stolze
- Bielefeld University, Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Universitätsstr. 27, 33615 Bielefeld, Germany
| | - Michael Beckstette
- Helmholtz Centre for Infection Research, Microbial Infection Biology / Experimental Immunology, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Carsten Jost
- Department Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Daniel Wibberg
- Bielefeld University, Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Universitätsstr. 27, 33615 Bielefeld, Germany
| | - Jochen Blom
- Department Bioinformatics and Systems Biology, Justus-Liebig University Gießen, Heinrich-Buff-Ring 58, 35392 Giessen, Germany
| | - Christian Henke
- Faculty of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Katharina Willenbücher
- Department Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Madis Rumming
- Faculty of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Antje Rademacher
- Department Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Alfred Pühler
- Bielefeld University, Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Universitätsstr. 27, 33615 Bielefeld, Germany
| | - Alexander Sczyrba
- Bielefeld University, Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Universitätsstr. 27, 33615 Bielefeld, Germany
- Faculty of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Andreas Schlüter
- Bielefeld University, Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Universitätsstr. 27, 33615 Bielefeld, Germany
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Abstract
The microbiome residing in anaerobic digesters drives the anaerobic digestion (AD) process to convert various feedstocks to biogas as a renewable source of energy. This microbiome has been investigated in numerous studies in the last century. The early studies used cultivation-based methods and analysis to identify the four guilds (or functional groups) of microorganisms. Molecular biology techniques overcame the limitations of cultivation-based methods and allowed the identification of unculturable microorganisms, revealing the high diversity of microorganisms involved in AD. In the past decade, omics technologies, including metataxonomics, metagenomics, metatranscriptomics, metaproteomics, and metametabolomics, have been or start to be used in comprehensive analysis and studies of biogas-producing microbiomes. In this chapter, we reviewed the utilities and limitations of these analysis methods, techniques, and technologies when they were used in studies of biogas-producing microbiomes, as well as the new information on diversity, composition, metabolism, and syntrophic interactions of biogas-producing microbiomes. We also discussed the current knowledge gaps and the research needed to further improve AD efficiency and stability.
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Bremges A, Fritz A, McHardy AC. CAMITAX: Taxon labels for microbial genomes. Gigascience 2020; 9:giz154. [PMID: 31909794 PMCID: PMC6946028 DOI: 10.1093/gigascience/giz154] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 11/23/2019] [Accepted: 12/10/2019] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The number of microbial genome sequences is increasing exponentially, especially thanks to recent advances in recovering complete or near-complete genomes from metagenomes and single cells. Assigning reliable taxon labels to genomes is key and often a prerequisite for downstream analyses. FINDINGS We introduce CAMITAX, a scalable and reproducible workflow for the taxonomic labelling of microbial genomes recovered from isolates, single cells, and metagenomes. CAMITAX combines genome distance-, 16S ribosomal RNA gene-, and gene homology-based taxonomic assignments with phylogenetic placement. It uses Nextflow to orchestrate reference databases and software containers and thus combines ease of installation and use with computational reproducibility. We evaluated the method on several hundred metagenome-assembled genomes with high-quality taxonomic annotations from the TARA Oceans project, and we show that the ensemble classification method in CAMITAX improved on all individual methods across tested ranks. CONCLUSIONS While we initially developed CAMITAX to aid the Critical Assessment of Metagenome Interpretation (CAMI) initiative, it evolved into a comprehensive software package to reliably assign taxon labels to microbial genomes. CAMITAX is available under Apache License 2.0 at https://github.com/CAMI-challenge/CAMITAX.
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Affiliation(s)
- Andreas Bremges
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Adrian Fritz
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Alice C McHardy
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
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Campanaro S, Treu L, Rodriguez-R LM, Kovalovszki A, Ziels RM, Maus I, Zhu X, Kougias PG, Basile A, Luo G, Schlüter A, Konstantinidis KT, Angelidaki I. New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:25. [PMID: 32123542 PMCID: PMC7038595 DOI: 10.1186/s13068-020-01679-y] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 02/08/2020] [Indexed: 05/20/2023]
Abstract
BACKGROUND Microorganisms in biogas reactors are essential for degradation of organic matter and methane production. However, a comprehensive genome-centric comparison, including relevant metadata for each sample, is still needed to identify the globally distributed biogas community members and serve as a reliable repository. RESULTS Here, 134 publicly available metagenomes derived from different biogas reactors were used to recover 1635 metagenome-assembled genomes (MAGs) representing different biogas bacterial and archaeal species. All genomes were estimated to be > 50% complete and nearly half ≥ 90% complete with ≤ 5% contamination. In most samples, specialized microbial communities were established, while only a few taxa were widespread among the different reactor systems. Metabolic reconstruction of the MAGs enabled the prediction of functional traits related to biomass degradation and methane production from waste biomass. An extensive evaluation of the replication index provided an estimation of the growth dynamics for microbes involved in different steps of the food chain. CONCLUSIONS The outcome of this study highlights a high flexibility of the biogas microbiome, allowing it to modify its composition and to adapt to the environmental conditions, including temperatures and a wide range of substrates. Our findings enhance our mechanistic understanding of the AD microbiome and substantially extend the existing repository of genomes. The established database represents a relevant resource for future studies related to this engineered ecosystem.
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Affiliation(s)
- Stefano Campanaro
- Department of Biology, University of Padova, Via U. Bassi 58/b, 35121 Padua, Italy
- CRIBI Biotechnology Center, University of Padova, 35131 Padua, Italy
| | - Laura Treu
- Department of Biology, University of Padova, Via U. Bassi 58/b, 35121 Padua, Italy
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Luis M. Rodriguez-R
- School of Civil & Environmental Engineering and School of Biological Sciences (Adjunct), Georgia Institute of Technology, 311 Ferst Drive, Atlanta, GA 30332-0512 USA
| | - Adam Kovalovszki
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Ryan M. Ziels
- Department of Civil Engineering, University of British Columbia, Vancouver, BC Canada
| | - Irena Maus
- Genome Research of Industrial Microorganisms, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany
| | - Xinyu Zhu
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Panagiotis G. Kougias
- Hellenic Agricultural Organization DEMETER, Soil and Water Resources Institute, Thermi-Thessaloniki, Greece
| | - Arianna Basile
- Department of Biology, University of Padova, Via U. Bassi 58/b, 35121 Padua, Italy
| | - Gang Luo
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai, 200433 China
| | - Andreas Schlüter
- Hellenic Agricultural Organization DEMETER, Soil and Water Resources Institute, Thermi-Thessaloniki, Greece
| | - Konstantinos T. Konstantinidis
- School of Civil & Environmental Engineering and School of Biological Sciences (Adjunct), Georgia Institute of Technology, 311 Ferst Drive, Atlanta, GA 30332-0512 USA
| | - Irini Angelidaki
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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Lian S, Wu L, Nikolausz M, Lechtenfeld OJ, Richnow HH. 2H and 13C isotope fractionation analysis of organophosphorus compounds for characterizing transformation reactions in biogas slurry: Potential for anaerobic treatment of contaminated biomass. WATER RESEARCH 2019; 163:114882. [PMID: 31352241 DOI: 10.1016/j.watres.2019.114882] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 07/10/2019] [Accepted: 07/16/2019] [Indexed: 06/10/2023]
Abstract
The ability of anaerobic digestion (AD) to eliminate organophosphorus model compounds (OPs) with structural elements of phosphate, phosphorothioate and phosphorodithioate esters was studied. The enzymatic mechanism of the first irreversible degradation reaction was characterized using metabolite pattern and kinetic 2H/13C-isotope effect in original, cell-free and heat sterilized biogas slurry. The isotope fractionation study suggests different modes of degradation reactions. Representatives for phosphate ester, tris(2-chloroethyl) phosphate and tris(1,3-dichloro-2-propyl) phosphate, were hydrolyzed in biogas slurry without carbon or hydrogen isotope fractionation. Representatives for phosphorodithioate, Dimethoate and Malathion, were degraded in original slurry yielding carbon enrichment factor (εC) of -0.6 ± 0.1‰ and -5.5 ± 0.1‰ (-0.9 ± 0.1‰ and -7.2 ± 0.5‰ in cell-free slurry), without hydrogen isotope fractionation. Phosphorothioate degradation represented by Parathion and Parathion-methyl yielded surprisingly different εC (-0.7 ± 0.2 and -3.6 ± 0.4‰) and εH (-33 ± 5 and -5 ± 1‰) in original slurry compared to cell-free slurry (εC = -2.5 ± 0.5 and -8.6 ± 1.4‰; εH = -61 ± 10 and -10 ± 3‰) suggesting H-C bond cleavage. Degradation of Parathion and Parathion-methyl in sterilized slurry gave carbon but not hydrogen fractionation implying relative thermostable enzymatic activity with different mechanism. The correlation of 2H and 13C stable isotope fractionation of Parathion in biogas slurry showed distinct pattern (Λoriginal = 31 ± 11, Λcell-free = 20 ± 2), indicating different mechanism from chemical hydrolysis. Overall, AD can be a potential treatment for OPs contaminated biomass or contaminated organic waste material.
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Affiliation(s)
- Shujuan Lian
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318, Leipzig, Germany.
| | - Langping Wu
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318, Leipzig, Germany.
| | - Marcell Nikolausz
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318, Leipzig, Germany.
| | - Oliver J Lechtenfeld
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318, Leipzig, Germany.
| | - Hans H Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318, Leipzig, Germany.
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27
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Heyer R, Schallert K, Siewert C, Kohrs F, Greve J, Maus I, Klang J, Klocke M, Heiermann M, Hoffmann M, Püttker S, Calusinska M, Zoun R, Saake G, Benndorf D, Reichl U. Metaproteome analysis reveals that syntrophy, competition, and phage-host interaction shape microbial communities in biogas plants. MICROBIOME 2019; 7:69. [PMID: 31029164 PMCID: PMC6486700 DOI: 10.1186/s40168-019-0673-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 03/26/2019] [Indexed: 05/30/2023]
Abstract
BACKGROUND In biogas plants, complex microbial communities produce methane and carbon dioxide by anaerobic digestion of biomass. For the characterization of the microbial functional networks, samples of 11 reactors were analyzed using a high-resolution metaproteomics pipeline. RESULTS Examined methanogenesis archaeal communities were either mixotrophic or strictly hydrogenotrophic in syntrophy with bacterial acetate oxidizers. Mapping of identified metaproteins with process steps described by the Anaerobic Digestion Model 1 confirmed its main assumptions and also proposed some extensions such as syntrophic acetate oxidation or fermentation of alcohols. Results indicate that the microbial communities were shaped by syntrophy as well as competition and phage-host interactions causing cell lysis. For the families Bacillaceae, Enterobacteriaceae, and Clostridiaceae, the number of phages exceeded up to 20-fold the number of host cells. CONCLUSION Phage-induced cell lysis might slow down the conversion of substrates to biogas, though, it could support the growth of auxotrophic microbes by cycling of nutrients.
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Affiliation(s)
- R. Heyer
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany
| | - K. Schallert
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany
| | - C. Siewert
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Sandtorstraße 1, 39106 Magdeburg, Germany
| | - F. Kohrs
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany
| | - J. Greve
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany
| | - I. Maus
- Center for Biotechnology (CeBiTec), University Bielefeld, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - J. Klang
- Department Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - M. Klocke
- Department Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - M. Heiermann
- Department Technology Assessment and Substance Cycles, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - M. Hoffmann
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Sandtorstraße 1, 39106 Magdeburg, Germany
| | - S. Püttker
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany
| | - M. Calusinska
- Environmental Research and Innovation (ERIN), Luxembourg Institute of Science and Technology, 41 rue du Brill, L-4422 Belvaux, Luxembourg
| | - R. Zoun
- Otto von Guericke University, Institute for Databases and Software Engineering, Universitätsplatz 2, 39106 Magdeburg, Germany
| | - G. Saake
- Otto von Guericke University, Institute for Databases and Software Engineering, Universitätsplatz 2, 39106 Magdeburg, Germany
| | - D. Benndorf
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Sandtorstraße 1, 39106 Magdeburg, Germany
| | - U. Reichl
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Sandtorstraße 1, 39106 Magdeburg, Germany
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Šafarič L, Shakeri Yekta S, Liu T, Svensson BH, Schnürer A, Bastviken D, Björn A. Dynamics of a Perturbed Microbial Community during Thermophilic Anaerobic Digestion of Chemically Defined Soluble Organic Compounds. Microorganisms 2018; 6:microorganisms6040105. [PMID: 30314333 PMCID: PMC6313639 DOI: 10.3390/microorganisms6040105] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 10/06/2018] [Accepted: 10/10/2018] [Indexed: 11/22/2022] Open
Abstract
Knowledge of microbial community dynamics in relation to process perturbations is fundamental to understand and deal with the instability of anaerobic digestion (AD) processes. This study aims to investigate the microbial community structure and function of a thermophilic AD process, fed with a chemically defined substrate, and its association with process performance stability. Next generation amplicon sequencing of 16S ribosomal RNA (rRNA) genes revealed that variations in relative abundances of the predominant bacterial species, Defluviitoga tunisiensis and Anaerobaculum hydrogeniformans, were not linked to the process performance stability, while dynamics of bacterial genera of low abundance, Coprothermobacter and Defluviitoga (other than D. tunisiensis), were associated with microbial community function and process stability. A decrease in the diversity of the archaeal community was observed in conjunction with process recovery and stable performance, implying that the high abundance of specific archaeal group(s) contributed to the stable AD. Dominance of hydrogenotrophic Methanoculleus particularly corresponded to an enhanced microbial acetate and propionate turnover capacity, whereas the prevalence of hydrogenotrophic Methanothermobacter and acetoclastic Methanosaeta was associated with instable AD. Acetate oxidation via syntrophic interactions between Coprothermobacter and Methanoculleus was potentially the main methane-formation pathway during the stable process. We observed that supplementation of Se and W to the medium improved the propionate turnover by the thermophilic consortium. The outcomes of our study provided insights into the community dynamics and trace element requirements in relation to the process performance stability of thermophilic AD.
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Affiliation(s)
- Luka Šafarič
- Department of Thematic Studies-Environmental Change, Linköping University, 581 83 Linköping, Sweden.
- Biogas Research Center, Linköping University, 581 83 Linköping, Sweden.
| | - Sepehr Shakeri Yekta
- Department of Thematic Studies-Environmental Change, Linköping University, 581 83 Linköping, Sweden.
- Biogas Research Center, Linköping University, 581 83 Linköping, Sweden.
| | - Tong Liu
- Department of Molecular Science, Swedish University of Agricultural Science, Uppsala BioCenter, 75007 Uppsala, Sweden.
| | - Bo H Svensson
- Department of Thematic Studies-Environmental Change, Linköping University, 581 83 Linköping, Sweden.
- Biogas Research Center, Linköping University, 581 83 Linköping, Sweden.
| | - Anna Schnürer
- Department of Thematic Studies-Environmental Change, Linköping University, 581 83 Linköping, Sweden.
- Biogas Research Center, Linköping University, 581 83 Linköping, Sweden.
- Department of Molecular Science, Swedish University of Agricultural Science, Uppsala BioCenter, 75007 Uppsala, Sweden.
| | - David Bastviken
- Department of Thematic Studies-Environmental Change, Linköping University, 581 83 Linköping, Sweden.
| | - Annika Björn
- Department of Thematic Studies-Environmental Change, Linköping University, 581 83 Linköping, Sweden.
- Biogas Research Center, Linköping University, 581 83 Linköping, Sweden.
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29
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Substrate-Induced Response in Biogas Process Performance and Microbial Community Relates Back to Inoculum Source. Microorganisms 2018; 6:microorganisms6030080. [PMID: 30081593 PMCID: PMC6163493 DOI: 10.3390/microorganisms6030080] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 08/01/2018] [Accepted: 08/02/2018] [Indexed: 12/31/2022] Open
Abstract
This study investigated whether biogas reactor performance, including microbial community development, in response to a change in substrate composition is influenced by initial inoculum source. For the study, reactors previously operated with the same grass–manure mixture for more than 120 days and started with two different inocula were used. These reactors initially showed great differences depending on inoculum source, but eventually showed similar performance and overall microbial community structure. At the start of the present experiment, the substrate was complemented with milled feed wheat, added all at once or divided into two portions. The starting hypothesis was that process performance depends on initial inoculum source and microbial diversity, and thus that reactor performance is influenced by the feeding regime. In response to the substrate change, all reactors showed increases and decreases in volumetric and specific methane production, respectively. However, specific methane yield and development of the microbial community showed differences related to the initial inoculum source, confirming the hypothesis. However, the different feeding regimes had only minor effects on process performance and overall community structure, but still induced differences in the cellulose-degrading community and in cellulose degradation.
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30
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Tomazetto G, Hahnke S, Wibberg D, Pühler A, Klocke M, Schlüter A. Proteiniphilum saccharofermentans str. M3/6 T isolated from a laboratory biogas reactor is versatile in polysaccharide and oligopeptide utilization as deduced from genome-based metabolic reconstructions. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2018; 18:e00254. [PMID: 29892569 PMCID: PMC5993710 DOI: 10.1016/j.btre.2018.e00254] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 04/26/2018] [Accepted: 04/26/2018] [Indexed: 12/16/2022]
Abstract
Proteiniphilum saccharofermentans str. M3/6T is a recently described species within the family Porphyromonadaceae (phylum Bacteroidetes), which was isolated from a mesophilic laboratory-scale biogas reactor. The genome of the strain was completely sequenced and manually annotated to reconstruct its metabolic potential regarding biomass degradation and fermentation pathways. The P. saccharofermentans str. M3/6T genome consists of a 4,414,963 bp chromosome featuring an average GC-content of 43.63%. Genome analyses revealed that the strain possesses 3396 protein-coding sequences. Among them are 158 genes assigned to the carbohydrate-active-enzyme families as defined by the CAZy database, including 116 genes encoding glycosyl hydrolases (GHs) involved in pectin, arabinogalactan, hemicellulose (arabinan, xylan, mannan, β-glucans), starch, fructan and chitin degradation. The strain also features several transporter genes, some of which are located in polysaccharide utilization loci (PUL). PUL gene products are involved in glycan binding, transport and utilization at the cell surface. In the genome of strain M3/6T, 64 PUL are present and most of them in association with genes encoding carbohydrate-active enzymes. Accordingly, the strain was predicted to metabolize several sugars yielding carbon dioxide, hydrogen, acetate, formate, propionate and isovalerate as end-products of the fermentation process. Moreover, P. saccharofermentans str. M3/6T encodes extracellular and intracellular proteases and transporters predicted to be involved in protein and oligopeptide degradation. Comparative analyses between P. saccharofermentans str. M3/6T and its closest described relative P. acetatigenes str. DSM 18083T indicate that both strains share a similar metabolism regarding decomposition of complex carbohydrates and fermentation of sugars.
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Affiliation(s)
- Geizecler Tomazetto
- Brazilian Bioethanol Science and Technology Laboratory – CTBE/CNPEM, 10000 Giuseppe Maximo Scolfaro St, Zip Code 13083-852 Campinas, SP, Brazil
| | - Sarah Hahnke
- Department Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany
| | - Alfred Pühler
- Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany
| | - Michael Klocke
- Department Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany
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31
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Han R, Yuan Y, Cao Q, Li Q, Chen L, Zhu D, Liu D. PCR-DGGE Analysis on Microbial Community Structure of Rural Household Biogas Digesters in Qinghai Plateau. Curr Microbiol 2017; 75:541-549. [PMID: 29234881 DOI: 10.1007/s00284-017-1414-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 12/05/2017] [Indexed: 12/16/2022]
Abstract
To investigate contribution of environmental factor(s) to microbial community structure(s) involved in rural household biogas fermentation at Qinghai Plateau, we collected slurry samples from 15 digesters, with low-temperature working conditions (11.1-15.7 °C) and evenly distributed at three counties (Datong, Huangyuan, and Ledu) with cold plateau climate, to perform polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and further sequencing. The bacterial communities in the total 15 digesters were classified into 38 genera with Mangroviflexus (12.1%) as the first dominant, and the archaeal communities into ten genera with Methanogenium (38.5%) as the most dominant. For each county, the digesters with higher biogas production, designated as HP digesters, exclusively had 1.6-3.1 °C higher fermentation temperature and the unique bacterial structure composition related, i.e., unclassified Clostridiales for all the HP digesters and unclassified Marinilabiliaceae and Proteiniclasticum for Ledu HP digesters. Regarding archaeal structure composition, Methanogenium exhibited significantly higher abundances at all the HP digesters and Thermogymnomonas was the unique species only identified at Ledu HP digesters with higher-temperature conditions. Redundancy analysis also confirmed the most important contribution of temperature to the microbial community structures investigated. This report emphasized the correlation between temperature and specific microbial community structure(s) that would benefit biogas production of rural household digesters at Qinghai Plateau.
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Affiliation(s)
- Rui Han
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, Hubei, China.,Qinghai Key Laboratory of Vegetable Genetics and Physiology, Academy of Agriculture and Forestry, Qinghai University, Xining, 810016, Qinghai, China
| | - Yongze Yuan
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, Hubei, China
| | - Qianwen Cao
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, Hubei, China
| | - Quanhui Li
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Academy of Agriculture and Forestry, Qinghai University, Xining, 810016, Qinghai, China
| | - Laisheng Chen
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Academy of Agriculture and Forestry, Qinghai University, Xining, 810016, Qinghai, China
| | - Derui Zhu
- Research Center of Basic Medical Sciences, Qinghai University Medical College, Xining, 810006, Qinghai, China.
| | - Deli Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, Hubei, China.
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