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Ascandari A, Aminu S, Safdi NEH, El Allali A, Daoud R. A bibliometric analysis of the global impact of metaproteomics research. Front Microbiol 2023; 14:1217727. [PMID: 37476667 PMCID: PMC10354264 DOI: 10.3389/fmicb.2023.1217727] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 06/20/2023] [Indexed: 07/22/2023] Open
Abstract
Background Metaproteomics is a subfield in meta-omics that is used to characterize the proteome of a microbial community. Despite its importance and the plethora of publications in different research area, scientists struggle to fully comprehend its functional impact on the study of microbiomes. In this study, bibliometric analyses are used to evaluate the current state of metaproteomic research globally as well as evaluate the specific contribution of Africa to this burgeoning research area. In this study, we use bibliometric analyses to evaluate the current state of metaproteomic research globally, identify research frontiers and hotspots, and further predict future trends in metaproteomics. The specific contribution of Africa to this research area was evaluated. Methods Relevant documents from 2004 to 2022 were extracted from the Scopus database. The documents were subjected to bibliometric analyses and visualization using VOS viewer and Biblioshiny package in R. Factors such as the trends in publication, country and institutional cooperation networks, leading scientific journals, author's productivity, and keywords analyses were conducted. The African publications were ranked using Field-Weighted Citation Impact (FWCI) scores. Results A total of 1,138 documents were included and the number of publications increased drastically from 2004 to 2022 with more publications (170) reported in 2021. In terms of publishers, Frontiers in Microbiology had the highest number of total publications (62). The United States of America (USA), Germany, China, and Canada, together with other European countries were the most productive. Institution-wise, the Helmholtz Zentrum für Umweltforschung, Germany had more publications while Max Plank Institute had the highest total collaborative link strength. Jehmlich N. was the most productive author whereas Hettich RL had the highest h-index of 63. Regarding Africa, only 2.2% of the overall publications were from the continent with more publication outputs from South Africa. More than half of the publications from the continent had an FWCI score ≥ 1. Conclusion The scientific outputs of metaproteomics are rapidly evolving with developed countries leading the way. Although Africa showed prospects for future progress, this could only be accelerated by providing funding, increased collaborations, and mentorship programs.
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Affiliation(s)
- AbdulAziz Ascandari
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Suleiman Aminu
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
- Department of Biochemistry, Ahmadu Bello University, Zaria, Nigeria
| | - Nour El Houda Safdi
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Achraf El Allali
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Rachid Daoud
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
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Mu L, Wang Y, Xu F, Li J, Tao J, Sun Y, Song Y, Duan Z, Li S, Chen G. Emerging Strategies for Enhancing Propionate Conversion in Anaerobic Digestion: A Review. Molecules 2023; 28:3883. [PMID: 37175291 PMCID: PMC10180298 DOI: 10.3390/molecules28093883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/18/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023] Open
Abstract
Anaerobic digestion (AD) is a triple-benefit biotechnology for organic waste treatment, renewable production, and carbon emission reduction. In the process of anaerobic digestion, pH, temperature, organic load, ammonia nitrogen, VFAs, and other factors affect fermentation efficiency and stability. The balance between the generation and consumption of volatile fatty acids (VFAs) in the anaerobic digestion process is the key to stable AD operation. However, the accumulation of VFAs frequently occurs, especially propionate, because its oxidation has the highest Gibbs free energy when compared to other VFAs. In order to solve this problem, some strategies, including buffering addition, suspension of feeding, decreased organic loading rate, and so on, have been proposed. Emerging methods, such as bioaugmentation, supplementary trace elements, the addition of electronic receptors, conductive materials, and the degasification of dissolved hydrogen, have been recently researched, presenting promising results. But the efficacy of these methods still requires further studies and tests regarding full-scale application. The main objective of this paper is to provide a comprehensive review of the mechanisms of propionate generation, the metabolic pathways and the influencing factors during the AD process, and the recent literature regarding the experimental research related to the efficacy of various strategies for enhancing propionate biodegradation. In addition, the issues that must be addressed in the future and the focus of future research are identified, and the potential directions for future development are predicted.
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Affiliation(s)
- Lan Mu
- School of Mechanical Engineering, Tianjin University of Commerce, Tianjin 300134, China; (L.M.)
| | - Yifan Wang
- School of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin 300134, China
| | - Fenglian Xu
- School of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin 300134, China
| | - Jinhe Li
- Tianjin Capital Environmental Protection Group Co., Ltd., Tianjin 300133, China
| | - Junyu Tao
- School of Mechanical Engineering, Tianjin University of Commerce, Tianjin 300134, China; (L.M.)
| | - Yunan Sun
- School of Mechanical Engineering, Tianjin University of Commerce, Tianjin 300134, China; (L.M.)
| | - Yingjin Song
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China;
| | - Zhaodan Duan
- School of Mechanical Engineering, Tianjin University of Commerce, Tianjin 300134, China; (L.M.)
| | - Siyi Li
- School of Mechanical Engineering, Tianjin University of Commerce, Tianjin 300134, China; (L.M.)
| | - Guanyi Chen
- School of Mechanical Engineering, Tianjin University of Commerce, Tianjin 300134, China; (L.M.)
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Cao Q, Zhang W, Lian T, Wang S, Yin F, Zhou T, Wei X, Dong H. Revealing mechanism of micro-aeration for enhancing volatile fatty acids production from swine manure. BIORESOURCE TECHNOLOGY 2022; 365:128140. [PMID: 36252761 DOI: 10.1016/j.biortech.2022.128140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Micro-aeration is considered a new strategy for improving volatile fatty acids (VFAs) production of agricultural waste. This study investigated the effect and mechanism of micro-aeration of air and oxygen (O2) on VFAs production from swine manure. The results showed that Air-micro-aeration had the most significant improvement effect, with the highest VFAs of 8.21 g/L, which was increased by 22.4%. Moreover, the mixing effects of different micro-aeration were limited, and the microbial communities significantly varied. Firmicutes and Bacteroidota were the dominant hydrolytic and acidogenic bacteria, and Air-micro-aeration preferentially promoted electron transfer activity and energy generation. Methanosarcina, Methanocorpusculum, and Methanobrevibacter can adapt to environmental changes according to their different oxygen tolerance, and the consumption and conversion of VFAs by methanogens were slow under Air-micro-aeration condition. This study revealed mechanism of micro-aeration for improving VFAs production from swine manure, providing a theoretical basis for micro-aeration regulation optimization.
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Affiliation(s)
- Qitao Cao
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Wanqin Zhang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Tianjing Lian
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China; College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, PR China
| | - Shunli Wang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Fubin Yin
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Tanlong Zhou
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Xiaoman Wei
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Hongmin Dong
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China.
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Zhang L, Yuan Y, Zhang Y, Liu Y. Exploring key factors in anaerobic syntrophic interactions: Biomass activity, microbial community, and morphology. BIORESOURCE TECHNOLOGY 2022; 363:127852. [PMID: 36067891 DOI: 10.1016/j.biortech.2022.127852] [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: 07/05/2022] [Revised: 08/20/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
The present work evaluated the impacts of microbial communities, biomass activity and sludge morphology on anaerobic syntrophic reactions. Experiments were conducted using mature floc sludge and granular sludge under different food/microbes ratios, and with different sludge types (floc sludge, concentrated floc sludge and granular sludge) and sludge morphology (granules, vortexed granules, and granules with different particle sizes). The results show that the intact granules achieved the most effective syntrophic reaction among all sludge types. The granule structure facilitated the enrichment of syntrophic acetate oxidation bacteria (g_Syner-01 and g_Mesotoga) and methanogens, which corresponds to their superior specific methanogenic activity and high production of communication compounds. Despite the high diffusion and substrate uptake capacities, the disintegrated granules had low H2 consumption rates, which led to poor syntrophic activities. The results underline the importance of sludge spatial structures in promoting excellent syntrophic activities and the development of diverse microbial communities.
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Affiliation(s)
- Lei Zhang
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Canada
| | - Yiyang Yuan
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Canada
| | - Yingdi Zhang
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Canada
| | - Yang Liu
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Canada.
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Current Trends in Biological Valorization of Waste-Derived Biomass: The Critical Role of VFAs to Fuel A Biorefinery. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8090445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The looming climate and energy crises, exacerbated by increased waste generation, are driving research and development of sustainable resource management systems. Research suggests that organic materials, such as food waste, grass, and manure, have potential for biotransformation into a range of products, including: high-value volatile fatty acids (VFAs); various carboxylic acids; bioenergy; and bioplastics. Valorizing these organic residues would additionally reduce the increasing burden on waste management systems. Here, we review the valorization potential of various sustainably sourced feedstocks, particularly food wastes and agricultural and animal residues. Such feedstocks are often micro-organism-rich and well-suited to mixed culture fermentations. Additionally, we touch on the technologies, mainly biological systems including anaerobic digestion, that are being developed for this purpose. In particular, we provide a synthesis of VFA recovery techniques, which remain a significant technological barrier. Furthermore, we highlight a range of challenges and opportunities which will continue to drive research and discovery within the field. Analysis of the literature reveals growing interest in the development of a circular bioeconomy, built upon a biorefinery framework, which utilizes biogenic VFAs for chemical, material, and energy applications.
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6
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Logan M, Tan LC, Nzeteu CO, Lens PNL. Enhanced anaerobic digestion of dairy wastewater in a granular activated carbon amended sequential batch reactor. GLOBAL CHANGE BIOLOGY. BIOENERGY 2022; 14:840-857. [PMID: 35915605 PMCID: PMC9324911 DOI: 10.1111/gcbb.12947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 02/21/2022] [Accepted: 03/29/2022] [Indexed: 06/15/2023]
Abstract
This study investigated the potential of granular activated carbon (GAC) supplementation to enhance anaerobic degradation of dairy wastewater. Two sequential batch reactors (SBRs; 0.8 L working volume), one control and another amended with GAC, were operated at 37°C and 1.5-1.6 m/h upflow velocity for a total of 120 days (four cycles of 30 days each). The methane production at the end of each cycle run increased by about 68%, 503%, 110%, and 125% in the GAC-amended SBR, compared with the Control SBR. Lipid degradation was faster in the presence of GAC. Conversely, the organic compounds, especially lipids, accumulated in the absence of the conductive material. In addition, a reduction in lag phase duration by 46%-100% was observed at all four cycles in the GAC-amended SBR. The peak methane yield rate was at least 2 folds higher with GAC addition in all cycles. RNA-based bacterial analysis revealed enrichment of Synergistes (0.8% to 29.2%) and Geobacter (0.4% to 11.3%) in the GAC-amended SBR. Methanolinea (85.8%) was the dominant archaea in the biofilm grown on GAC, followed by Methanosaeta (11.3%), at RNA level. Overall, this study revealed that GAC supplementation in anaerobic digesters treating dairy wastewater can promote stable and efficient methane production, accelerate lipid degradation and might promote the activity of electroactive microorganisms.
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Affiliation(s)
| | - Lea Chua Tan
- National University of Ireland, GalwayGalwayIreland
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7
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Ketsub N, Whatmore P, Abbasabadi M, Doherty WOS, Kaparaju P, O'Hara IM, Zhang Z. Effects of pretreatment methods on biomethane production kinetics and microbial community by solid state anaerobic digestion of sugarcane trash. BIORESOURCE TECHNOLOGY 2022; 352:127112. [PMID: 35381335 DOI: 10.1016/j.biortech.2022.127112] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 06/14/2023]
Abstract
Solid state anaerobic digestion (SS-AD) of lignocellulose is effective in improving biomethane productivity but is limited by low biomass digestibility and lack of substrate-specific working microorganisms. In this study, the effects of different pretreatment methods on biomethane production by SS-AD of sugarcane trash were studied. The biomethane production, fitted to a modified Gompertz's model, predicted a maximum methane yield of 214.2 L/kg volatile solids (VS) and productivity of 6.9 L/kg VS/day from KOH-pretreated trash, respectively. Microbial community analysis showed that bacterial community was significantly associated with volatile acids and pretreatment types while archaeal community was significantly associated with methane yield. Microbial community dynamics was revealed in SS-AD. Main genera related to pretreatment method were identified and discussed. This study generated important information on SS-AD of lignocellulosic biomass pretreated by different methods, which is useful for developing bioaugmentation strategies to improve biomethane production by SS-AD.
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Affiliation(s)
- Napong Ketsub
- Centre for Agriculture and the Bioeconomy, Faculty of Science, Queensland University of Technology, Brisbane, Queensland 4000, Australia; School of Mechanical, Medical and Process Engineering, Faculty of Engineering, Queensland University of Technology, Brisbane, Queensland 4000, Australia
| | - Paul Whatmore
- Bioinformatics Research Officer, Division of Research & Innovation, Queensland University of Technology, Brisbane, Queensland 4000, Australia
| | - Mahsa Abbasabadi
- Centre for Agriculture and the Bioeconomy, Faculty of Science, Queensland University of Technology, Brisbane, Queensland 4000, Australia; School of Biology and Environmental Sciences, Faculty of Science, Queensland University of Technology, Brisbane, Queensland 4000, Australia
| | - William O S Doherty
- Centre for Agriculture and the Bioeconomy, Faculty of Science, Queensland University of Technology, Brisbane, Queensland 4000, Australia; School of Mechanical, Medical and Process Engineering, Faculty of Engineering, Queensland University of Technology, Brisbane, Queensland 4000, Australia
| | - Prasad Kaparaju
- School of Engineering and Built Environment, Griffith University, Brisbane, Queensland 4111, Australia
| | - Ian M O'Hara
- Centre for Agriculture and the Bioeconomy, Faculty of Science, Queensland University of Technology, Brisbane, Queensland 4000, Australia; School of Mechanical, Medical and Process Engineering, Faculty of Engineering, Queensland University of Technology, Brisbane, Queensland 4000, Australia; ARC Centre of Excellence in Synthetic Biology, QUT, Brisbane, QLD 4000, Australia
| | - Zhanying Zhang
- Centre for Agriculture and the Bioeconomy, Faculty of Science, Queensland University of Technology, Brisbane, Queensland 4000, Australia; School of Mechanical, Medical and Process Engineering, Faculty of Engineering, Queensland University of Technology, Brisbane, Queensland 4000, Australia; ARC Centre of Excellence in Synthetic Biology, QUT, Brisbane, QLD 4000, Australia.
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8
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Biogas Production and Microbial Communities of Mesophilic and Thermophilic Anaerobic Co-Digestion of Animal Manures and Food Wastes in Costa Rica. ENERGIES 2022. [DOI: 10.3390/en15093252] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Biomass generated from agricultural operations in Costa Rica represents an untapped renewable resource for bioenergy generation. This study investigated the effects of two temperatures and three mixture ratios of manures and food wastes on biogas production and microbial community structure. Increasing the amount of fruit and restaurant wastes in the feed mixture significantly enhanced the productivity of the systems (16% increase in the mesophilic systems and 41% in the thermophilic). The methane content of biogas was also favored at higher temperatures. Beta diversity analysis, based on high-throughput sequencing of 16S rRNA gene, showed that microbial communities of the thermophilic digestions were more similar to each other than the mesophilic digestions. Species richness of the thermophilic digestions was significantly greater than the corresponding mesophilic digestions (F = 40.08, p = 0.003). The mesophilic digesters were dominated by Firmicutes and Bacteroidetes while in thermophilic digesters, the phyla Firmicutes and Chloroflexi accounted for up to 90% of all sequences. Methanosarcina represented the key methanogen and was more abundant in thermophilic digestions. These results demonstrate that increasing digestion temperature and adding food wastes can alleviate the negative impact of low C:N ratios on anaerobic digestion.
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9
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An Q, Chen D, Chen H, Yue X, Wang L. Modification of hydro-chars by non-thermal plasma to enhance co-anaerobic digestion and degradation of sewage sludge pyrolysis oil. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 307:114531. [PMID: 35078068 DOI: 10.1016/j.jenvman.2022.114531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 01/08/2022] [Accepted: 01/14/2022] [Indexed: 06/14/2023]
Abstract
The pyrolysis oil produced from the sewage sludge pyrolysis process is a complex admixture of organic substances, which is difficult to be degraded in a normal anaerobic digestion (AD) process. In this study, the hydro-chars produced at 200, 240, and 280 °C were modified by non-thermal plasma (NTP) and then they were used to promote pyrolysis oil degradation and biogas production in a co-AD digester. The experimental results revealed that after NTP modification, the specific surface areas of the hydro-chars produced at 200 °C (SW200+P) and 240 °C were increased from 28.0 to 39.3 m2g-1 and from 36.2 to 45.4 m2g-1, respectively. Their pore volumes also increased by more than 10%. The SW200+P hydro-char exhibited the highest chemical oxygen demand (COD) removal rate (60.49%) and the highest CH4 yield, which is 6.3 times of the digester with pyrolysis oil but without hydro-char addition (PO + CC). Additionally, the benzene series in the pyrolysis oil can be completely degraded in all digesters with the hydro-char addition. With addition of the SW200+P hydro-char, the Clostridia increased most significantly to become the predominant bacteria community at the class level, and the Methanosarcina became the predominant archaea community at the genus level, which contributed to the increased CH4 yield. The hydro-char addition also increased Dietzia and Cellulosimicrobium, which promoted the degradation of benzene series in the pyrolysis oil. The investigation results suggest that the NTP modification technique can be a potential solution to effectively utilize the hydro-char and help pyrolysis oil degradation via the co-AD process.
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Affiliation(s)
- Qing An
- Thermal and Environmental Engineering Institute, Mechanical Engineering College, Tongji University, Shanghai, 201800, China
| | - Dezhen Chen
- Thermal and Environmental Engineering Institute, Mechanical Engineering College, Tongji University, Shanghai, 201800, China.
| | - Hui Chen
- School of Mechanical Engineering, Shanghai Dianji University, Shanghai, 201306, China.
| | - Xia Yue
- Thermal and Environmental Engineering Institute, Mechanical Engineering College, Tongji University, Shanghai, 201800, China
| | - Lei Wang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
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Bio-Based Processes for Material and Energy Production from Waste Streams under Acidic Conditions. FERMENTATION 2022. [DOI: 10.3390/fermentation8030115] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The revolutionary transformation from petrol-based production to bio-based production is becoming urgent in line with the rapid industrialization, depleting resources, and deterioration of the ecosystem. Bio-based production from waste-streams is offering a sustainable and environmentally friendly solution. It offers several advantages, such as a longer operation period, less competition for microorganisms, higher efficiency, and finally, lower process costs. In the current study, several bio-based products (organic acids, biomethane, biohydrogen, and metal leachates) produced under acidic conditions are reviewed regarding their microbial pathways, processes, and operational conditions. Furthermore, the limitations both in the production process and in the scale-up are evaluated with future recommendations.
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Llamas M, Greses S, Tomás-Pejó E, González-Fernández C. Carboxylic acids production via anaerobic fermentation: Microbial communities' responses to stepwise and direct hydraulic retention time decrease. BIORESOURCE TECHNOLOGY 2022; 344:126282. [PMID: 34752887 DOI: 10.1016/j.biortech.2021.126282] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/29/2021] [Accepted: 10/31/2021] [Indexed: 05/11/2023]
Abstract
Carboxylic acids, traditionally produced from fossil fuels, might be generated from renewable biomass resources via anaerobic fermentation. Considering that the microbial activity of this bioprocess is ruled by the imposed hydraulic retention time (HRT), this investigation explored the relationship between process stability and microbial community. Stepwise and direct HRT reduction strategies were assessed in terms of waste bioconversion into volatile fatty acids (VFAs). Microbial community dynamics revealed a microbial specialization along the HRT decrease. The direct implementation of low HRT resulted in drastic microbial fluctuations, leading to process failure at HRT below 6 days. Stepwise strategy for HRT reduction favored microbial adaptation, supporting maximum bioconversions efficiencies (32 % VFACOD/tCODin) at low HRT values (HRT 4 days). Microbial similarity analysis revealed Clostridiales, Lactobacillales and Bacteroidales orders as keystone microorganisms involved in VFAs production, being responsible for protein degradation and propionic acid accumulation.
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Affiliation(s)
- Mercedes Llamas
- Biotechnological Processes Unit, IMDEA Energy, Madrid, Spain
| | - Silvia Greses
- Biotechnological Processes Unit, IMDEA Energy, Madrid, Spain
| | - Elia Tomás-Pejó
- Biotechnological Processes Unit, IMDEA Energy, Madrid, Spain
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Steinberg LM, Martino AJ, House CH. Convergent Microbial Community Formation in Replicate Anaerobic Reactors Inoculated from Different Sources and Treating Ersatz Crew Waste. Life (Basel) 2021; 11:life11121374. [PMID: 34947905 PMCID: PMC8706314 DOI: 10.3390/life11121374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/25/2021] [Accepted: 12/02/2021] [Indexed: 11/16/2022] Open
Abstract
Future manned space travel will require efficient recycling of nutrients from organic waste back into food production. Microbial systems are a low-energy, efficient means of nutrient recycling, but their use in a life support system requires predictability and reproducibility in community formation and reactor performance. To assess the reproducibility of microbial community formation in fixed-film reactors, we inoculated replicate anaerobic reactors from two methanogenic inocula: a lab-scale fixed-film, plug-flow anaerobic reactor and an acidic transitional fen. Reactors were operated under identical conditions, and we assessed reactor performance and used 16s rDNA amplicon sequencing to determine microbial community formation. Reactor microbial communities were dominated by similar groups, but differences in community membership persisted in reactors inoculated from different sources. Reactor performance overlapped, suggesting a convergence of both reactor communities and organic matter mineralization. The results of this study suggest an optimized microbial community could be preserved and used to start new, or restart failed, anaerobic reactors in a life support system with predictable reactor performance.
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Affiliation(s)
| | - Amanda J. Martino
- Biology Department, School of STEAM, Saint Francis University, Loretto, PA 15940, USA;
| | - Christopher H. House
- Department of Geosciences, Earth and Environmental Systems Institute, College of Earth and Mineral Sciences, The Pennsylvania State University, University Park, State College, PA 16802, USA
- Correspondence: (L.M.S.); (C.H.H.)
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Rahman MS, Hoque MN, Puspo JA, Islam MR, Das N, Siddique MA, Hossain MA, Sultana M. Microbiome signature and diversity regulates the level of energy production under anaerobic condition. Sci Rep 2021; 11:19777. [PMID: 34611238 PMCID: PMC8492712 DOI: 10.1038/s41598-021-99104-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/13/2021] [Indexed: 02/08/2023] Open
Abstract
The microbiome of the anaerobic digester (AD) regulates the level of energy production. To assess the microbiome diversity and composition in different stages of anaerobic digestion, we collected 16 samples from the AD of cow dung (CD) origin. The samples were categorized into four groups (Group-I, Group-II, Group-III and Group-IV) based on the level of energy production (CH4%), and sequenced through whole metagenome sequencing (WMS). Group-I (n = 2) belonged to initial time of energy production whereas Group-II (n = 5), Group-III (n = 5), and Group-IV (n = 4) had 21-34%, 47-58% and 71-74% of CH4, respectively. The physicochemical analysis revealed that level of energy production (CH4%) had significant positive correlation with digester pH (r = 0.92, p < 0.001), O2 level (%) (r = 0.54, p < 0.05), and environmental temperature (°C) (r = 0.57, p < 0.05). The WMS data mapped to 2800 distinct bacterial, archaeal and viral genomes through PathoScope (PS) and MG-RAST (MR) analyses. We detected 768, 1421, 1819 and 1774 bacterial strains in Group-I, Group-II, Group-III and Group-IV, respectively through PS analysis which were represented by Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, Spirochaetes and Fibrobacteres phyla (> 93.0% of the total abundances). Simultaneously, 343 archaeal strains were detected, of which 95.90% strains shared across four metagenomes. We identified 43 dominant species including 31 bacterial and 12 archaeal species in AD microbiomes, of which only archaea showed positive correlation with digester pH, CH4 concentration, pressure and temperature (Spearman correlation; r > 0.6, p < 0.01). The indicator species analysis showed that the species Methanosarcina vacuolate, Dehalococcoides mccartyi, Methanosarcina sp. Kolksee and Methanosarcina barkeri were highly specific for energy production. The correlation network analysis showed that different strains of Euryarcheota and Firmicutes phyla exhibited significant correlation (p = 0.021, Kruskal-Wallis test; with a cutoff of 1.0) with the highest level (74.1%) of energy production (Group-IV). In addition, top CH4 producing microbiomes showed increased genomic functional activities related to one carbon and biotin metabolism, oxidative stress, proteolytic pathways, membrane-type-1-matrix-metalloproteinase (MT1-MMP) pericellular network, acetyl-CoA production, motility and chemotaxis. Importantly, the physicochemical properties of the AD including pH, CH4 concentration (%), pressure, temperature and environmental temperature were found to be positively correlated with these genomic functional potentials and distribution of ARGs and metal resistance pathways (Spearman correlation; r > 0.5, p < 0.01). This study reveals distinct changes in composition and diversity of the AD microbiomes including different indicator species, and their genomic features that are highly specific for energy production.
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Affiliation(s)
- M. Shaminur Rahman
- grid.8198.80000 0001 1498 6059Department of Microbiology, University of Dhaka, Dhaka, 1000 Bangladesh
| | - M. Nazmul Hoque
- grid.8198.80000 0001 1498 6059Department of Microbiology, University of Dhaka, Dhaka, 1000 Bangladesh ,grid.443108.a0000 0000 8550 5526Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706 Bangladesh
| | - Joynob Akter Puspo
- grid.8198.80000 0001 1498 6059Department of Microbiology, University of Dhaka, Dhaka, 1000 Bangladesh
| | - M. Rafiul Islam
- grid.8198.80000 0001 1498 6059Department of Microbiology, University of Dhaka, Dhaka, 1000 Bangladesh
| | - Niloy Das
- grid.8198.80000 0001 1498 6059Department of Microbiology, University of Dhaka, Dhaka, 1000 Bangladesh ,Surge Engineering (www.surgeengineering.com), Dhaka, 1205 Bangladesh
| | - Mohammad Anwar Siddique
- grid.8198.80000 0001 1498 6059Department of Microbiology, University of Dhaka, Dhaka, 1000 Bangladesh
| | - M. Anwar Hossain
- grid.8198.80000 0001 1498 6059Department of Microbiology, University of Dhaka, Dhaka, 1000 Bangladesh ,Present Address: Jashore University of Science and Technology, Jashore, 7408 Bangladesh
| | - Munawar Sultana
- grid.8198.80000 0001 1498 6059Department of Microbiology, University of Dhaka, Dhaka, 1000 Bangladesh
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14
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Silva I, Jorge C, Brito L, Duarte E. A pig slurry feast/famine feeding regime strategy to improve mesophilic anaerobic digestion efficiency and digestate hygienisation. WASTE MANAGEMENT & RESEARCH : THE JOURNAL OF THE INTERNATIONAL SOLID WASTES AND PUBLIC CLEANSING ASSOCIATION, ISWA 2021; 39:947-955. [PMID: 33280536 DOI: 10.1177/0734242x20972794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The increasing concentration of livestock farms results in large amounts of waste production and the need for their management. The study of anaerobic digestion (AD) technology, under mesophilic conditions, applied to pig slurry is of the upmost importance for biogas recovery and sanitised digestate, contributing to a circular economy. The assessment of the effects of a feast/famine regime on biogas and biomethane (bio-CH4) yield with different feeding frequencies was performed. The evaluation was made in regards to three scenarios: the first is based on daily feeding (FR1); in the second, the feeding occurs once every two days (FR2); and in the third, the feeding happens once every three days (FR3). The results demonstrate that the biogas and methane yield increased by 34% and 37% between FR1 and FR3. The stability inside the reactor was maintained since specific loading energetic rate values did not exceed the recommended limit (0.4 d-1). It was also possible to conclude that the AD technology was efficient to sanitise the pig slurry, with the count of Escherichia coli going from 1 × 105 colony-forming units (CFU) g-1 to less than 100 CFU g-1, meeting the legal requirements for agricultural valorisation. The total anaerobic mesophile plate counts were significantly (p < 0.1) reduced from feeding to digestate, and the plate counts of Clostridia were significantly (p < 0.05) increased, reflecting the changes in the composition of the microbiota. The increasing yield in bio-CH4 in accordance with Clostridium counts suggests this genus as a positive microbiological key indicator of the AD performance.
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Affiliation(s)
- I Silva
- LEAF - Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, Lisbon, Portugal
| | - C Jorge
- Luke - Natural Resources Institute Finland, Helsinki, Finland
- CEF - Forest Research Center, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, Lisbon, Portugal
| | - L Brito
- LEAF - Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, Lisbon, Portugal
| | - E Duarte
- LEAF - Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, Lisbon, Portugal
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15
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Saha S, Basak B, Hwang JH, Salama ES, Chatterjee PK, Jeon BH. Microbial Symbiosis: A Network towards Biomethanation. Trends Microbiol 2020; 28:968-984. [DOI: 10.1016/j.tim.2020.03.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/20/2020] [Accepted: 03/25/2020] [Indexed: 11/28/2022]
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16
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The significance of microbial community functions and symbiosis in enhancing methane production during anaerobic digestion: a review. Symbiosis 2020. [DOI: 10.1007/s13199-020-00734-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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17
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Poirier S, Déjean S, Midoux C, Lê Cao KA, Chapleur O. Integrating independent microbial studies to build predictive models of anaerobic digestion inhibition by ammonia and phenol. BIORESOURCE TECHNOLOGY 2020; 316:123952. [PMID: 32771938 DOI: 10.1016/j.biortech.2020.123952] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/28/2020] [Accepted: 07/31/2020] [Indexed: 05/23/2023]
Abstract
Anaerobic digestion (AD) is a process that can efficiently degrade organic waste into renewable energies. AD failure is however common as the underpinning microbial mechanisms are highly vulnerable to a wide range of inhibitory compounds. Sequencing technologies enable the identification of microbial indicators of digesters inhibition, but existing studies are limited. They used different inocula, substrates, sites and types of reactors and reported different or contradictory indicators. Our aim was to identify a robust signature of microbial indicators of phenol and ammonia inhibitions across four independent AD microbial studies. To identify such signature, we applied an original multivariate integrative method on two in-house studies, then validated our approach by predicting the inhibitory status of samples from two other studies with more than 90% accuracy. Our approach shows how we can efficiently leverage on existing studies to extract reproducible microbial community patterns and predict AD inhibition to improve AD microbial management.
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Affiliation(s)
- Simon Poirier
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement, 92761 Antony, France
| | - Sébastien Déjean
- Toulouse Mathematics Institute, UMR 5219 CNRS, Toulouse University, Toulouse, France
| | - Cédric Midoux
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement, 92761 Antony, France
| | - Kim-Anh Lê Cao
- Melbourne Integrative Genomics, School of Mathematics and Statistics, The University of Melbourne, Parkville, Victoria, Australia
| | - Olivier Chapleur
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement, 92761 Antony, France.
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18
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Chen J, Li H, Zhang Z, He C, Shi Q, Jiao N, Zhang Y. DOC dynamics and bacterial community succession during long-term degradation of Ulva prolifera and their implications for the legacy effect of green tides on refractory DOC pool in seawater. WATER RESEARCH 2020; 185:116268. [PMID: 32784034 DOI: 10.1016/j.watres.2020.116268] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 07/29/2020] [Accepted: 08/03/2020] [Indexed: 06/11/2023]
Abstract
Under climate warming and coastal eutrophication, outbreaks of green tides have increased in recent decades; e.g., the world's largest green tide caused by Ulva prolifera has occurred in the Yellow Sea for 13 consecutive years. The massive assemblage of macroalgae absorbs large amounts of atmospheric CO2 and converts it into biomass. After the green tide, millions of tons of the macroalgal biomass sink to the seabed to be degraded eventually; this inevitably has a significant impact on the coastal organic carbon pool and microbial community. However, this impact is poorly understood. Here, the degradation of Ulva prolifera over 520 days revealed that relatively sufficient degradation of the macroalgae occurred at ca. 7 months. The rapid release of dissolved organic carbon (DOC) mainly occurred in the first week, which not only increased the size and diversity of the DOC pool in a short time but also promoted the rapid growth of bacteria and led to hypoxia and acidification of the seawater. After that, the labile portion of DOC was gradually used up by bacteria within one month, while the degradation of semi-labile or semi-refractory DOC occurred in half a year. The remaining DOC existed in the form of refractory DOC (RDOC), resisting bacterial consumption and remaining stable for 10 months. During the long-term degradation process, bacterial community structure and metabolic function showed obvious successional characteristics, driving the gradual transformation of DOC from labile to refractory through the microbial carbon pump mechanism. After the long-term degradation, the remaining RDOC accounted for approximately 1.6% of the macroalgal carbon biomass. As RDOC can maintain long-term stability, we propose that the frequent outbreaks of green tides not only affect microbial processes but also may have an important cumulative effect on the coastal RDOC pool.
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Affiliation(s)
- Jing Chen
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hongmei Li
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zenghu Zhang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Chen He
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, 102249, China
| | - Quan Shi
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, 102249, China
| | - Nianzhi Jiao
- State Key Laboratory for Marine Environmental Science, Xiamen University, Xiamen, 361100, China.
| | - Yongyu Zhang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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19
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Wang Z, Yun S, Shi J, Han F, Liu B, Wang R, Li X. Critical evidence for direct interspecies electron transfer with tungsten-based accelerants: An experimental and theoretical investigation. BIORESOURCE TECHNOLOGY 2020; 311:123519. [PMID: 32446236 DOI: 10.1016/j.biortech.2020.123519] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 05/05/2020] [Accepted: 05/07/2020] [Indexed: 06/11/2023]
Abstract
Accelerants can significantly enhance the biodegradability in anaerobic digestion (AD), which can be attributed to the direct interspecies electron transfer (DIET) mechanism. However, critical evidence for DIET mechanism is absent. In this work, nano-scale tungsten (W)-based compounds (WC, W2N, and W18O49) are employed to clarify the roles of W-based accelerants in AD systems. A DIET mechanism based on the W-based accelerants is proposed, and three critical pieces of evidence are provided: (i) First-principle density functional theory calculations provide theoretical evidence, illustrating that W-based accelerants are of zero band gap. (ii) Electrical conductivity evaluation further elucidates that W-based accelerants have superior electronic transport. (iii) Pyrosequencing of 16S rRNA gene confirms the existence of acetogens and methanogens in AD systems, which can act as electron-donor bacteria and electron-acceptor archaea, respectively. Combining theoretical with experimental results, the critical evidence provides a general strategy for understanding the DIET mechanism of accelerant in AD systems.
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Affiliation(s)
- Ziqi Wang
- Functional Materials Laboratory (FML), School of Materials Science and Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, China
| | - Sining Yun
- Functional Materials Laboratory (FML), School of Materials Science and Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, China.
| | - Jing Shi
- Functional Materials Laboratory (FML), School of Materials Science and Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, China
| | - Feng Han
- Functional Materials Laboratory (FML), School of Materials Science and Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, China
| | - Bingyin Liu
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, China
| | - Ru Wang
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, China
| | - Xue Li
- Functional Materials Laboratory (FML), School of Materials Science and Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, China
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20
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Villa Gomez DK, Becerra Castañeda P, Montoya Rosales JDJ, González Rodríguez LM. Anaerobic digestion of bean straw applying a fungal pre-treatment and using cow manure as co-substrate. ENVIRONMENTAL TECHNOLOGY 2020; 41:2863-2874. [PMID: 30811276 DOI: 10.1080/09593330.2019.1587004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 02/18/2019] [Indexed: 06/09/2023]
Abstract
The significant amounts of agriculture residues such as bean straw (BS) in rural areas, advises its valorisation for energy recovery. The feasibility of using BS for biogas production through anaerobic digestion was assessed. Prior to this, a fungal pre-treatment to hydrolyse BS with Pleutorus ostreatus was studied at 30°C and 100 rpm in orbital incubators with 1, 10 and 30 mg fungus/g straw for 14, 21 and 28 days. Then, anaerobic digestion experiments were performed in batch with cow manure (CM) as co-substrate and pre-treated BS at ratios (g/g total solids) of 1/2, 1/3, 1/5 and 0/1. Maximum lignin (18%) and hemicellulose (44%) degradation occurred at 30 mg fungus/g straw and 28 days, along with the highest total methane yield (38 mL CH4/g VS loaded). The total amount of methane decreased when increasing CM in the experiments (701.4-191.5 mL CH4), suggesting inhibition owed to a component of CM. Self-sustained biogas production of BS occurred due to the presence of bacteria (i.e. Bacilli and Bacteroidia) and archea (i.e. Methanobacteria and Methanomicrobia). However, the usage of a full-active inoculum should be studied for higher biogas production rates.
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Affiliation(s)
| | - Patricia Becerra Castañeda
- Unidad Profesional Interdisciplinaria De Ingeniería Campus Zacatecas, Instituto Politécnico Nacional, Zacatecas, México
| | - Jose de Jesus Montoya Rosales
- Unidad Profesional Interdisciplinaria De Ingeniería Campus Zacatecas, Instituto Politécnico Nacional, Zacatecas, México
| | - Luis Mario González Rodríguez
- Unidad Profesional Interdisciplinaria De Ingeniería Campus Zacatecas, Instituto Politécnico Nacional, Zacatecas, México
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21
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Cardona L, Cao KAL, Puig-Castellví F, Bureau C, Madigou C, Mazéas L, Chapleur O. Integrative Analyses to Investigate the Link between Microbial Activity and Metabolite Degradation during Anaerobic Digestion. J Proteome Res 2020; 19:3981-3992. [DOI: 10.1021/acs.jproteome.0c00251] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Laëtitia Cardona
- Université Paris-Saclay, INRAE, PROSE, 1 rue Pierre-Gilles de Gennes, CS 10030, 92761 Antony Cedex, France
| | - Kim Anh Lê Cao
- Melbourne Integrative Genomics, School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Francesc Puig-Castellví
- Université Paris-Saclay, INRAE, PROSE, 1 rue Pierre-Gilles de Gennes, CS 10030, 92761 Antony Cedex, France
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 75005 Paris, France
| | - Chrystelle Bureau
- Université Paris-Saclay, INRAE, PROSE, 1 rue Pierre-Gilles de Gennes, CS 10030, 92761 Antony Cedex, France
| | - Céline Madigou
- Acquisitions et Analyses de Données pour l’Histoire naturelle, 2AD—UMS 2700 CNRS MNHN, Muséum national d’Histoire naturelle, CP26, 57 rue Cuvier, 75231 Paris Cedex 05, France
| | - Laurent Mazéas
- Université Paris-Saclay, INRAE, PROSE, 1 rue Pierre-Gilles de Gennes, CS 10030, 92761 Antony Cedex, France
| | - Olivier Chapleur
- Université Paris-Saclay, INRAE, PROSE, 1 rue Pierre-Gilles de Gennes, CS 10030, 92761 Antony Cedex, France
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22
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Han W, He P, Lin Y, Shao L, Lü F. A Methanogenic Consortium Was Active and Exhibited Long-Term Survival in an Extremely Acidified Thermophilic Bioreactor. Front Microbiol 2019; 10:2757. [PMID: 32038509 PMCID: PMC6988822 DOI: 10.3389/fmicb.2019.02757] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 11/12/2019] [Indexed: 11/29/2022] Open
Abstract
Acid crisis characterized by acid accumulation and/or low pH is a common reason for the failure of anaerobic digestion (AD), which is usually applied for wastewater and waste treatment. Acid-tolerant methanogens are rarely reported to be active in the artificial anaerobic digester. In this study, we observed that the thermophilic methanogenesis by a consortium in the form of flocs and not granules could still be recovered during long-term operation at acetate concentration of up to 104 mM and pH 5.5 by adjusting the pH gradually or directly to pH 5.5 or 5.0. The acclimation process involving the gradual decrease in pH could enhance the resistance of the consortium against extreme acidification. The stable isotopic signature analysis of biogas revealed that Methanosarcina, which produced methane through acetoclastic methanogenesis (AM) pathway, was the predominant methane producer when the pH was decreased gradually to 5.0. Meanwhile, the abundance of Coprothermobacter increased with a decrease in pH. Contrastingly, when directly subjected to an environment of pH 5.5 and 104 mM acetate (15.84-mM free acetic acid) after a 42-day lag phase, Methanothermobacter was the predominant methanogen. Methanothermobacter initiated methane production through the hydrogenotrophic pathway and formed syntrophic relationship/consortium with the potential acetate-oxidizing bacteria, Thermacetogenium and Coprothermobacter. Comparative metagenomic and metatranscriptomic analysis on this self-adapted and acid-tolerant consortium revealed that the genes, such as GroEL, DnaK, CheY, and flagellum-related genes (FlaA, FlgE, and FliC) from Anaerobaculum, Thermacetogenium, and Coprothermobacter were highly overexpressed in response to system acidification. Microbial self-adaptation patterns (community structure adjustment, methanogenesis pathway shift, and transcriptional regulation) of thermophilic methanogenic consortium to gradual and sudden acidification were evaluated by integrated stable isotopic signature and comparative meta-omic approaches. The study elucidated the acid-resistant mechanism of thermophilic methanogenic consortium and deepened our knowledge of the function, interaction, and microbial characteristics of Methanosarcina, Methanothermobacter, and Coprothermobacter under extreme acidic environment.
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Affiliation(s)
- Wenhao Han
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai, China.,Shanghai Institute of Pollution Control and Ecological Security, Shanghai, China
| | - Pinjing He
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai, China.,Institute of Waste Treatment and Reclamation, Tongji University, Shanghai, China
| | - Yucheng Lin
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai, China.,Shanghai Institute of Pollution Control and Ecological Security, Shanghai, China
| | - Liming Shao
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai, China.,Institute of Waste Treatment and Reclamation, Tongji University, Shanghai, China
| | - Fan Lü
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai, China.,Institute of Waste Treatment and Reclamation, Tongji University, Shanghai, China
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23
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Atasoy M, Eyice O, Schnürer A, Cetecioglu Z. Volatile fatty acids production via mixed culture fermentation: Revealing the link between pH, inoculum type and bacterial composition. BIORESOURCE TECHNOLOGY 2019; 292:121889. [PMID: 31394468 DOI: 10.1016/j.biortech.2019.121889] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 07/09/2019] [Accepted: 07/24/2019] [Indexed: 06/10/2023]
Abstract
The aim of the study was to investigate the effects of operational parameters, inoculum type and bacterial community on mixed culture fermentation to produce one dominant acid type in the mixture of volatile fatty acids (VFA). The study was performed using three different inocula (large&small granular and slurry) with glucose under various initial pH. The VFA production efficiency reached to 0,97 (gCOD/gSCOD) by granular sludge. VFA composition was changed by initial pH: in neutral conditions, acetic acid; in acidic conditions, acetic and butyric acids, in alkali conditions butyric acid were dominated, respectively. The VFA production was positively affected by the high relative abundance of Firmicutes. On the contrary, a negative correlation was seen between VFA production and the relative abundance of Chloroflexi. The results revealed the physical sludge structure of inoculum was the key factor for production efficiency, whereas, pH was the most important parameter to affect VFA composition.
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Affiliation(s)
- Merve Atasoy
- Department of Chemical Engineering, KTH Royal Institute of Technology, SE-100 44, Sweden
| | - Ozge Eyice
- School of Biological and Chemical Sciences, Queen Mary University of London, E1 4NS, UK
| | - Anna Schnürer
- Department of Molecular Sciences, Biocenter, Swedish University of Agricultural Sciences, SE 750 07, Sweden
| | - Zeynep Cetecioglu
- Department of Chemical Engineering, KTH Royal Institute of Technology, SE-100 44, Sweden.
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24
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Saha S, Jeon BH, Kurade MB, Govindwar SP, Chatterjee PK, Oh SE, Roh HS, Lee SS. Interspecies microbial nexus facilitated methanation of polysaccharidic wastes. BIORESOURCE TECHNOLOGY 2019; 289:121638. [PMID: 31212174 DOI: 10.1016/j.biortech.2019.121638] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 06/05/2019] [Accepted: 06/10/2019] [Indexed: 06/09/2023]
Abstract
Compositional variations in organic wastes influence microbial abundancy and syntrophy during anaerobic digestion (AD), impacting the normal performance of digesters for methanation. Investigation of the microbial dynamics during AD following augmentation with polysaccharidic wastes (PW) revealed the association of effective digester performance and methane yields with the microbial nexus. Dominance of the acidogenic saccharolytic genera, Prevotella, Eubacterium, and Lachnoclostridium, enhanced the utilization of carbohydrates (54%) in PW-augmented digesters. Spearman's rs correlation showed dynamic interspecies interactions among acetogenic syntrophs, and that of iron oxidizers/reducers with acetoclastic and hydrogenotrophic methanogens. Propionate oxidizers in Chloroflexi (i.e., Bellilinea, Levilinea, and Longilinea) exhibited positive associations with acetoclastic methanogens. Increase in the population of acetoclastic methanogens (Methanosaeta, 77% and Methanosarcina, 9%) accelerated the methanogenic activity of PW-augmented digesters by 7 times during the exponential phase, increasing the methane yield (75%) compared to the control. Thus, microbial syntrophy facilitated the effective methanation of PW during AD process.
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Affiliation(s)
- Shouvik Saha
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, Republic of Korea
| | - Byong-Hun Jeon
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, Republic of Korea.
| | - Mayur B Kurade
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, Republic of Korea
| | - Sanjay P Govindwar
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, Republic of Korea
| | - Pradip K Chatterjee
- Energy Research and Technology Group, CSIR Central Mechanical Engineering Research Institute, Durgapur 713-209, India
| | - Sang-Eun Oh
- Department of Biological Environment, Kangwon National University, Chuncheon, Gangwon-do 24341, Republic of Korea
| | - Hyun-Seog Roh
- Department of Environmental Engineering, Yonsei University, Wonju, Gangwon-do 26493, Republic of Korea
| | - Sean S Lee
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, Republic of Korea
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25
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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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26
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Bertucci M, Calusinska M, Goux X, Rouland-Lefèvre C, Untereiner B, Ferrer P, Gerin PA, Delfosse P. Carbohydrate Hydrolytic Potential and Redundancy of an Anaerobic Digestion Microbiome Exposed to Acidosis, as Uncovered by Metagenomics. Appl Environ Microbiol 2019; 85:e00895-19. [PMID: 31152018 PMCID: PMC6643232 DOI: 10.1128/aem.00895-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 05/26/2019] [Indexed: 12/22/2022] Open
Abstract
Increased hydrolysis of easily digestible biomass may lead to acidosis of anaerobic reactors and decreased methane production. Previously, it was shown that the structure of microbial communities changed during acidosis; however, once the conditions are back to optimal, biogas (initially CO2) production quickly restarts. This suggests the retention of the community functional redundancy during the process failure. In this study, with the use of metagenomics and downstream bioinformatics analyses, we characterize the carbohydrate hydrolytic potential of the microbial community, with a special focus on acidosis. To that purpose, carbohydrate-active enzymes were identified, and to further link the community hydrolytic potential with key microbes, bacterial genomes were reconstructed. In addition, we characterized biochemically the specificity and activity of selected enzymes, thus verifying the accuracy of the in silico predictions. The results confirm the retention of the community hydrolytic potential during acidosis and indicate Bacteroidetes to be largely involved in biomass degradation. Bacteroidetes showed higher diversity and genomic content of carbohydrate hydrolytic enzymes that might favor the dominance of this phylum over other bacteria in some anaerobic reactors. The combination of bioinformatic analyses and activity tests enabled us to propose a model of acetylated glucomannan degradation by BacteroidetesIMPORTANCE The enzymatic hydrolysis of lignocellulosic biomass is mainly driven by the action of carbohydrate-active enzymes. By characterizing the gene profiles at the different stages of the anaerobic digestion experiment, we showed that the microbiome retains its hydrolytic functional redundancy even during severe acidosis, despite significant changes in taxonomic composition. By analyzing reconstructed bacterial genomes, we demonstrate that Bacteroidetes hydrolytic gene diversity likely favors the abundance of this phylum in some anaerobic digestion systems. Further, we observe genetic redundancy within the Bacteroidetes group, which accounts for the preserved hydrolytic potential during acidosis. This work also uncovers new polysaccharide utilization loci involved in the deconstruction of various biomasses and proposes the model of acetylated glucomannan degradation by Bacteroidetes Acetylated glucomannan-enriched biomass is a common substrate for many industries, including pulp and paper production. Using naturally evolved cocktails of enzymes for biomass pretreatment could be an interesting alternative to the commonly used chemical pretreatments.
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Affiliation(s)
- Marie Bertucci
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, Belvaux, Luxembourg
- Laboratory of Bioengineering, Earth and Life Institute, Applied Microbiology, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Magdalena Calusinska
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, Belvaux, Luxembourg
| | - Xavier Goux
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, Belvaux, Luxembourg
| | - Corinne Rouland-Lefèvre
- Institute of Ecology and Environmental Sciences, Research Institute Development, Sorbonne Universités, Bondy, France
| | - Boris Untereiner
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, Belvaux, Luxembourg
| | - Pau Ferrer
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, Belvaux, Luxembourg
| | - Patrick A Gerin
- Laboratory of Bioengineering, Earth and Life Institute, Applied Microbiology, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Philippe Delfosse
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, Belvaux, Luxembourg
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27
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Nordgård ASR, Bergland WH, Bakke R, Østgaard K, Bakke I. Mapping anaerobic sludge bed community adaptations to manure supernatant in biogas reactors. Sci Rep 2018; 8:15870. [PMID: 30367088 PMCID: PMC6203818 DOI: 10.1038/s41598-018-34088-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 10/07/2018] [Indexed: 12/05/2022] Open
Abstract
In upflow anaerobic sludge bed (UASB) reactors, biomass present as granules allows for long solids retention time. Here, granules from a process treating pulp and paper industrial wastewater were successfully applied as inoculum in UASB reactors treating pig manure supernatant, despite high particle content and high ammonium concentrations in the influent. We did a detailed characterization of archaeal and bacterial communities associated with the inoculum and with the aggregated and dispersed fractions of the influent and the reactors after one year of operation. The granular communities underwent major changes and adapted to the highly distinct conditions without disintegration of the granules. Although the granules persisted in the reactors, non-granular aggregates accumulated, and partly replaced the granules. Particles introduced to the reactors by the pig manure influent apparently contributed both as food and biofilm growth support. Archaeal communities in the dispersed reactor phase were similar to those dispersed in the influents, implying successful retention and little loss of archaeal biomass due to detachment or disintegration of granules and other aggregates. Unique bacterial communities developed in the dispersed fraction of the reactors despite of low hydraulic retention times. They probably consisted of fast growing organisms consuming readily degradable organic matter.
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Affiliation(s)
- Anna Synnøve Røstad Nordgård
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Wenche Hennie Bergland
- Department of Process, Energy and Environmental Technology, University College of Southeast Norway (USN), Kjølnes ring 56, 3918, Porsgrunn, Norway
| | - Rune Bakke
- Department of Process, Energy and Environmental Technology, University College of Southeast Norway (USN), Kjølnes ring 56, 3918, Porsgrunn, Norway
| | - Kjetill Østgaard
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Ingrid Bakke
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway.
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