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Wang H, Fu X, Huang H, Shen D, Fan D, Zhu L, Dai X, Dong B. Bioenergy recovery and carbon emissions benefits of short-term bio-thermophilic pretreatment on low organic sewage sludge anaerobic digestion: A pilot-scale study. J Environ Sci (China) 2025; 148:321-335. [PMID: 39095168 DOI: 10.1016/j.jes.2023.08.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/19/2023] [Accepted: 08/20/2023] [Indexed: 08/04/2024]
Abstract
Sewage sludge in cities of Yangzi River Belt, China, generally exhibits a lower organic content and higher silt contentdue to leakage of drainage system, which caused low bioenergy recovery and carbon emission benefits in conventional anaerobic digestion (CAD). Therefore, this paper is on a pilot scale, a bio-thermophilic pretreatment anaerobic digestion (BTPAD) for low organic sludge (volatile solids (VS) of 4%) was operated with a long-term continuous flow of 200 days. The VS degradation rate and CH4 yield of BTPAD increased by 19.93% and 53.33%, respectively, compared to those of CAD. The analysis of organic compositions in sludge revealed that BTPAD mainly improved the hydrolysis of proteins in sludge. Further analysis of microbial community proportions by high-throughput sequencing revealed that the short-term bio-thermophilic pretreatment was enriched in Clostridiales, Coprothermobacter and Gelria, was capable of hydrolyzing acidified proteins, and provided more volatile fatty acid (VFA) for the subsequent reaction. Biome combined with fluorescence quantitative polymerase chain reaction (PCR) analysis showed that the number of bacteria with high methanogenic capacity in BTPAD was much higher than that in CAD during the medium temperature digestion stage, indicating that short-term bio-thermophilic pretreatment could provide better methanogenic conditions for BTPAD. Furthermore, the greenhouse gas emission footprint analysis showed that short-term bio-thermophilic pretreatment could reduce the carbon emission of sludge anaerobic digestion system by 19.18%.
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Affiliation(s)
- Hui Wang
- College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Xiang Fu
- College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Haozhe Huang
- College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Danni Shen
- Yangtze Eco-Environment Engineering Research Center, China Three Gorges Corporation, Beijing 100038, China; Yangtze River Eco-Environmental Engineering Research Center, Shanghai Investigation, Design and Research Institute Co., LTD, Shanghai 200092, China
| | - Dongdong Fan
- China Construction Third Engineering Bureau First Engineering Co., Ltd., Wuhan 430000, China
| | - Liming Zhu
- China Construction Third Engineering Bureau First Engineering Co., Ltd., Wuhan 430000, China
| | - Xiaohu Dai
- College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Bin Dong
- College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Yangtze Eco-Environment Engineering Research Center, China Three Gorges Corporation, Beijing 100038, China.
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2
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Wu M, Yang ZH, Jiang TB, Zhang WW, Wang ZW, Hou QX. Enhancing sludge methanogenesis with changed micro-environment of anaerobic microorganisms by Fenton iron mud. CHEMOSPHERE 2023; 341:139884. [PMID: 37648172 DOI: 10.1016/j.chemosphere.2023.139884] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 06/14/2023] [Accepted: 08/17/2023] [Indexed: 09/01/2023]
Abstract
Conductive materials have been demonstrated to enhance sludge methanogenesis, but few researches have concentrated on the interaction among conductive materials, microorganisms and their immediate living environment. In this study, Fenton iron mud with a high abundance of Fe(III) was recycled and applied in anaerobic reactors to promote anaerobic digestion (AD) process. The results show that the primary content of extracellular polymeric substances (EPS) such as polysaccharides and proteins increased significantly, possibly promoting microbial aggregation. Furthermore, with the increment of redox mediators including humic substances in EPS and Fe(III) introduced by Fenton iron mud, the direct interspecies electron transfer (DIET) between methanogens and interacting bacteria could be accelerated, which enhanced the rate of methanogenesis in anaerobic digestion (35.21 ± 4.53% increase compared to the control). The further analysis of the anaerobic microbial community confirmed the fact that Fenton iron mud enriched functional microorganisms, such as the abundance of CO2-reducing (e.g. Chloroflexi) and Fe(III)-reducing bacteria (e.g., Tepidimicrobium), thereby expediting the electron transfer reaction in the AD process via microbial DIET and dissimilatory iron reduction (DIR). This work will make it possible for using the recycled hazardous material - Fenton iron mud to improve the performance of anaerobic granular sludge during methanogenesis.
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Affiliation(s)
- Ming Wu
- Tianjin Key Laboratory of Pulp and Paper, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Zhen-Hu Yang
- Tianjin Key Laboratory of Pulp and Paper, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Tong-Bao Jiang
- Tianjin Key Laboratory of Pulp and Paper, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Wen-Wen Zhang
- Tianjin Key Laboratory of Pulp and Paper, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Zhi-Wei Wang
- College of Light Industry and Food Engineering, Guangxi University, Nanning, 530004, China
| | - Qing-Xi Hou
- Tianjin Key Laboratory of Pulp and Paper, Tianjin University of Science & Technology, Tianjin, 300457, China.
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Hassa J, Tubbesing TJ, Maus I, Heyer R, Benndorf D, Effenberger M, Henke C, Osterholz B, Beckstette M, Pühler A, Sczyrba A, Schlüter A. Uncovering Microbiome Adaptations in a Full-Scale Biogas Plant: Insights from MAG-Centric Metagenomics and Metaproteomics. Microorganisms 2023; 11:2412. [PMID: 37894070 PMCID: PMC10608942 DOI: 10.3390/microorganisms11102412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 10/29/2023] Open
Abstract
The current focus on renewable energy in global policy highlights the importance of methane production from biomass through anaerobic digestion (AD). To improve biomass digestion while ensuring overall process stability, microbiome-based management strategies become more important. In this study, metagenomes and metaproteomes were used for metagenomically assembled genome (MAG)-centric analyses to investigate a full-scale biogas plant consisting of three differentially operated digesters. Microbial communities were analyzed regarding their taxonomic composition, functional potential, as well as functions expressed on the proteome level. Different abundances of genes and enzymes related to the biogas process could be mostly attributed to different process parameters. Individual MAGs exhibiting different abundances in the digesters were studied in detail, and their roles in the hydrolysis, acidogenesis and acetogenesis steps of anaerobic digestion could be assigned. Methanoculleus thermohydrogenotrophicum was an active hydrogenotrophic methanogen in all three digesters, whereas Methanothermobacter wolfeii was more prevalent at higher process temperatures. Further analysis focused on MAGs, which were abundant in all digesters, indicating their potential to ensure biogas process stability. The most prevalent MAG belonged to the class Limnochordia; this MAG was ubiquitous in all three digesters and exhibited activity in numerous pathways related to different steps of AD.
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Affiliation(s)
- Julia Hassa
- Genome Research of Industrial Microorganisms, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany; (J.H.)
| | - Tom Jonas Tubbesing
- Computational Metagenomics Group, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; (T.J.T.)
| | - Irena Maus
- Genome Research of Industrial Microorganisms, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany; (J.H.)
| | - Robert Heyer
- Multidimensional Omics Data Analyses Group, Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Bunsen-Kirchhoff-Straße 11, Dortmund 44139, Germany
- Multidimensional Omics Data Analyses Group, Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Dirk Benndorf
- Biosciences and Process Engineering, Anhalt University of Applied Sciences, Bernburger Straße 55, Postfach 1458, 06366 Köthen, Germany
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
| | - Mathias Effenberger
- Bavarian State Research Center for Agriculture, Institute for Agricultural Engineering and Animal Husbandry, Vöttinger Straße 36, 85354 Freising, Germany
| | - Christian Henke
- Computational Metagenomics Group, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; (T.J.T.)
| | - Benedikt Osterholz
- Computational Metagenomics Group, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; (T.J.T.)
| | - Michael Beckstette
- Computational Metagenomics Group, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; (T.J.T.)
| | - Alfred Pühler
- Genome Research of Industrial Microorganisms, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany; (J.H.)
| | - Alexander Sczyrba
- Computational Metagenomics Group, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; (T.J.T.)
| | - Andreas Schlüter
- Genome Research of Industrial Microorganisms, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany; (J.H.)
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Wirth R, Bagi Z, Shetty P, Szuhaj M, Cheung TTS, Kovács KL, Maróti G. Inter-kingdom interactions and stability of methanogens revealed by machine-learning guided multi-omics analysis of industrial-scale biogas plants. THE ISME JOURNAL 2023:10.1038/s41396-023-01448-3. [PMID: 37286740 DOI: 10.1038/s41396-023-01448-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/23/2023] [Accepted: 05/26/2023] [Indexed: 06/09/2023]
Abstract
Multi-omics analysis is a powerful tool for the detection and study of inter-kingdom interactions, such as those between bacterial and archaeal members of complex biogas-producing microbial communities. In the present study, the microbiomes of three industrial-scale biogas digesters, each fed with different substrates, were analysed using a machine-learning guided genome-centric metagenomics framework complemented with metatranscriptome data. This data permitted us to elucidate the relationship between abundant core methanogenic communities and their syntrophic bacterial partners. In total, we detected 297 high-quality, non-redundant metagenome-assembled genomes (nrMAGs). Moreover, the assembled 16 S rRNA gene profiles of these nrMAGs showed that the phylum Firmicutes possessed the highest copy number, while the representatives of the archaeal domain had the lowest. Further investigation of the three anaerobic microbial communities showed characteristic alterations over time but remained specific to each industrial-scale biogas plant. The relative abundance of various microorganisms as revealed by metagenome data was independent from corresponding metatranscriptome activity data. Archaea showed considerably higher activity than was expected from their abundance. We detected 51 nrMAGs that were present in all three biogas plant microbiomes with different abundances. The core microbiome correlated with the main chemical fermentation parameters, and no individual parameter emerged as a predominant shaper of community composition. Various interspecies H2/electron transfer mechanisms were assigned to hydrogenotrophic methanogens in the biogas plants that ran on agricultural biomass and wastewater. Analysis of metatranscriptome data revealed that methanogenesis pathways were the most active of all main metabolic pathways.
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Affiliation(s)
- Roland Wirth
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Zoltán Bagi
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Prateek Shetty
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
| | - Márk Szuhaj
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | | | - Kornél L Kovács
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary.
- Faculty of Water Sciences, University of Public Service, Baja, Hungary.
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5
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Rather MA, Agarwal D, Bhat TA, Khan IA, Zafar I, Kumar S, Amin A, Sundaray JK, Qadri T. Bioinformatics approaches and big data analytics opportunities in improving fisheries and aquaculture. Int J Biol Macromol 2023; 233:123549. [PMID: 36740117 DOI: 10.1016/j.ijbiomac.2023.123549] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023]
Abstract
Aquaculture has witnessed an excellent growth rate during the last two decades and offers huge potential to provide nutritional as well as livelihood security. Genomic research has contributed significantly toward the development of beneficial technologies for aquaculture. The existing high throughput technologies like next-generation technologies generate oceanic data which requires extensive analysis using appropriate tools. Bioinformatics is a rapidly evolving science that involves integrating gene based information and computational technology to produce new knowledge for the benefit of aquaculture. Bioinformatics provides new opportunities as well as challenges for information and data processing in new generation aquaculture. Rapid technical advancements have opened up a world of possibilities for using current genomics to improve aquaculture performance. Understanding the genes that govern economically relevant characteristics, necessitates a significant amount of additional research. The various dimensions of data sources includes next-generation DNA sequencing, protein sequencing, RNA sequencing gene expression profiles, metabolic pathways, molecular markers, and so on. Appropriate bioinformatics tools are developed to mine the biologically relevant and commercially useful results. The purpose of this scoping review is to present various arms of diverse bioinformatics tools with special emphasis on practical translation to the aquaculture industry.
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Affiliation(s)
- Mohd Ashraf Rather
- Division of Fish Genetics and Biotechnology, Faculty of Fisheries Ganderbal, Sher-e- Kashmir University of Agricultural Science and Technology, Kashmir, India.
| | - Deepak Agarwal
- Institute of Fisheries Post Graduation Studies OMR Campus, Vaniyanchavadi, Chennai, India
| | | | - Irfan Ahamd Khan
- Division of Fish Genetics and Biotechnology, Faculty of Fisheries Ganderbal, Sher-e- Kashmir University of Agricultural Science and Technology, Kashmir, India
| | - Imran Zafar
- Department of Bioinformatics and Computational Biology, Virtual University Punjab, Pakistan
| | - Sujit Kumar
- Department of Bioinformatics and Computational Biology, Virtual University Punjab, Pakistan
| | - Adnan Amin
- Postgraduate Institute of Fisheries Education and Research Kamdhenu University, Gandhinagar-India University of Kurasthra, India; Department of Aquatic Environmental Management, Faculty of Fisheries Rangil- Ganderbel -SKUAST-K, India
| | - Jitendra Kumar Sundaray
- ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha 751002, India
| | - Tahiya Qadri
- Division of Food Science and Technology, SKUAST-K, Shalimar, India
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6
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Wi J, Lee S, Ahn H. Influence of Dairy Manure as Inoculum Source on Anaerobic Digestion of Swine Manure. Bioengineering (Basel) 2023; 10:bioengineering10040432. [PMID: 37106619 PMCID: PMC10135913 DOI: 10.3390/bioengineering10040432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 03/30/2023] Open
Abstract
Inoculation is a widely used method to improve the efficiency of anaerobic digestion (AD) with a high organic load. This study was conducted to prove the potential of dairy manure as an inoculum source for AD of swine manure. Furthermore, an appropriate inoculum-to-substrate (I/S) ratio was determined to improve methane yield and reduce the required time of AD. We carried out 176 days of anaerobic digestion for five different I/S ratios (3, 1, and 0.3 on a volatile solid basis, dairy manure alone, and swine manure alone) of manure, using solid container submerged lab-scale reactors in mesophilic conditions. As a result, solid-state swine manure inoculated with dairy manure could be digested without inhibition caused by ammonia and volatile fatty acid accumulation. The highest methane yield potential was observed in I/S ratios 1 and 0.3, as 133 and 145 mL CH4·g−1-VS, respectively. The lag phase of swine manure alone was more extended, 41 to 47 days, than other treatments containing dairy manure, directly related to tardy startup. These results revealed that dairy manure can be used as an inoculum source for AD of swine manure. The proper I/S ratios leading to successful AD of swine manure were 1 and 0.3.
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7
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Liu Y, Zhao L, Qiu Z, Yuan H. The gut microbiota diversity of five Orthoptera (Insecta, Polyneoptera) insects determined by DNA metabarcoding. Biodivers Data J 2023; 11:e98162. [PMID: 38327358 PMCID: PMC10848783 DOI: 10.3897/bdj.11.e98162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 02/28/2023] [Indexed: 03/17/2023] Open
Abstract
Most orthopteran insects are phytophagous and some are important pests in agriculture and forests. Many intestinal microflora of Orthoptera insects have been reported, primarily from Acridoidea and there have been few reports of other taxa. In this study, we collected 15 individuals representing five species (Ruspolialineosa, Tetrixjaponica, Erianthusversicolor, Gryllotalpaorientalis and Teleogryllusemma) belonging to five orthopteran superfamilies (Tettigonioidea, Tetrigoidea, Eumastacoidea, Gryllotalpoidea and Grylloidea) to characterise and compare the gut microbiota with greater taxonomic width by performing sequencing analysis of the 16S rRNA V4 region in gut material. A total of 606,053 high-quality sequences and 3,105 OTUs were acquired from 15 gut samples representing 24 phyla, 48 classes, 69 orders, 133 families and 219 genera. Firmicutes and bacteria were the most abundant phyla, followed by Bacteroidetes, Cyanobacteria, Actinobacteria and Acidobacteria. At the genus level, Serratia, Citrobacter, Wolbachia, Lactobacillus and Parabacteroides were the most predominant genera in R.lineosa, T.japonica, E.versicolor, G.orientalis and T.emma, respectively. Both Principal Coordinates Analysis (PCoA) and heatmap results revealed significant differences in bacterial community composition across species. Additionally, alpha diversity analysis indicated the bacterial richness was significantly different amongst the five species.
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Affiliation(s)
- Yantong Liu
- School of Basic Medical Sciences, Xi’an Medical University, xi'an, ChinaSchool of Basic Medical Sciences, Xi’an Medical Universityxi'anChina
| | - Lina Zhao
- College of Life Sciences, Shaanxi Normal University, xi'an, ChinaCollege of Life Sciences, Shaanxi Normal Universityxi'anChina
| | - Zhongying Qiu
- School of Basic Medical Sciences, Xi’an Medical University, xi'an, ChinaSchool of Basic Medical Sciences, Xi’an Medical Universityxi'anChina
| | - Hao Yuan
- School of Basic Medical Sciences, Xi’an Medical University, xi'an, ChinaSchool of Basic Medical Sciences, Xi’an Medical Universityxi'anChina
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8
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A Review of Basic Bioinformatic Techniques for Microbial Community Analysis in an Anaerobic Digester. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9010062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Biogas production involves various types of intricate microbial populations in an anaerobic digester (AD). To understand the anaerobic digestion system better, a broad-based study must be conducted on the microbial population. Deep understanding of the complete metagenomics including microbial structure, functional gene form, similarity/differences, and relationships between metabolic pathways and product formation, could aid in optimization and enhancement of AD processes. With advancements in technologies for metagenomic sequencing, for example, next generation sequencing and high-throughput sequencing, have revolutionized the study of microbial dynamics in anaerobic digestion. This review includes a brief introduction to the basic process of metagenomics research and includes a detailed summary of the various bioinformatics approaches, viz., total investigation of data obtained from microbial communities using bioinformatics methods to expose metagenomics characterization. This includes (1) methods of DNA isolation and sequencing, (2) investigation of anaerobic microbial communities using bioinformatics techniques, (3) application of the analysis of anaerobic microbial community and biogas production, and (4) restriction and prediction of bioinformatics analysis on microbial metagenomics. The review has been concluded, giving a summarized insight into bioinformatic tools and also promoting the future prospects of integrating humungous data with artificial intelligence and neural network software.
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Köller N, Hahnke S, Zverlov V, Wibberg D, Klingl A, Busche T, Klocke M, Pühler A, Schlüter A, Liebl W, Maus I. Anaeropeptidivorans aminofermentans gen. nov., sp. nov., a mesophilic proteolytic salt-tolerant bacterium isolated from a laboratory-scale biogas fermenter, and emended description of Clostridium colinum. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748496 DOI: 10.1099/ijsem.0.005668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
An anaerobic bacterial strain, designated strain M3/9T, was isolated from a laboratory-scale biogas fermenter fed with maize silage supplemented with 5 % wheat straw. Cells were straight, non-motile rods, which stained Gram-negative. Optimal growth occurred between 30 and 40°C, at pH 7.5-8.5, and up to 3.9 % (w/v) NaCl was tolerated. When grown on peptone from casein and soymeal, strain M3/9T produced mainly acetic acid, ethanol, and isobutyric acid. The major cellular fatty acids of the novel strain were C16 : 0 and C16 : 0 DMA. The genome of strain M3/9T is 3757 330 bp in size with a G+C content of 38.45 mol%. Phylogenetic analysis allocated strain M3/9T within the family Lachnospiraceae with Clostridium colinum DSM 6011T and Anaerotignum lactatifermentans DSM 14214T being the most closely related species sharing 57.86 and 56.99% average amino acid identity and 16S rRNA gene sequence similarities of 91.58 and 91.26 %, respectively. Based on physiological, chemotaxonomic and genetic data, we propose the description of a novel species and genus Anaeropeptidivorans aminofermentans gen. nov., sp. nov., represented by the type strain M3/9T (=DSM 100058T=LMG 29527T). In addition, an emended description of Clostridium colinum is provided.
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Affiliation(s)
- Nora Köller
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Sarah Hahnke
- Department of Human Medicine, University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
| | - Vladimir Zverlov
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany.,Institute for Bio- and Geosciences (IBG-5), Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
| | - Andreas Klingl
- Plant Development, Department Biology I - Botany, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
| | - Tobias Busche
- Medical Faculty OWL & Centrum für Biotechnologie (CeBiTec), 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
| | - Alfred Pühler
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Wolfgang Liebl
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Irena Maus
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany.,Institute for Bio- and Geosciences (IBG-5), Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
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10
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Sánchez-Sánchez C, Aranda-Medina M, Rodríguez A, Hernández A, Córdoba MG, Cuadros-Blázquez F, Ruiz-Moyano S. Development of real-time PCR methods for the quantification of Methanoculleus, Methanosarcina and Methanobacterium in anaerobic digestion. J Microbiol Methods 2022; 199:106529. [PMID: 35772572 DOI: 10.1016/j.mimet.2022.106529] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/18/2022] [Accepted: 06/22/2022] [Indexed: 12/27/2022]
Abstract
Anaerobic digestion is a growing technology to manage organic waste and produce bioenergy. To promote this technology, it is essential to know, at the molecular level, the dynamics of microbial communities, specifically the methanogenic community. In the present study, three primer pairs were selected from seven primer pairs which were designed and tested with different concentrations and conditions to detect Methanosarcina, Methanoculleus and Methanobacterium by real-time PCR based on the SYBR Green System. The functionality of the developed methods was demonstrated by the high linear relationship of the standard curves, and the specificity of each primer was empirically verified by testing DNA isolated from methane-producing and non-producing strains. These assays also exhibited good repeatability and reproducibility, which indicates the robustness of the methods. The described primers were successfully used to investigate the methanogenic communities of 10 samples from an anaerobic co-digestion. The genus Methanosarcina was the dominant methanogenic group.
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Affiliation(s)
- Consolación Sánchez-Sánchez
- Departamento de Física Aplicada, Escuela de Ingenierías Agrarias, Universidad de Extremadura, Avda, de Adolfo Suárez S/n, 06007 Badajoz, Spain
| | - Mercedes Aranda-Medina
- Expresión Gráfica, Escuela de Ingenierías Industriales, Campus Universitario, Avda de Elvas sn, 06006 Badajoz, Spain
| | - Alicia Rodríguez
- Instituto Universitario de Investigación de Recursos Agrarios (INURA), Escuela de Ingenierías Agrarias, Universidad de Extremadura, Avda. Adolfo Suarez, s/n, 06071 Badajoz, Spain.
| | - Alejandro Hernández
- Instituto Universitario de Investigación de Recursos Agrarios (INURA), Escuela de Ingenierías Agrarias, Universidad de Extremadura, Avda. Adolfo Suarez, s/n, 06071 Badajoz, Spain
| | - María G Córdoba
- Instituto Universitario de Investigación de Recursos Agrarios (INURA), Escuela de Ingenierías Agrarias, Universidad de Extremadura, Avda. Adolfo Suarez, s/n, 06071 Badajoz, Spain
| | - Francisco Cuadros-Blázquez
- Departamento de Física Aplicada, Escuela de Ingenierías Agrarias, Universidad de Extremadura, Avda, de Adolfo Suárez S/n, 06007 Badajoz, Spain
| | - Santiago Ruiz-Moyano
- Instituto Universitario de Investigación de Recursos Agrarios (INURA), Escuela de Ingenierías Agrarias, Universidad de Extremadura, Avda. Adolfo Suarez, s/n, 06071 Badajoz, Spain
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Kim NK, Lee SH, Kim Y, Park HD. Current understanding and perspectives in anaerobic digestion based on genome-resolved metagenomic approaches. BIORESOURCE TECHNOLOGY 2022; 344:126350. [PMID: 34813924 DOI: 10.1016/j.biortech.2021.126350] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/09/2021] [Accepted: 11/11/2021] [Indexed: 06/13/2023]
Abstract
Anaerobic digestion (AD) is a technique that can be used to treat high concentrations of various organic wastes using a consortium of functionally diverse microorganisms under anaerobic conditions. Methane gas, a beneficial by-product of the AD process, is a renewable energy source that can replace fossil fuels following purification. However, detailed functional roles and metabolic interactions between microbial populations involved in organic waste removal and methanogenesis are yet to be known. Recent metagenomic approaches based on advanced high-throughput sequencing techniques have enabled the exploration of holistic microbial taxonomy and functionality of complex microbial populations involved in the AD process. Gene-centric and genome-centric analyses based on metagenome-assembled genomes are a platform that can be used to study the composition of microbial communities and their roles during AD. This review looks at how these up-to-date metagenomic analyses can be applied to promote our understanding and improved the development of the AD process.
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Affiliation(s)
- Na-Kyung Kim
- School of Civil, Environmental and Architectural Engineering, Korea University, Seoul, South Korea
| | - Sang-Hoon Lee
- School of Civil, Environmental and Architectural Engineering, Korea University, Seoul, South Korea
| | - Yonghoon Kim
- School of Civil, Environmental and Architectural Engineering, Korea University, Seoul, South Korea
| | - Hee-Deung Park
- School of Civil, Environmental and Architectural Engineering, Korea University, Seoul, South Korea.
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12
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Singh A, Moestedt J, Berg A, Schnürer A. Microbiological Surveillance of Biogas Plants: Targeting Acetogenic Community. Front Microbiol 2021; 12:700256. [PMID: 34484143 PMCID: PMC8415747 DOI: 10.3389/fmicb.2021.700256] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 07/21/2021] [Indexed: 11/15/2022] Open
Abstract
Acetogens play a very important role in anaerobic digestion and are essential in ensuring process stability. Despite this, targeted studies of the acetogenic community in biogas processes remain limited. Some efforts have been made to identify and understand this community, but the lack of a reliable molecular analysis strategy makes the detection of acetogenic bacteria tedious. Recent studies suggest that screening of bacterial genetic material for formyltetrahydrofolate synthetase (FTHFS), a key marker enzyme in the Wood-Ljungdahl pathway, can give a strong indication of the presence of putative acetogens in biogas environments. In this study, we applied an acetogen-targeted analyses strategy developed previously by our research group for microbiological surveillance of commercial biogas plants. The surveillance comprised high-throughput sequencing of FTHFS gene amplicons and unsupervised data analysis with the AcetoScan pipeline. The results showed differences in the acetogenic community structure related to feed substrate and operating parameters. They also indicated that our surveillance method can be helpful in the detection of community changes before observed changes in physico-chemical profiles, and that frequent high-throughput surveillance can assist in management towards stable process operation, thus improving the economic viability of biogas plants. To our knowledge, this is the first study to apply a high-throughput microbiological surveillance approach to visualise the potential acetogenic population in commercial biogas digesters.
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Affiliation(s)
- Abhijeet Singh
- Anaerobic Microbiology and Biotechnology Group, Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jan Moestedt
- Tekniska Verken i Linköping AB, Department R&D, Linköping, Sweden
| | | | - Anna Schnürer
- Anaerobic Microbiology and Biotechnology Group, Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
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13
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Structure of Microbial Communities When Complementary Effluents Are Anaerobically Digested. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11031293] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Olive oil and pig productions are important industries in Portugal that generate large volumes of wastewater with high organic load and toxicity, raising environmental concerns. The principal objective of this study is to energetically valorize these organic effluents—piggery effluent and olive mill wastewater—through the anaerobic digestion to the biogas/methane production, by means of the effluent complementarity concept. Several mixtures of piggery effluent were tested, with an increasing percentage of olive mill wastewater. The best performance was obtained for samples of piggery effluent alone and in admixture with 30% of OMW, which provided the same volume of biogas (0.8 L, 70% CH4), 63/75% COD removal, and 434/489 L CH4/kg SVin, respectively. The validation of the process was assessed by molecular evaluation through Next Generation Sequencing (NGS) of the 16S rRNA gene. The structure of the microbial communities for both samples, throughout the anaerobic process, was characterized by the predominance of bacterial populations belonging to the phylum Firmicutes, mainly Clostridiales, with Bacteroidetes being the subdominant populations. Archaea populations belonging to the genus Methanosarcina became predominant throughout anaerobic digestion, confirming the formation of methane mainly from acetate, in line with the greatest removal of volatile fatty acids (VFAs) in these samples.
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14
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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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15
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Kumar Awasthi M, Ravindran B, Sarsaiya S, Chen H, Wainaina S, Singh E, Liu T, Kumar S, Pandey A, Singh L, Zhang Z. Metagenomics for taxonomy profiling: tools and approaches. Bioengineered 2020; 11:356-374. [PMID: 32149573 PMCID: PMC7161568 DOI: 10.1080/21655979.2020.1736238] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 02/20/2020] [Accepted: 02/21/2020] [Indexed: 12/25/2022] Open
Abstract
The study of metagenomics is an emerging field that identifies the total genetic materials in an organism along with the set of all genetic materials like deoxyribonucleic acid and ribose nucleic acid, which play a key role with the maintenance of cellular functions. The best part of this technology is that it gives more flexibility to environmental microbiologists to instantly pioneer the immense genetic variability of microbial communities. However, it is intensively complex to identify the suitable sequencing measures of any specific gene that can exclusively indicate the involvement of microbial metagenomes and be able to advance valuable results about these communities. This review provides an overview of the metagenomic advancement that has been advantageous for aggregation of more knowledge about specific genes, microbial communities and its metabolic pathways. More specific drawbacks of metagenomes technology mainly depend on sequence-based analysis. Therefore, this 'targeted based metagenomics' approach will give comprehensive knowledge about the ecological, evolutionary and functional sequence of significantly important genes that naturally exist in living beings either human, animal and microorganisms from distinctive ecosystems.
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Affiliation(s)
- Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province, China
- Swedish Centre for Resource Recovery, University of Borås, Borås, Sweden
| | - B. Ravindran
- Department of Environmental Energy and Engineering, Kyonggi University Youngtong-Gu, Suwon, South Korea
| | - Surendra Sarsaiya
- Key Laboratory of Basic Pharmacology of Ministry of Education, Zunyi Medical University, Zunyi, Guizhou, China
| | - Hongyu Chen
- Institute of Biology, Freie Universität Berlin Altensteinstr, Berlin, Germany
| | - Steven Wainaina
- Swedish Centre for Resource Recovery, University of Borås, Borås, Sweden
| | - Ekta Singh
- CSIR-National Environmental Engineering Research Institute, Nagpur, India
| | - Tao Liu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Sunil Kumar
- CSIR-National Environmental Engineering Research Institute, Nagpur, India
| | - Ashok Pandey
- Centre for Innovation and Translational Research CSIR-Indian Institute of Toxicology Research, Lucknow, India
| | - Lal Singh
- CSIR-National Environmental Engineering Research Institute, Nagpur, India
| | - Zengqiang Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province, China
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16
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Microalgae Cultivation Technologies as an Opportunity for Bioenergetic System Development—Advantages and Limitations. SUSTAINABILITY 2020. [DOI: 10.3390/su12239980] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Microalgal biomass is currently considered as a sustainable and renewable feedstock for biofuel production (biohydrogen, biomethane, biodiesel) characterized by lower emissions of hazardous air pollutants than fossil fuels. Photobioreactors for microalgae growth can be exploited using many industrial and domestic wastes. It allows locating the commercial microalgal systems in areas that cannot be employed for agricultural purposes, i.e., near heating or wastewater treatment plants and other industrial facilities producing carbon dioxide and organic and nutrient compounds. Despite their high potential, the large-scale algal biomass production technologies are not popular because the systems for biomass production, separation, drainage, and conversion into energy carriers are difficult to explicitly assess and balance, considering the ecological and economical concerns. Most of the studies presented in the literature have been carried out on a small, laboratory scale. This significantly limits the possibility of obtaining reliable data for a comprehensive assessment of the efficiency of such solutions. Therefore, there is a need to verify the results in pilot-scale and the full technical-scale studies. This study summarizes the strengths and weaknesses of microalgal biomass production technologies for bioenergetic applications.
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17
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Vendruscolo ECG, Mesa D, Rissi DV, Meyer BH, de Oliveira Pedrosa F, de Souza EM, Cruz LM. Microbial communities network analysis of anaerobic reactors fed with bovine and swine slurry. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 742:140314. [PMID: 33167293 DOI: 10.1016/j.scitotenv.2020.140314] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 05/18/2020] [Accepted: 06/15/2020] [Indexed: 05/28/2023]
Abstract
Anaerobic digestion can produce biogas as an eco-friendly energy source, driven by a microbial community-dependent process and, as such, suffer influences from many biotic and abiotic factors. Understanding the players and how they interact, the mechanisms involved, what the factors are, and how they influence the biogas process and production is an important way to better control it and make it more efficient. Metagenomic approach is a powerful tool to assess microbial diversity and further, allow correlating changes in microbial communities with multiple factors in virtually all environments. In the present study, we used metagenomic approach to assess microbial community structure changes in two biodigesters, differing in their biogas production capacity, architecture, and feed. A total of 1,440,096 reads of the 16S rRNA gene V4 region were obtained and analyzed. The main bacterial phyla were Firmicutes and Bacteroidetes in both biodigesters, but the biodiversity was greater in the Upflow Anaerobic Sludge Blanket (UASB) reactor fed with bovine manure than in the Continuous Stirred Tank Reactor (CSTR) fed with swine manure, which also correlated with an increase in biogas or methane production. Microbial community structure associated with biodigesters changed seasonally and depended on animal growth stage. Random forest algorithm analysis revealed key microbial taxa for each biodigester. Candidatus Cloacomonas, Methanospirillum, and Methanosphaera were the marker taxa for UASB and the archaea groups Methanobrevibacter and Candidatus Methanoplasma were the marker taxa for CSTR. A high abundance of Candidatus Methanoplasma and Marinimicrobia SAR406 clade suggested lower increments in methane production. Network analysis pointed to negative and positive associations and specific key groups, essential in maintaining the anaerobic digestion (AD) process, as being uncultured Parcubacteria bacteria, Candidatus Cloacomonas, and Candidatus Methanoplasma groups, whose functions in AD require investigation.
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Affiliation(s)
| | - Dany Mesa
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Av. Coronel Francisco H. dos Santos,100, CP 19031, Centro Politécnico, Curitiba, PR, 81531-980, Brazil
| | - Daniel Vasconcelos Rissi
- Sector of Professional and Technological Education, Federal University of Paraná, R. Dr. Alcides Vieira Arcoverde, 1225 - Jardim das Américas, Curitiba, PR, 81520-260, Brazil
| | - Bruno Henrique Meyer
- Department of Informatics, Federal University of Paraná, R. Evaristo F. Ferreira da Costa, 383-391 - Jardim das Américas, Curitiba, PR, 82590-300, Brazil
| | - Fábio de Oliveira Pedrosa
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Av. Coronel Francisco H. dos Santos,100, CP 19031, Centro Politécnico, Curitiba, PR, 81531-980, Brazil
| | - Emanuel Maltempi de Souza
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Av. Coronel Francisco H. dos Santos,100, CP 19031, Centro Politécnico, Curitiba, PR, 81531-980, Brazil
| | - Leonardo Magalhães Cruz
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Av. Coronel Francisco H. dos Santos,100, CP 19031, Centro Politécnico, Curitiba, PR, 81531-980, Brazil; Department of Informatics, Federal University of Paraná, R. Evaristo F. Ferreira da Costa, 383-391 - Jardim das Américas, Curitiba, PR, 82590-300, Brazil
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18
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Luo L, Zhang C, Zhang Z, Peng J, Han Y, Wang P, Kong X, Rizwan HM, Zhang D, Su P, Liu Y. Differences in Tetracycline Antibiotic Resistance Genes and Microbial Community Structure During Aerobic Composting and Anaerobic Digestion. Front Microbiol 2020; 11:583995. [PMID: 33178166 PMCID: PMC7596291 DOI: 10.3389/fmicb.2020.583995] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/18/2020] [Indexed: 12/14/2022] Open
Abstract
Antibiotics are widely added to swine forage and are the main reason for the environmental accumulation of antibiotic resistance genes (ARGs) in swine manure-dwelling microorganisms. Aerobic composting (AC) and anaerobic digestion (AD) are efficient methods for converting swine manure to bio-fertilizer while degrading residual antibiotics. However, the influence of these methods on ARG accumulation and the difference in their efficiency have rarely been investigated. In this study, we explored the variations in four tetracycline antibiotics (TCs) and their associated ARGs and in microbial communities after AC and AD treatment. After full-scale manure AC and AD, the four TCs were removed effectively. AD had a higher TC removal efficiency than AC and a slower rate of TC-associated ARG accumulation. In addition, the community structure was more stable in the AC and AD manures than in untreated manure, and the relationship among microbial species also evolved into competition from mutualism after both AC and AD treatment. It was also speculated that the genera Acholeplasma and Arthrobacter were the possible hosts of tetO, tetW, and tetQ; the shift in the prokaryotic community composition and the alleviation of selective pressure by TC degradation led to decreased relative abundance of ARGs in AD- and AC-treated manure.
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Affiliation(s)
- Luyun Luo
- Yangtze Normal University, Chongqing, China
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Chengjia Zhang
- College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Zhuo Zhang
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Jing Peng
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Yongqin Han
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Pei Wang
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Xiaoting Kong
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Hamid Muhammad Rizwan
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Deyong Zhang
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Pin Su
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Yong Liu
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha, China
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19
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Ferraro A, Massini G, Mazzurco Miritana V, Rosa S, Signorini A, Fabbricino M. A novel enrichment approach for anaerobic digestion of lignocellulosic biomass: Process performance enhancement through an inoculum habitat selection. BIORESOURCE TECHNOLOGY 2020; 313:123703. [PMID: 32580121 DOI: 10.1016/j.biortech.2020.123703] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/12/2020] [Accepted: 06/15/2020] [Indexed: 06/11/2023]
Abstract
Inocula enrichment was performed using an innovative habitat-based selection approach to improve wheat straw (WS) anaerobic digestion (AD) efficiency. The procedure was carried out by sequentially re-inoculating the primary microbial community seven times in subsequent anaerobic reactors containing untreated WS. Re-inocula were performed at different re-inoculum times (24, 48, and 96 h) by moving a porous support mimicking a rumen structure from one batch to the next (S-tests) or re-inoculating only the culture medium (C-tests). Highest H2 production yields were observed after four and five re-inocula (0.08 ± 0.02 NmL h-1 gVS-1 and 0.09 ± 0.02 NmL h-1 gVS-1) for S-24 and S-48, respectively. For S-96, higher CH4 yields were observed after the start-up test and sixth re-inoculum (0.05 ± 0.003 NmL h-1 gVS-1 and 0.04 ± 0.005 NmL h-1 gVS-1, respectively). Accordingly, S-96 showed the highest active Archaea component (7%). C-test microbial communities were dominated by fermenting, hydrogen-producing bacteria and showed lower microbial community diversity than S-tests.
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Affiliation(s)
- Alberto Ferraro
- Department of Civil, Architectural and Environmental Engineering, University of Naples "Federico II", Via Claudio 21, 80125 Naples, Italy.
| | - Giulia Massini
- Department of Energy Technologies, Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Via Anguillarese 301, 00123 Rome, Italy
| | - Valentina Mazzurco Miritana
- Department of Energy Technologies, Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Via Anguillarese 301, 00123 Rome, Italy
| | - Silvia Rosa
- Department of Energy Technologies, Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Via Anguillarese 301, 00123 Rome, Italy
| | - Antonella Signorini
- Department of Energy Technologies, Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Via Anguillarese 301, 00123 Rome, Italy
| | - Massimiliano Fabbricino
- Department of Civil, Architectural and Environmental Engineering, University of Naples "Federico II", Via Claudio 21, 80125 Naples, Italy
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20
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Fontana A, Soldano M, Bellassi P, Fabbri C, Gallucci F, Morelli L, Cappa F. Dynamics of Clostridium genus and hard-cheese spoiling Clostridium species in anaerobic digesters treating agricultural biomass. AMB Express 2020; 10:102. [PMID: 32488433 PMCID: PMC7266885 DOI: 10.1186/s13568-020-01040-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 05/26/2020] [Indexed: 11/29/2022] Open
Abstract
Biogas plants are a widespread renewable energy technology. However, the use of digestate for agronomic purposes has often been a matter of concern. It is controversial whether biogas plants might harbor some pathogenic clostridial species, which represent a biological risk. Moreover, the inhabitance of Clostridium hard-cheese spoiling species in anaerobic digesters can be problematic for hard-cheese manufacturing industries, due to the issue of cheese blowing defects. This study investigated the effect of mesophilic anaerobic digestion processes on the Clostridium consortia distribution over time. Specifically, three lab-scale CSTRs treating agricultural biomass were characterized by considering both the whole microbial community and the cultivable clostridial spores. It is assessed an overall reduction of the Clostridium genus during the anaerobic digestion process. Moreover, it was evidenced a slight, but steady decrease of the cultivable clostridial spores, mainly represented by two pathogenic species, C. perfringens and C. bifermentans, and one hard-cheese spoiling species, C. butyricum. Thus, it is revealed an overall reduction of the clostridial population abundance after the mesophilic anaerobic digestion treatment of agricultural biomass.
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Affiliation(s)
- Alessandra Fontana
- Department for Sustainable Food Process - DiSTAS, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122, Piacenza, Italy.
| | - Mariangela Soldano
- Centro Ricerche Produzioni Animali - C.R.P.A. S.p.A., Viale Timavo, 43/2, 42121, Reggio Emilia, Italy
| | - Paolo Bellassi
- Department for Sustainable Food Process - DiSTAS, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122, Piacenza, Italy
| | - Claudio Fabbri
- Centro Ricerche Produzioni Animali - C.R.P.A. S.p.A., Viale Timavo, 43/2, 42121, Reggio Emilia, Italy
| | - Francesco Gallucci
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria - CREA, Via della Pascolare, 16, Monterotondo, 00015, Rome, Italy
| | - Lorenzo Morelli
- Department for Sustainable Food Process - DiSTAS, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122, Piacenza, Italy
- Centro Ricerche Biotecnologiche, Università Cattolica del Sacro Cuore, Via Milano, 24, 26100, Cremona, Italy
| | - Fabrizio Cappa
- Department for Sustainable Food Process - DiSTAS, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122, Piacenza, Italy
- Centro Ricerche Biotecnologiche, Università Cattolica del Sacro Cuore, Via Milano, 24, 26100, Cremona, Italy
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21
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Lee CG, Baba Y, Asano R, Fukuda Y, Tada C, Nakai Y. Identification of bacteria involved in the decomposition of lignocellulosic biomass treated with cow rumen fluid by metagenomic analysis. J Biosci Bioeng 2020; 130:137-141. [PMID: 32331776 DOI: 10.1016/j.jbiosc.2020.03.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 02/25/2020] [Accepted: 03/20/2020] [Indexed: 10/24/2022]
Abstract
We had developed a new pretreatment system using cow rumen fluid to improve the methane production from lignocellulosic substrates. However, the pretreatment conditions differ from the in-situ rumen environment, therefore different microbes may be involved in plant cell wall decomposition. In the current study, shotgun metagenomic analysis using MiSeq platform was performed to elucidate the bacteria which produce cellulase and hemicellulase in this pretreatment system. The rumen fluid which contained waste paper pieces (0.1% w/v) were incubated at 37°C during 120 h. The fluid samples were collected from the reactor at each time-point and analyzed for chemical properties. Rumen microbial DNA was extracted from 0-h and 60-h samples and subjected to shotgun-metagenomic analysis. After pretreatment, approximately half of cellulose and hemicellulose contents of the waste paper were decomposed and some volatile fatty acids were accumulated. Clostridia (e.g., Ruminococcus and Clostridium) were the predominant bacteria before and after 60-h pretreatment, and their relative abundance was increased during pretreatment. However, Prevotella and Fibrobacter, one of the most dominant bacteria in-situ rumen fluid, were observed less than 3% before incubation and they were decreased after pretreatment. Genes encoding cellulase and hemicellulase were mainly found in Ruminococcus, Clostridium, and Caldicellulosiruptor. Calicellulosiruptor, which had not been previously identified as the predominant genus in lignocellulose decomposition in in-situ rumen conditions, might be considered as the main fibrolytic bacterium in this system. Thus, this study demonstrated that the composition of fibrolytic bacteria in this system was greatly different from those in the in-situ rumen.
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Affiliation(s)
- Chol Gyu Lee
- Graduate School of Agricultural Science, Tohoku University, Osaki, Miyagi 989-6711, Japan.
| | - Yasunori Baba
- Graduate School of Agricultural Science, Tohoku University, Osaki, Miyagi 989-6711, Japan.
| | - Ryoki Asano
- Department of Biotechnology, Faculty of Bioresource Sciences, Akita Prefectural University, Akita, Akita 010-0195, Japan.
| | - Yasuhiro Fukuda
- Graduate School of Agricultural Science, Tohoku University, Osaki, Miyagi 989-6711, Japan.
| | - Chika Tada
- Graduate School of Agricultural Science, Tohoku University, Osaki, Miyagi 989-6711, Japan.
| | - Yutaka Nakai
- Graduate School of Agricultural Science, Tohoku University, Osaki, Miyagi 989-6711, Japan.
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Diverse Microbial Community Profiles of Propionate-Degrading Cultures Derived from Different Sludge Sources of Anaerobic Wastewater Treatment Plants. Microorganisms 2020; 8:microorganisms8020277. [PMID: 32085468 PMCID: PMC7074800 DOI: 10.3390/microorganisms8020277] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/13/2020] [Accepted: 02/16/2020] [Indexed: 11/16/2022] Open
Abstract
Anaerobic digestion (AD) has been used for wastewater treatment and production of renewable energy or biogas. Propionate accumulation is one of the important problems leading to an unstable system and low methane production. Revealing propionate-degrading microbiome is necessary to gain a better knowledge for alleviation of the problem. Herein, we systematically investigated the propionate-degrading cultures enriched from various anaerobic sludge sources of agro-industrial wastewater treatment plants using 16S rRNA gene sequencing. Different microbial profiles were shown even though the methanogenic activities of all cultures were similar. Interestingly, non-classical propionate-degrading key players Smithella, Syntrophomonas, and Methanosaeta were observed as common prevalent taxa in our enriched cultures. Moreover, different hydrogenotrophic methanogens were found specifically to the different sludge sources. The enriched culture of high salinity sludge showed a distinct microbial profile compared to the others, containing mainly Thermovirga, Anaerolinaceae, Methanosaeta, Syntrophobactor, and Methanospirillum. Our microbiome analysis revealed different propionate-degrading community profiles via mainly the Smithella pathway and offers inside information for microbiome manipulation in AD systems to increase biogas production corresponding to their specific microbial communities.
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Wang H, Lim TT, Duong C, Zhang W, Xu C, Yan L, Mei Z, Wang W. Long-Term Mesophilic Anaerobic Co-Digestion of Swine Manure with Corn Stover and Microbial Community Analysis. Microorganisms 2020; 8:microorganisms8020188. [PMID: 32013160 PMCID: PMC7074675 DOI: 10.3390/microorganisms8020188] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/28/2020] [Accepted: 01/28/2020] [Indexed: 01/12/2023] Open
Abstract
Long-term anaerobic co-digestion of swine manure (SM) and corn stover (CS) was conducted using semi-continuously loaded digesters under mesophilic conditions. A preliminary test was first conducted to test the effects of loading rates, and results indicated the 3 g-VS L−1 d−1 was the optimal loading rate. Based on the preliminary results, a verification replicated test was conducted with 3 g-VS L−1 d−1 loading rate and different SM/CS ratios (1:1, 2:1 and 1:2). Results showed that a SM/CS ratio of 2/1 was optimal, based on maximum observed methane-VSdes generation and carbon conversion efficiency (72.56 ± 3.40 mL g−1 and 40.59%, respectively). Amplicon sequencing analysis suggested that microbial diversity was increased with CS loading. Amino-acid-degrading bacteria were abundant in the treatment groups. Archaea Methanoculleus could enhance biogas and methane productions.
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Affiliation(s)
- Haipeng Wang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Agro-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (H.W.); (W.Z.); (C.X.); (L.Y.)
| | - Teng Teeh Lim
- Agriculture Systems Management, Division of Food Systems and Bioengineering, University of Missouri, Columbia, MO 65211-5200, USA; (T.T.L.); (C.D.)
| | - Cuong Duong
- Agriculture Systems Management, Division of Food Systems and Bioengineering, University of Missouri, Columbia, MO 65211-5200, USA; (T.T.L.); (C.D.)
| | - Wei Zhang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Agro-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (H.W.); (W.Z.); (C.X.); (L.Y.)
| | - Congfeng Xu
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Agro-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (H.W.); (W.Z.); (C.X.); (L.Y.)
| | - Lei Yan
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Agro-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (H.W.); (W.Z.); (C.X.); (L.Y.)
| | - Zili Mei
- Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture and Rural Affairs, Chengdu 610041, China;
| | - Weidong Wang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Agro-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (H.W.); (W.Z.); (C.X.); (L.Y.)
- Correspondence: ; Tel.: +86-13836729365
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Lasrado D, Ahankari S, Kar K. Nanocellulose‐based polymer composites for energy applications—A review. J Appl Polym Sci 2020. [DOI: 10.1002/app.48959] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Dylan Lasrado
- School of Mechanical Engineering, Student of EngineeringVIT University Vellore Tamil Nadu 632014 India
| | - Sandeep Ahankari
- School of Mechanical EngineeringVIT University Vellore Tamil Nadu 632014 India
| | - Kamal Kar
- Department of Mechanical Engineering and Materials Science ProgrammeIIT Kanpur Kanpur Uttar Pradesh 208016 India
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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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Genome-Centered Metagenomics Analysis Reveals the Microbial Interactions of a Syntrophic Consortium during Methane Generation in a Decentralized Wastewater Treatment System. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app10010135] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The application of anaerobic digestors to decentralized wastewater treatment systems (DWTS) has gained momentum worldwide due to their ease of operation, high efficiency, and ability to recycle wastewater. However, the microbial mechanisms responsible for the high efficiency and ability of DWTS to recycle wastewater are still unclear. In this study, the microbial community structure and function of two different anaerobic bioreactors (a primary sludge digestor, PSD, and anaerobic membrane bioreactor, AnMBR) of a DWTS located in Germany was investigated using 16S rRNA gene amplicon and metagenomic sequencing, respectively. The results showed that the microbial community structure was remarkably different in PSD and AnMBR. Methanobacteriaceae and Syntrophaceae were identified as the families that significantly differed in abundance between these two bioreactors. We also used genome-centered metagenomics to predict the microbial interactions and methane-generating pathway, which yielded 21 near-complete assembled genomes (MAGs) (average completeness of 93.0% and contamination of 2.9%). These MAGs together represented the majority of the microbial community. MAGs affiliated with methanogenic archaea, including Methanobacterium sp., Methanomicrobiales archaea, Methanomassiliicoccales archaea, and Methanosaeta concilii, were recruited, along with other syntrophic bacterial MAGs associated with anaerobic digestion. Key genes encoding enzymes involved in specific carbohydrate-active and methanogenic pathways in MAGs were identified to illustrate the microbial functions and interactions that occur during anaerobic digestion in the wastewater treatment. From the MAG information, it was predicted that bacteria affiliated with Bacteroidetes, Prolixibacteraceae, and Synergistaceae were the key bacteria involved in anaerobic digestion. In the methane production step, Methanobacterium sp. performed hydrogenotrophic methanogenesis, which reduced carbon dioxide to methane with hydrogen as the primary electron donor. Taken together, our findings provide a clear understanding of the methane-generating pathways and highlight the syntrophic interactions that occur during anaerobic digestion in DWTS.
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Genome Analyses and Genome-Centered Metatranscriptomics of Methanothermobacter wolfeii Strain SIV6, Isolated from a Thermophilic Production-Scale Biogas Fermenter. Microorganisms 2019; 8:microorganisms8010013. [PMID: 31861790 PMCID: PMC7022856 DOI: 10.3390/microorganisms8010013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/13/2019] [Accepted: 12/16/2019] [Indexed: 12/18/2022] Open
Abstract
In the thermophilic biogas-producing microbial community, the genus Methanothermobacter was previously described to be frequently abundant. The aim of this study was to establish and analyze the genome sequence of the archaeal strain Methanothermobacter wolfeii SIV6 originating from a thermophilic industrial-scale biogas fermenter and compare it to related reference genomes. The circular chromosome has a size of 1,686,891 bases, featuring a GC content of 48.89%. Comparative analyses considering three completely sequenced Methanothermobacter strains revealed a core genome of 1494 coding sequences and 16 strain specific genes for M. wolfeii SIV6, which include glycosyltransferases and CRISPR/cas associated genes. Moreover, M. wolfeii SIV6 harbors all genes for the hydrogenotrophic methanogenesis pathway and genome-centered metatranscriptomics indicates the high metabolic activity of this strain, with 25.18% of all transcripts per million (TPM) belong to the hydrogenotrophic methanogenesis pathway and 18.02% of these TPM exclusively belonging to the mcr operon. This operon encodes the different subunits of the enzyme methyl-coenzyme M reductase (EC: 2.8.4.1), which catalyzes the final and rate-limiting step during methanogenesis. Finally, fragment recruitment of metagenomic reads from the thermophilic biogas fermenter on the SIV6 genome showed that the strain is abundant (1.2%) within the indigenous microbial community. Detailed analysis of the archaeal isolate M. wolfeii SIV6 indicates its role and function within the microbial community of the thermophilic biogas fermenter, towards a better understanding of the biogas production process and a microbial-based management of this complex process.
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Heyer R, Schallert K, Büdel A, Zoun R, Dorl S, Behne A, Kohrs F, Püttker S, Siewert C, Muth T, Saake G, Reichl U, Benndorf D. A Robust and Universal Metaproteomics Workflow for Research Studies and Routine Diagnostics Within 24 h Using Phenol Extraction, FASP Digest, and the MetaProteomeAnalyzer. Front Microbiol 2019; 10:1883. [PMID: 31474963 PMCID: PMC6707425 DOI: 10.3389/fmicb.2019.01883] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 07/30/2019] [Indexed: 01/29/2023] Open
Abstract
The investigation of microbial proteins by mass spectrometry (metaproteomics) is a key technology for simultaneously assessing the taxonomic composition and the functionality of microbial communities in medical, environmental, and biotechnological applications. We present an improved metaproteomics workflow using an updated sample preparation and a new version of the MetaProteomeAnalyzer software for data analysis. High resolution by multidimensional separation (GeLC, MudPIT) was sacrificed to aim at fast analysis of a broad range of different samples in less than 24 h. The improved workflow generated at least two times as many protein identifications than our previous workflow, and a drastic increase of taxonomic and functional annotations. Improvements of all aspects of the workflow, particularly the speed, are first steps toward potential routine clinical diagnostics (i.e., fecal samples) and analysis of technical and environmental samples. The MetaProteomeAnalyzer is provided to the scientific community as a central remote server solution at www.mpa.ovgu.de.
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Affiliation(s)
- Robert Heyer
- Bioprocess Engineering, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Kay Schallert
- Bioprocess Engineering, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Anja Büdel
- Bioprocess Engineering, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Roman Zoun
- Database Research Group, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Sebastian Dorl
- Bioinformatics Research Group, University of Applied Sciences Upper Austria, Hagenberg, Austria
| | | | - Fabian Kohrs
- Bioprocess Engineering, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Sebastian Püttker
- Bioprocess Engineering, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Corina Siewert
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems Magdeburg, Magdeburg, Germany
| | - Thilo Muth
- Bioinformatics Unit (MF 1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin, Germany
| | - Gunter Saake
- Database Research Group, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Udo Reichl
- Bioprocess Engineering, Otto von Guericke University Magdeburg, Magdeburg, Germany
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems Magdeburg, Magdeburg, Germany
| | - Dirk Benndorf
- Bioprocess Engineering, Otto von Guericke University Magdeburg, Magdeburg, Germany
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems Magdeburg, Magdeburg, Germany
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Spatial Variations of Bacterial Communities of an Anaerobic Lagoon-Type Biodigester Fed with Dairy Manure. Processes (Basel) 2019. [DOI: 10.3390/pr7070408] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Anaerobic digestion technology is being widely employed for sustainable management of organic wastes generated in animal farms, industries, etc. Nevertheless, biodigester microbiome is still considered a “black box” because it is regulated by different physico-chemical and operational factors. In this study, the bacterial diversity and composition in different sites of a full-scale lagoon type biodigester (23,000 m3) fed with dairy manure, viz., the influent, beginning, middle, final and effluent were analyzed. The biodigester registered a total of 1445 OTUs, which demonstrated the complex microbial ecosystem in it. Of them, only six OTUs were shared among all the different sampling points. The most abundant phyla belonged to Firmicutes, Proteobacteria, Latescibacteria and Thermotogae. The Simpson and Shannon index showed that the highest microbial diversity was observed in the beginning point of the biodigester, meanwhile, the lowest diversity was recorded in the middle. Based on the UniFrac distances, microbial communities with high similarity were recorded in the middle and final of the biodigester. It can be clearly observed that bacterial communities varied at the different points of the biodigester. However, based on metagenome predictions using PICRUSt, it was found that independent of the differences in taxonomy and location, bacterial communities maintained similar metabolic functions.
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Schiebenhoefer H, Van Den Bossche T, Fuchs S, Renard BY, Muth T, Martens L. Challenges and promise at the interface of metaproteomics and genomics: an overview of recent progress in metaproteogenomic data analysis. Expert Rev Proteomics 2019; 16:375-390. [PMID: 31002542 DOI: 10.1080/14789450.2019.1609944] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION The study of microbial communities based on the combined analysis of genomic and proteomic data - called metaproteogenomics - has gained increased research attention in recent years. This relatively young field aims to elucidate the functional and taxonomic interplay of proteins in microbiomes and its implications on human health and the environment. Areas covered: This article reviews bioinformatics methods and software tools dedicated to the analysis of data from metaproteomics and metaproteogenomics experiments. In particular, it focuses on the creation of tailored protein sequence databases, on the optimal use of database search algorithms including methods of error rate estimation, and finally on taxonomic and functional annotation of peptide and protein identifications. Expert opinion: Recently, various promising strategies and software tools have been proposed for handling typical data analysis issues in metaproteomics. However, severe challenges remain that are highlighted and discussed in this article; these include: (i) robust false-positive assessment of peptide and protein identifications, (ii) complex protein inference against a background of highly redundant data, (iii) taxonomic and functional post-processing of identification data, and finally, (iv) the assessment and provision of metrics and tools for quantitative analysis.
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Affiliation(s)
- Henning Schiebenhoefer
- a Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure , Robert Koch Institute , Berlin , Germany
| | - Tim Van Den Bossche
- b VIB - UGent Center for Medical Biotechnology, VIB , Ghent , Belgium.,c Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences , Ghent University , Ghent , Belgium
| | - Stephan Fuchs
- d FG13 Division of Nosocomial Pathogens and Antibiotic Resistances , Robert Koch Institute , Wernigerode , Germany
| | - Bernhard Y Renard
- a Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure , Robert Koch Institute , Berlin , Germany
| | - Thilo Muth
- a Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure , Robert Koch Institute , Berlin , Germany
| | - Lennart Martens
- b VIB - UGent Center for Medical Biotechnology, VIB , Ghent , Belgium.,c Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences , Ghent University , Ghent , Belgium
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31
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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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Planý M, Czolderová M, Kraková L, Puškárová A, Bučková M, Šoltys K, Budiš J, Szemes T, Mackulak T, Wu JH, Pangallo D. Biogas production: evaluation of the influence of K2FeO4 pretreatment of maple leaves (Acer platanoides) on microbial consortia composition. Bioprocess Biosyst Eng 2019; 42:1151-1163. [DOI: 10.1007/s00449-019-02112-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 03/20/2019] [Indexed: 10/27/2022]
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Improved Methanogenic Communities for Biogas Production. BIOFUEL AND BIOREFINERY TECHNOLOGIES 2019. [DOI: 10.1007/978-3-030-10516-7_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Qiu L, Tao X, Xiong H, Yu J, Wei H. Lactobacillus plantarum ZDY04 exhibits a strain-specific property of lowering TMAO via the modulation of gut microbiota in mice. Food Funct 2018; 9:4299-4309. [PMID: 30039147 DOI: 10.1039/c8fo00349a] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Trimethylamine N-oxide (TMAO), which is oxidized from trimethylamine (TMA) by hepatic flavin-containing monooxygenases (FMOs), promotes the development of atherosclerosis and is a new target for the prevention and treatment of cardiovascular disease from the perspective of intestinal flora. TMA is transformed by intestinal flora from TMA-containing nutrients, such as choline. Some small molecular agents lower serum TMAO and/or cecal TMA levels. However, probiotics that can effectively reduce serum TMAO levels are currently lacking. In this work, five potentially probiotic strains were administered to mice supplemented with 1.3% choline. Only Lactobacillus plantarum ZDY04 significantly reduced serum TMAO and cecal TMA levels by modulating the relative abundance of the families Lachnospiraceae, Erysipelotrichaceae and Bacteroidaceae and the genus Mucispirillum in mice and not by influencing the expression levels of hepatic FMO3 and metabolizing choline, TMA, and TMAO. In addition, L. plantarum ZDY04 can significantly inhibit the development of TMAO-induced atherosclerosis in ApoE-/- 1.3% choline-fed mice as compared with the untreated PBS group. In conclusion, the use of L. plantarum ZDY04 may be an alternative approach to reduce serum TMAO levels and TMAO-induced atherosclerosis in mice.
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Affiliation(s)
- Liang Qiu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi 330047, P. R. China.
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35
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Ferguson RMW, Coulon F, Villa R. Understanding microbial ecology can help improve biogas production in AD. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 642:754-763. [PMID: 29920462 DOI: 10.1016/j.scitotenv.2018.06.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 06/01/2018] [Accepted: 06/01/2018] [Indexed: 06/08/2023]
Abstract
454-Pyrosequencing and lipid fingerprinting were used to link anaerobic digestion (AD) process parameters (pH, alkalinity, volatile fatty acids (VFAs), biogas production and methane content) with the reactor microbial community structure and composition. AD microbial communities underwent stress conditions after changes in organic loading rate and digestion substrates. 454-Pyrosequencing analysis showed that, irrespectively of the substrate digested, methane content and pH were always significantly, and positively, correlated with community evenness. In AD, microbial communities with more even distributions of diversity are able to use parallel metabolic pathways and have greater functional stability; hence, they are capable of adapting and responding to disturbances. In all reactors, a decrease in methane content to <30% was always correlated with a 50% increase of Firmicutes sequences (particularly in operational taxonomic units (OTUs) related to Ruminococcaceae and Veillonellaceae). Whereas digesters producing higher methane content (above 60%), contained a high number of sequences related to Synergistetes and unidentified bacterial OTUs. Finally, lipid fingerprinting demonstrated that, under stress, the decrease in archaeal biomass was higher than the bacterial one, and that archaeal Phospholipid etherlipids (PLEL) levels were correlated to reactor performances. These results demonstrate that, across a number of parameters such as lipids, alpha and beta diversity, and OTUs, knowledge of the microbial community structure can be used to predict, monitor, or optimise AD performance.
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Affiliation(s)
- Robert M W Ferguson
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Frédéric Coulon
- School of Water, Energy and Environment, Cranfield University, Cranfield, MK43 0AL, UK
| | - Raffaella Villa
- School of Water, Energy and Environment, Cranfield University, Cranfield, MK43 0AL, UK.
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Campanaro S, Treu L, Kougias PG, Luo G, Angelidaki I. Metagenomic binning reveals the functional roles of core abundant microorganisms in twelve full-scale biogas plants. WATER RESEARCH 2018; 140:123-134. [PMID: 29704757 DOI: 10.1016/j.watres.2018.04.043] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Revised: 03/22/2018] [Accepted: 04/16/2018] [Indexed: 05/07/2023]
Abstract
The aim of this work was to elucidate the microbial ecology in twelve mesophilic and thermophilic full-scale biogas plants using a genome-centric metagenomic approach. In this study both biogas plants treating manure and those treating sludge from waste water treatment plants were considered. The identification of 132 Metagenome-Assembled Genomes (MAGs) and analysis of their abundance profile in different samples allowed the identification of the most abundant core members of the anaerobic digestion microbiome. Canonical correspondence analysis was used to determine the influence of biotic and environmental factors on MAGs abundance and to investigate the methanogenic performance of the biogas plants. Prediction of the functional properties of MAGs was obtained analyzing their KEGG pathways and their carbohydrate active domains. Network analysis allowed investigation of species-species associations and shed light on syntrophic interactions between members belonging to the anaerobic digestion dark matter (phylum Fermentibacteria). By stratifying and comparing different levels of information, it was predicted that some MAGs have a crucial role in the manure-supplemented thermophilic biogas plants and it was highlighted the importance of the glycine cleavage system in complementing the "truncated" Wood-Ljungdahl pathway.
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Affiliation(s)
- Stefano Campanaro
- Department of Biology, University of Padua, Via U. Bassi 58/b, 35121 Padova, Italy
| | - Laura Treu
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark
| | - Panagiotis G Kougias
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark.
| | - Gang Luo
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, 200433, Shanghai, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China.
| | - Irini Angelidaki
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark
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Treu L, Kougias PG, de Diego-Díaz B, Campanaro S, Bassani I, Fernández-Rodríguez J, Angelidaki I. Two-year microbial adaptation during hydrogen-mediated biogas upgrading process in a serial reactor configuration. BIORESOURCE TECHNOLOGY 2018; 264:140-147. [PMID: 29800774 DOI: 10.1016/j.biortech.2018.05.070] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 05/17/2018] [Accepted: 05/18/2018] [Indexed: 05/07/2023]
Abstract
Microbial dynamics in an upgrading biogas reactor system undergoing a more than two years-period at stable operating conditions were explored. The carbon dioxide generated during biomass degradation in the first reactor of the system was converted to methane into the secondary reactor by addition of external hydrogen. Considering the overall efficiency, the long-term operation period resulted in an improved biogas upgrading performance (99% methane content). However, a remarkable accumulation of acetate was revealed, indicating the enhancement of homoacetogenic activity. For this reason, a shift in the anaerobic digestion microbiome was expected and evaluated by 16S rRNA amplicon analysis. Results demonstrated that the most abundant archaeal species identified in the first time point, Candidatus Methanoculleus thermohydrogenotrophicum, was replaced by Methanothermobacter thermautotrophicus, becoming dominant after the community adaptation. The most interesting taxonomic units were clustered by relative abundance and six main long-term adaptation trends were found, characterizing functionally related microbes (e.g. homoacetogens).
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Affiliation(s)
- L Treu
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark
| | - P G Kougias
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark.
| | - B de Diego-Díaz
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark; Department of Chemistry, University of Navarra, Spain
| | - S Campanaro
- Department of Biology, University of Padua, Via U. Bassi 58/b, 35131 Padova, Italy
| | - I Bassani
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark
| | | | - I Angelidaki
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark
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Spatial Distribution and Diverse Metabolic Functions of Lignocellulose-Degrading Uncultured Bacteria as Revealed by Genome-Centric Metagenomics. Appl Environ Microbiol 2018; 84:AEM.01244-18. [PMID: 30006398 DOI: 10.1128/aem.01244-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 07/06/2018] [Indexed: 12/25/2022] Open
Abstract
The mechanisms by which specific anaerobic microorganisms remain firmly attached to lignocellulosic material, allowing them to efficiently decompose organic matter, have yet to be elucidated. To circumvent this issue, microbiomes collected from anaerobic digesters treating pig manure and meadow grass were fractionated to separate the planktonic microbes from those adhered to lignocellulosic substrate. Assembly of shotgun reads, followed by a binning process, recovered 151 population genomes, 80 out of which were completely new and were not previously deposited in any database. Genome coverage allowed the identification of microbial spatial distribution in the engineered ecosystem. Moreover, a composite bioinformatic analysis using multiple databases for functional annotation revealed that uncultured members of the Bacteroidetes and Firmicutes follow diverse metabolic strategies for polysaccharide degradation. The structure of cellulosome in Firmicutes species can differ depending on the number and functional roles of carbohydrate-binding modules. In contrast, members of the Bacteroidetes are able to adhere to and degrade lignocellulose due to the presence of multiple carbohydrate-binding family 6 modules in beta-xylosidase and endoglucanase proteins or S-layer homology modules in unknown proteins. This study combines the concept of variability in spatial distribution with genome-centric metagenomics, allowing a functional and taxonomical exploration of the biogas microbiome.IMPORTANCE This work contributes new knowledge about lignocellulose degradation in engineered ecosystems. Specifically, the combination of the spatial distribution of uncultured microbes with genome-centric metagenomics provides novel insights into the metabolic properties of planktonic and firmly attached to plant biomass bacteria. Moreover, the knowledge obtained in this study enabled us to understand the diverse metabolic strategies for polysaccharide degradation in different species of Bacteroidetes and Clostridiales Even though structural elements of cellulosome were restricted to Clostridiales species, our study identified a putative mechanism in Bacteroidetes species for biomass decomposition, which is based on a gene cluster responsible for cellulose degradation, disaccharide cleavage to glucose, and transport to cytoplasm.
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Wirth R, Lakatos G, Böjti T, Maróti G, Bagi Z, Rákhely G, Kovács KL. Anaerobic gaseous biofuel production using microalgal biomass – A review. Anaerobe 2018; 52:1-8. [DOI: 10.1016/j.anaerobe.2018.05.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 05/16/2018] [Accepted: 05/22/2018] [Indexed: 12/17/2022]
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Wenzel L, Heyer R, Schallert K, Löser L, Wünschiers R, Reichl U, Benndorf D. SDS-PAGE fractionation to increase metaproteomic insight into the taxonomic and functional composition of microbial communities for biogas plant samples. Eng Life Sci 2018; 18:498-509. [PMID: 32624931 DOI: 10.1002/elsc.201800062] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 05/14/2018] [Accepted: 05/28/2018] [Indexed: 11/08/2022] Open
Abstract
Metaproteomics represent an important tool for the taxonomic and functional investigation of microbial communities in humans, environment, and technical applications. Due to the high complexity of the microbial communities, protein, and peptide fractionation is applied to improve the characterization of taxonomic and functional composition of microbial communities. In order to target scientific questions regarding taxonomic and functional composition adequately, a tradeoff between the number of fractions analyzed and the required depth of information has to be found. Two samples of a biogas plant were analyzed by either single LC-MS/MS measurement (1D) or LC-MS/MS measurements of fractions obtained after SDS-PAGE (2D) separation. Fractionation with SDS-PAGE increased the number of identified spectra by 273%, the number of peptides by 95%, and the number of metaproteins by 59%. Rarefaction plots of species and metaproteins against identified spectra showed that 2D separation was sufficient to identify most microbial families but not all metaproteins. More reliable quantitative comparison could be achieved with 2D. 1D separation enabled high-throughput analysis of samples, however, depth in functional descriptions and reliability of quantification were lost. Nevertheless, the proteotyping of multiple samples was still possible. 2D separations provided more reliable quantitative data combined with a deeper insight into the taxonomic and functional composition of the microbial communities. Regarding taxonomic and functional composition, metaproteomics based on 2D is just the tip of an iceberg.
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Affiliation(s)
- Lisa Wenzel
- Bioprocess Engineering Otto von Guericke University Magdeburg Germany
| | - Robert Heyer
- Bioprocess Engineering Otto von Guericke University Magdeburg Germany
| | - Kay Schallert
- Bioprocess Engineering Otto von Guericke University Magdeburg Germany
| | - Lucy Löser
- Applied Computer Sciences and Biosciences University of Applied Science Mittweida Mittweida Germany
| | - Röbbe Wünschiers
- Applied Computer Sciences and Biosciences University of Applied Science Mittweida Mittweida Germany
| | - Udo Reichl
- Bioprocess Engineering Otto von Guericke University Magdeburg Germany.,Bioprocess Engineering Max Planck Institute for Dynamics of Complex Technical Systems Magdeburg Germany
| | - Dirk Benndorf
- Bioprocess Engineering Otto von Guericke University Magdeburg Germany.,Bioprocess Engineering Max Planck Institute for Dynamics of Complex Technical Systems Magdeburg Germany
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Schmidt A, Sturm G, Lapp CJ, Siebert D, Saravia F, Horn H, Ravi PP, Lemmer A, Gescher J. Development of a production chain from vegetable biowaste to platform chemicals. Microb Cell Fact 2018; 17:90. [PMID: 29898726 PMCID: PMC6001048 DOI: 10.1186/s12934-018-0937-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 05/30/2018] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND A future bioeconomy relies on the development of technologies to convert waste into valuable compounds. We present here an attempt to design a biotechnological cascade for the conversion of vegetable waste into acetoin and electrical energy. RESULTS A vegetable waste dark fermentation effluent containing mainly acetate, butyrate and propionate was oxidized in a bioelectrochemical system. The achieved average current at a constant anode potential of 0 mV against standard hydrogen electrode was 177.5 ± 52.5 µA/cm2. During this step, acetate and butyrate were removed from the effluent while propionate was the major remaining component of the total organic carbon content comprising on average 75.6%. The key players with regard to carbon oxidation and electrode reduction were revealed using amplicon sequencing and metatranscriptomic analysis. Using nanofiltration, it was possible to concentrate the propionate in the effluent. The effluent was revealed to be a suitable medium for biotechnological production strains. As a proof of principle, the propionate in the effluent of the bioelectrochemical system was converted into the platform chemical acetoin with a carbon recovery of 86%. CONCLUSIONS To the best of our knowledge this is the first report on a full biotechnological production chain leading from vegetable waste to the production of a single valuable platform chemical that integrates carbon elimination steps leading to the production of the valuable side product electrical energy.
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Affiliation(s)
- Annemarie Schmidt
- Department Applied Biology, Institute for Applied Biosciences, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Gunnar Sturm
- Department Applied Biology, Institute for Applied Biosciences, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Christian Jonas Lapp
- Department Applied Biology, Institute for Applied Biosciences, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Daniel Siebert
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| | - Florencia Saravia
- Chair of Water Chemistry and Water Technology, Karlsruhe Institute of Technology, Engler-Bunte-Institut, Karlsruhe, Germany
| | - Harald Horn
- Chair of Water Chemistry and Water Technology, Karlsruhe Institute of Technology, Engler-Bunte-Institut, Karlsruhe, Germany
| | - Padma Priya Ravi
- State Institute of Agricultural Engineering and Bioenergy, University of Hohenheim, Stuttgart, Germany
| | - Andreas Lemmer
- State Institute of Agricultural Engineering and Bioenergy, University of Hohenheim, Stuttgart, Germany
| | - Johannes Gescher
- Department Applied Biology, Institute for Applied Biosciences, Karlsruhe Institute of Technology, Karlsruhe, Germany. .,Institute for Biological Interfaces, Karlsruhe Institute of Technology, Karlsruhe, Germany.
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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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Hassa J, Maus I, Off S, Pühler A, Scherer P, Klocke M, Schlüter A. Metagenome, metatranscriptome, and metaproteome approaches unraveled compositions and functional relationships of microbial communities residing in biogas plants. Appl Microbiol Biotechnol 2018; 102:5045-5063. [PMID: 29713790 PMCID: PMC5959977 DOI: 10.1007/s00253-018-8976-7] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 03/27/2018] [Accepted: 03/28/2018] [Indexed: 12/15/2022]
Abstract
The production of biogas by anaerobic digestion (AD) of agricultural residues, organic wastes, animal excrements, municipal sludge, and energy crops has a firm place in sustainable energy production and bio-economy strategies. Focusing on the microbial community involved in biomass conversion offers the opportunity to control and engineer the biogas process with the objective to optimize its efficiency. Taxonomic profiling of biogas producing communities by means of high-throughput 16S rRNA gene amplicon sequencing provided high-resolution insights into bacterial and archaeal structures of AD assemblages and their linkages to fed substrates and process parameters. Commonly, the bacterial phyla Firmicutes and Bacteroidetes appeared to dominate biogas communities in varying abundances depending on the apparent process conditions. Regarding the community of methanogenic Archaea, their diversity was mainly affected by the nature and composition of the substrates, availability of nutrients and ammonium/ammonia contents, but not by the temperature. It also appeared that a high proportion of 16S rRNA sequences can only be classified on higher taxonomic ranks indicating that many community members and their participation in AD within functional networks are still unknown. Although cultivation-based approaches to isolate microorganisms from biogas fermentation samples yielded hundreds of novel species and strains, this approach intrinsically is limited to the cultivable fraction of the community. To obtain genome sequence information of non-cultivable biogas community members, metagenome sequencing including assembly and binning strategies was highly valuable. Corresponding research has led to the compilation of hundreds of metagenome-assembled genomes (MAGs) frequently representing novel taxa whose metabolism and lifestyle could be reconstructed based on nucleotide sequence information. In contrast to metagenome analyses revealing the genetic potential of microbial communities, metatranscriptome sequencing provided insights into the metabolically active community. Taking advantage of genome sequence information, transcriptional activities were evaluated considering the microorganism's genetic background. Metaproteome studies uncovered enzyme profiles expressed by biogas community members. Enzymes involved in cellulose and hemicellulose decomposition and utilization of other complex biopolymers were identified. Future studies on biogas functional microbial networks will increasingly involve integrated multi-omics analyses evaluating metagenome, transcriptome, proteome, and metabolome datasets.
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Affiliation(s)
- Julia Hassa
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstrasse 27, 33615, Bielefeld, Germany
| | - Irena Maus
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstrasse 27, 33615, Bielefeld, Germany
| | - Sandra Off
- Dept. Biotechnologie, Hochschule für angewandte Wissenschaften (HAW) Hamburg Ulmenliet 20, 21033, Hamburg, Germany
| | - Alfred Pühler
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstrasse 27, 33615, Bielefeld, Germany
| | - Paul Scherer
- Dept. Biotechnologie, Hochschule für angewandte Wissenschaften (HAW) Hamburg Ulmenliet 20, 21033, Hamburg, Germany
| | - Michael Klocke
- Dept. Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy, Max-Eyth-Allee 100, 14469, Potsdam, Germany
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstrasse 27, 33615, Bielefeld, Germany.
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Hassa J, Maus I, Off S, Pühler A, Scherer P, Klocke M, Schlüter A. Metagenome, metatranscriptome, and metaproteome approaches unraveled compositions and functional relationships of microbial communities residing in biogas plants. Appl Microbiol Biotechnol 2018. [PMID: 29713790 DOI: 10.1007/s00253-018-8976-7)] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The production of biogas by anaerobic digestion (AD) of agricultural residues, organic wastes, animal excrements, municipal sludge, and energy crops has a firm place in sustainable energy production and bio-economy strategies. Focusing on the microbial community involved in biomass conversion offers the opportunity to control and engineer the biogas process with the objective to optimize its efficiency. Taxonomic profiling of biogas producing communities by means of high-throughput 16S rRNA gene amplicon sequencing provided high-resolution insights into bacterial and archaeal structures of AD assemblages and their linkages to fed substrates and process parameters. Commonly, the bacterial phyla Firmicutes and Bacteroidetes appeared to dominate biogas communities in varying abundances depending on the apparent process conditions. Regarding the community of methanogenic Archaea, their diversity was mainly affected by the nature and composition of the substrates, availability of nutrients and ammonium/ammonia contents, but not by the temperature. It also appeared that a high proportion of 16S rRNA sequences can only be classified on higher taxonomic ranks indicating that many community members and their participation in AD within functional networks are still unknown. Although cultivation-based approaches to isolate microorganisms from biogas fermentation samples yielded hundreds of novel species and strains, this approach intrinsically is limited to the cultivable fraction of the community. To obtain genome sequence information of non-cultivable biogas community members, metagenome sequencing including assembly and binning strategies was highly valuable. Corresponding research has led to the compilation of hundreds of metagenome-assembled genomes (MAGs) frequently representing novel taxa whose metabolism and lifestyle could be reconstructed based on nucleotide sequence information. In contrast to metagenome analyses revealing the genetic potential of microbial communities, metatranscriptome sequencing provided insights into the metabolically active community. Taking advantage of genome sequence information, transcriptional activities were evaluated considering the microorganism's genetic background. Metaproteome studies uncovered enzyme profiles expressed by biogas community members. Enzymes involved in cellulose and hemicellulose decomposition and utilization of other complex biopolymers were identified. Future studies on biogas functional microbial networks will increasingly involve integrated multi-omics analyses evaluating metagenome, transcriptome, proteome, and metabolome datasets.
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Affiliation(s)
- Julia Hassa
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstrasse 27, 33615, Bielefeld, Germany
| | - Irena Maus
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstrasse 27, 33615, Bielefeld, Germany
| | - Sandra Off
- Dept. Biotechnologie, Hochschule für angewandte Wissenschaften (HAW) Hamburg Ulmenliet 20, 21033, Hamburg, Germany
| | - Alfred Pühler
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstrasse 27, 33615, Bielefeld, Germany
| | - Paul Scherer
- Dept. Biotechnologie, Hochschule für angewandte Wissenschaften (HAW) Hamburg Ulmenliet 20, 21033, Hamburg, Germany
| | - Michael Klocke
- Dept. Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy, Max-Eyth-Allee 100, 14469, Potsdam, Germany
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstrasse 27, 33615, Bielefeld, Germany.
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Jahan Z, Niazi MBK, Hägg MB, Gregersen ØW. Cellulose nanocrystal/PVA nanocomposite membranes for CO2/CH4 separation at high pressure. J Memb Sci 2018. [DOI: 10.1016/j.memsci.2018.02.061] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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De Vrieze J, Pinto AJ, Sloan WT, Ijaz UZ. The active microbial community more accurately reflects the anaerobic digestion process: 16S rRNA (gene) sequencing as a predictive tool. MICROBIOME 2018; 6:63. [PMID: 29609653 PMCID: PMC5879801 DOI: 10.1186/s40168-018-0449-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 03/16/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUND Amplicon sequencing methods targeting the 16S rRNA gene have been used extensively to investigate microbial community composition and dynamics in anaerobic digestion. These methods successfully characterize amplicons but do not distinguish micro-organisms that are actually responsible for the process. In this research, the archaeal and bacterial community of 48 full-scale anaerobic digestion plants were evaluated on DNA (total community) and RNA (active community) level via 16S rRNA (gene) amplicon sequencing. RESULTS A significantly higher diversity on DNA compared with the RNA level was observed for archaea, but not for bacteria. Beta diversity analysis showed a significant difference in community composition between the DNA and RNA of both bacteria and archaea. This related with 25.5 and 42.3% of total OTUs for bacteria and archaea, respectively, that showed a significant difference in their DNA and RNA profiles. Similar operational parameters affected the bacterial and archaeal community, yet the differentiating effect between DNA and RNA was much stronger for archaea. Co-occurrence networks and functional prediction profiling confirmed the clear differentiation between DNA and RNA profiles. CONCLUSIONS In conclusion, a clear difference in active (RNA) and total (DNA) community profiles was observed, implying the need for a combined approach to estimate community stability in anaerobic digestion.
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Affiliation(s)
- Jo De Vrieze
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
- Infrastructure and Environment Research Division, School of Engineering, University of Glasgow, Rankine Building, Oakfield Avenue, Glasgow, G12 8LT UK
| | - Ameet J. Pinto
- Northeastern University, 360 Huntington Avenue, Boston, MA 02115 USA
| | - William T. Sloan
- Infrastructure and Environment Research Division, School of Engineering, University of Glasgow, Rankine Building, Oakfield Avenue, Glasgow, G12 8LT UK
| | - Umer Zeeshan Ijaz
- Infrastructure and Environment Research Division, School of Engineering, University of Glasgow, Rankine Building, Oakfield Avenue, Glasgow, G12 8LT UK
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Wolters B, Jacquiod S, Sørensen SJ, Widyasari-Mehta A, Bech TB, Kreuzig R, Smalla K. Bulk soil and maize rhizosphere resistance genes, mobile genetic elements and microbial communities are differently impacted by organic and inorganic fertilization. FEMS Microbiol Ecol 2018; 94:4867966. [DOI: 10.1093/femsec/fiy027] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 02/15/2018] [Indexed: 12/30/2022] Open
Affiliation(s)
- Birgit Wolters
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11–12, 38104 Braunschweig, Germany
- Technische Universität Braunschweig, Institute of Environmental and Sustainable Chemistry, Hagenring 30, 38106 Braunschweig, Germany
| | - Samuel Jacquiod
- Section of Microbiology, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Arum Widyasari-Mehta
- Technische Universität Braunschweig, Institute of Environmental and Sustainable Chemistry, Hagenring 30, 38106 Braunschweig, Germany
| | - Tina B Bech
- Geological Survey of Denmark and Greenland (GEUS), Department of Geochemistry, Øster Voldgade 10, 1350 Copenhagen K, Denmark
| | - Robert Kreuzig
- Technische Universität Braunschweig, Institute of Environmental and Sustainable Chemistry, Hagenring 30, 38106 Braunschweig, Germany
| | - Kornelia Smalla
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11–12, 38104 Braunschweig, Germany
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Pandey P, Chiu C, Miao M, Wang Y, Settles M, del Rio NS, Castillo A, Souza A, Pereira R, Jeannotte R. 16S rRNA analysis of diversity of manure microbial community in dairy farm environment. PLoS One 2018; 13:e0190126. [PMID: 29304047 PMCID: PMC5755784 DOI: 10.1371/journal.pone.0190126] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 12/08/2017] [Indexed: 01/01/2023] Open
Abstract
Dairy farms generate a considerable amount of manure, which is applied in cropland as fertilizer. While the use of manure as fertilizer reduces the application of chemical fertilizers, the main concern with regards to manure application is microbial pollution. Manure is a reservoir of a broad range of microbial populations, including pathogens, which have potential to cause contamination and pose risks to public and animal health. Despite the widespread use of manure fertilizer, the change in microbial diversity of manure under various treatment processes is still not well-understood. We hypothesize that the microbial population of animal waste changes with manure handling used in a farm environment. Consequential microbial risk caused by animal manure may depend on manure handling. In this study, a reconnaissance effort for sampling dairy manure in California Central Valley followed by 16S rRNA analysis of content and diversity was undertaken to understand the microbiome of manure after various handling processes. The microbial community analysis of manure revealed that the population in liquid manure differs from that in solid manure. For instance, the bacteria of genus Sulfuriomonas were unique in liquid samples, while the bacteria of genus Thermos were observed only in solid samples. Bacteria of genus Clostridium were present in both solid and liquid samples. The population among liquid samples was comparable, as was the population among solid samples. These findings suggest that the mode of manure application (i.e., liquid versus solid) could have a potential impact on the microbiome of cropland receiving manure as fertilizers.
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Affiliation(s)
- Pramod Pandey
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, United States of America
- * E-mail: (PP); (RJ)
| | - Colleen Chiu
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, United States of America
- Department of Plant Sciences, College of Agricultural and Environmental Sciences, University of California, Davis, California, United States of America
| | - Max Miao
- Department of Plant Sciences, College of Agricultural and Environmental Sciences, University of California, Davis, California, United States of America
- Department of Plant Pathology, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Yi Wang
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, United States of America
- Department of Biological and Agricultural Engineering, University of California, Davis, California, United States of America
| | - Matthew Settles
- Genome Center Bioinformatics Core, University of California, Davis, California, United States of America
| | - Noelia Silva del Rio
- University of California Cooperative Extension, Veterinary Medicine Teaching and Research Center, Tulare, California, United States of America
| | - Alejandro Castillo
- University of California Cooperative Extension, Merced, California, United States of America
| | - Alex Souza
- University of California Cooperative Extension, Tulare, California, United States of America
| | - Richard Pereira
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Richard Jeannotte
- Department of Plant Sciences, College of Agricultural and Environmental Sciences, University of California, Davis, California, United States of America
- Universidad de Tarapacá, Arica, Chile
- * E-mail: (PP); (RJ)
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49
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Grohmann A, Fehrmann S, Vainshtein Y, Haag NL, Wiese F, Stevens P, Naegele HJ, Oechsner H, Hartsch T, Sohn K, Grumaz C. Microbiome dynamics and adaptation of expression signatures during methane production failure and process recovery. BIORESOURCE TECHNOLOGY 2018; 247:347-356. [PMID: 28954247 DOI: 10.1016/j.biortech.2017.08.214] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 08/30/2017] [Accepted: 08/31/2017] [Indexed: 06/07/2023]
Abstract
This study aimed to uncover microbial dynamics and transcriptional adaptations during mesophilic AD of maize silage and slurry. While one digester performed under optimal conditions, the investigations also evaluated the microbiome during a temperature drop mediated process failure accompanied by acidification and how it contributed to a process recovery. Composition and pathway activities were analyzed by whole genome shotgun (WGS) and metatranscriptome sequencing, respectively. A biodiversity of 112 species was observed with noticeable shifts over process time. Although four distinct groups of microbes could be identified with a correlating versatility according to substrate and to process disturbance, also tremendous effects on gene expression were monitored especially of the archaeal methane metabolism. Particularly, the expression of acetogenotrophic methanogenesis related genes was identified to be relevant for process regeneration.
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Affiliation(s)
- Anja Grohmann
- University of Stuttgart IGVP, Pfaffenwaldring 31, 70569 Stuttgart, Germany
| | | | | | - Nicola L Haag
- University of Hohenheim, State Institute of Agricultural Engineering and Bioenergy, Garbenstrasse 9, 70599 Stuttgart, Germany
| | | | - Philip Stevens
- Fraunhofer IGB, Nobelstrasse 12, 70569 Stuttgart, Germany
| | - Hans-Joachim Naegele
- University of Hohenheim, State Institute of Agricultural Engineering and Bioenergy, Garbenstrasse 9, 70599 Stuttgart, Germany
| | - Hans Oechsner
- University of Hohenheim, State Institute of Agricultural Engineering and Bioenergy, Garbenstrasse 9, 70599 Stuttgart, Germany
| | - Thomas Hartsch
- Genedata GmbH, Fürstenrieder Strasse 281, 81377 Munich, Germany
| | - Kai Sohn
- Fraunhofer IGB, Nobelstrasse 12, 70569 Stuttgart, Germany
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50
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Mulat DG, Huerta SG, Kalyani D, Horn SJ. Enhancing methane production from lignocellulosic biomass by combined steam-explosion pretreatment and bioaugmentation with cellulolytic bacterium Caldicellulosiruptor bescii. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:19. [PMID: 29422947 PMCID: PMC5787918 DOI: 10.1186/s13068-018-1025-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 01/13/2018] [Indexed: 05/07/2023]
Abstract
BACKGROUND Biogas production from lignocellulosic biomass is generally considered to be challenging due to the recalcitrant nature of this biomass. In this study, the recalcitrance of birch was reduced by applying steam-explosion (SE) pretreatment (210 °C and 10 min). Moreover, bioaugmentation with the cellulolytic bacterium Caldicellulosiruptor bescii was applied to possibly enhance the methane production from steam-exploded birch in an anaerobic digestion (AD) process under thermophilic conditions (62 °C). RESULTS Overall, the combined SE and bioaugmentation enhanced the methane yield up to 140% compared to untreated birch, while SE alone contributed to the major share of methane enhancement by 118%. The best methane improvement of 140% on day 50 was observed in bottles fed with pretreated birch and bioaugmentation with lower dosages of C. bescii (2 and 5% of inoculum volume). The maximum methane production rate also increased from 4-mL CH4/g VS (volatile solids)/day for untreated birch to 9-14-mL CH4/g VS/day for steam-exploded birch with applied bioaugmentation. Bioaugmentation was particularly effective for increasing the initial methane production rate of the pretreated birch yielding 21-44% more methane than the pretreated birch without applied bioaugmentation. The extent of solubilization of the organic matter was increased by more than twofold when combined SE pretreatment and bioaugmentation was used in comparison with the methane production from untreated birch. The beneficial effects of SE and bioaugmentation on methane yield indicated that biomass recalcitrance and hydrolysis step are the limiting factors for efficient AD of lignocellulosic biomass. Microbial community analysis by 16S rRNA amplicon sequencing showed that the microbial community composition was altered by the pretreatment and bioaugmentation processes. Notably, the enhanced methane production by pretreatment and bioaugmentation was well correlated with the increase in abundance of key bacterial and archaeal communities, particularly the hydrolytic bacterium Caldicoprobacter, several members of syntrophic acetate oxidizing bacteria and the hydrogenotrophic Methanothermobacter. CONCLUSION Our findings demonstrate the potential of combined SE and bioaugmentation for enhancing methane production from lignocellulosic biomass.
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Affiliation(s)
- Daniel Girma Mulat
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O.Box 5003, 1432 Ås, Norway
| | - Silvia Greses Huerta
- Department of Chemical Engineering, University of Valencia, P.O.Box 46100, Valencia, Spain
| | - Dayanand Kalyani
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O.Box 5003, 1432 Ås, Norway
| | - Svein Jarle Horn
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O.Box 5003, 1432 Ås, Norway
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