1
|
Hu P, Qian Y, Radian A, Xu M, Guo C, Gu JD. A global metagenomics-based analysis of BPA degradation and its coupling with nitrogen, sulfur, and methane metabolism in landfill leachates. JOURNAL OF HAZARDOUS MATERIALS 2024; 477:135395. [PMID: 39106729 DOI: 10.1016/j.jhazmat.2024.135395] [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: 05/28/2024] [Revised: 07/14/2024] [Accepted: 07/30/2024] [Indexed: 08/09/2024]
Abstract
Microbial metabolism in landfill leachate systems is critically important in driving the degradation reactions of organic pollutants, including the emerging pollutant bisphenol A (BPA). However, little research has addressed the microbial degradation of BPA in landfill leachate and its interactions with nitrogen (N), sulfur (S), and methane (CH4) metabolism on a global scale. To this end, in this study on a global scale, an extremely high concentration of BPA was detected throughout the global landfill leachates. Subsequent reconstructive analyses of metagenomic datasets from 113 sites worldwide revealed that the predominant BPA-degrading microflora included Proteobacteria, Firmicutes, and Bacteroidota. Further metabolic analyses revealed that all four biochemical pathways involved in the degradation of BPA were achieved through biochemical cooperation between different bacterial members of the community. In addition, BPA degraders have also been found to actively collaborate synergistically with non-BPA degraders in the N and S removal as well as CH4 catabolism in landfill leachates. Collectively, this study not only provides insights into the dominant microbial communities and specific types of BPA-degrading microbial members in the community of landfill leachates worldwide, but also reveals the synergistic interactions between BPA mineralization and N, S, and CH4 metabolism. These findings offer valuable and important insights for future comprehensive and in-depth investigations into BPA metabolism in different environments.
Collapse
Affiliation(s)
- Pengfei Hu
- Civil and Environmental Engineering, Technion - Israel Institute of Technology, Haifa 320003, Israel; Environmental Science and Engineering Research Group, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, The People's Republic of China
| | - Youfen Qian
- Civil and Environmental Engineering, Technion - Israel Institute of Technology, Haifa 320003, Israel; Environmental Science and Engineering Research Group, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, The People's Republic of China
| | - Adi Radian
- Civil and Environmental Engineering, Technion - Israel Institute of Technology, Haifa 320003, Israel
| | - Meiying Xu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, The People's Republic of China
| | - Changhong Guo
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang 150025, The People's Republic of China
| | - Ji-Dong Gu
- Civil and Environmental Engineering, Technion - Israel Institute of Technology, Haifa 320003, Israel; Environmental Science and Engineering Research Group, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, The People's Republic of China; Guangdong Provincial Key Laboratory of Materials and Technologies for Energy Conversion, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, The People's Republic of China.
| |
Collapse
|
2
|
Chen X, Zang C, Xie Y, Wang K, Li Y, Lv R, Wen B, Cui Z, Yuan X. Porous hollow microspheres based on industrial solid waste enhance biomethane recovery from corn straw. BIORESOURCE TECHNOLOGY 2024; 412:131395. [PMID: 39216699 DOI: 10.1016/j.biortech.2024.131395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 08/20/2024] [Accepted: 08/28/2024] [Indexed: 09/04/2024]
Abstract
The increasing production of industrial solid waste requires better disposal solutions. Porous hollow microspheres (PHM) are small inorganic materials with high surface area and adsorption capacity, but their potential for use in anaerobic digestion (AD) has not been explored. With PHM as additive, the effects of different industrial solid wastes (waste glass, steel slag, and fly ash) with different loadings (2 %-8 %), respectively, on the AD of corn straw were investigated in this study. The results showed that PHM could supplement trace elements and promote biofilm formation, which effectively shortened the lag period (25.00-60.87 %) and increased the methane yield (4.75 %-16.28 %). The 2 % PHM loading based on steel slag gave the highest methane yield (300.16 NmL/g VSadd). Microbial and PICRUSt2 analyses indicated that PHM enriched hydrolytic and acidogenic bacteria, increased the abundance of methanogenesis-related enzyme genes. This study provides a theoretical basis for the comprehensive utilization of coupled industrial and agricultural wastes.
Collapse
Affiliation(s)
- Xiaotian Chen
- College of Agronomy/Center of Biomass Engineering, China Agricultural University, Beijing 100193, China
| | - Changchang Zang
- College of Agronomy/Center of Biomass Engineering, China Agricultural University, Beijing 100193, China
| | - Yuting Xie
- College of Agronomy/Center of Biomass Engineering, China Agricultural University, Beijing 100193, China
| | - Ke Wang
- Beijing Huaqi Eco-Tech Co., LTD, Beijing 102200, China
| | - Yang Li
- Beijing Huaqi Eco-Tech Co., LTD, Beijing 102200, China
| | - Ruifang Lv
- Beijing Huaqi Eco-Tech Co., LTD, Beijing 102200, China
| | - Boting Wen
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Zongjun Cui
- College of Agronomy/Center of Biomass Engineering, China Agricultural University, Beijing 100193, China
| | - Xufeng Yuan
- College of Agronomy/Center of Biomass Engineering, China Agricultural University, Beijing 100193, China.
| |
Collapse
|
3
|
Bizzotto E, Fraulini S, Zampieri G, Orellana E, Treu L, Campanaro S. MICROPHERRET: MICRObial PHEnotypic tRait ClassifieR using Machine lEarning Techniques. ENVIRONMENTAL MICROBIOME 2024; 19:58. [PMID: 39113074 PMCID: PMC11308548 DOI: 10.1186/s40793-024-00600-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 07/24/2024] [Indexed: 08/10/2024]
Abstract
BACKGROUND In recent years, there has been a rapid increase in the number of microbial genomes reconstructed through shotgun sequencing, and obtained by newly developed approaches including metagenomic binning and single-cell sequencing. However, our ability to functionally characterize these genomes by experimental assays is orders of magnitude less efficient. Consequently, there is a pressing need for the development of swift and automated strategies for the functional classification of microbial genomes. RESULTS The present work leverages a suite of supervised machine learning algorithms to establish a range of 86 metabolic and other ecological functions, such as methanotrophy and plastic degradation, starting from widely obtainable microbial genome annotations. Tests performed on independent datasets demonstrated robust performance across complete, fragmented, and incomplete genomes above a 70% completeness level for most of the considered functions. Application of the algorithms to the Biogas Microbiome database yielded predictions broadly consistent with current biological knowledge and correctly detecting functionally-related nuances of archaeal genomes. Finally, a case study focused on acetoclastic methanogenesis demonstrated how the developed machine learning models can be refined or expanded with models describing novel functions of interest. CONCLUSIONS The resulting tool, MICROPHERRET, incorporates a total of 86 models, one for each tested functional class, and can be applied to high-quality microbial genomes as well as to low-quality genomes derived from metagenomics and single-cell sequencing. MICROPHERRET can thus aid in understanding the functional role of newly generated genomes within their micro-ecological context.
Collapse
Affiliation(s)
- Edoardo Bizzotto
- Department of Biology, University of Padova, Padova, 35131, Italy
| | - Sofia Fraulini
- Department of Biology, University of Padova, Padova, 35131, Italy
| | - Guido Zampieri
- Department of Biology, University of Padova, Padova, 35131, Italy.
| | - Esteban Orellana
- Department of Biology, University of Padova, Padova, 35131, Italy
| | - Laura Treu
- Department of Biology, University of Padova, Padova, 35131, Italy
| | | |
Collapse
|
4
|
Chang H, Du B, He K, Yin Q, Wu G. Mechanistic understanding of acclimation and energy metabolism of acetoclastic methanogens under different substrate to microorganism ratios. ENVIRONMENTAL RESEARCH 2024; 252:118911. [PMID: 38604482 DOI: 10.1016/j.envres.2024.118911] [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: 01/18/2024] [Revised: 04/05/2024] [Accepted: 04/08/2024] [Indexed: 04/13/2024]
Abstract
Mechanistic understanding of acetoclastic methanogenesis is pivotal for optimizing anaerobic digestion for efficient methane production. In this study, two different operational modes, continuous flow reactor (CFR) and sequencing batch reactor (SBR), accompanied with solids retention times (SRT) of 10 days (SBR10d and CFR10d) and 25 days (SBR25d and CFR25d) were implemented to elucidate their impacts on microbial communities and energy metabolism of methanogens in acetate-fed systems. Microbial community analysis revealed that the relative abundance of Methanosarcina (16.0%-46.0%) surpassed Methanothrix (3.7%-22.9%) in each reactor. SBRs had the potential to enrich both Methanothrix and Methanosarcina. Compared to SBRs, CFRs had lower total relative abundance of methanogens. Methanosarcina exhibited a superior enrichment in reactors with 10-day SRT, while Methanothrix preferred to be acclimated in reactors with 25-day SRT. The operational mode and SRT were also observed to affect the distribution of acetate-utilizing bacteria, including Pseudomonas, Desulfocurvus, Mesotoga, and Thauera. Regarding enzymes involved in energy metabolism, Ech and Vho/Vht demonstrated higher relative abundances at 10-day SRT compared to 25-day SRT, whereas Fpo and MtrA-H showed higher relative abundances in SBRs than those in CFRs. The relative abundance of genes encoding ATPase harbored by Methanothrix was higher than Methanosarcina at 25-day SRT. Additionally, the relative abundance of V/A-type ATPase (typically for methanogens) was observed higher in SBRs compared to CFRs, while the F-type ATPase (typically for bacteria) exhibited higher relative abundance in CFRs than that in SBRs.
Collapse
Affiliation(s)
- Huanhuan Chang
- Civil Engineering, School of Engineering, College of Science and Engineering, University of Galway, Galway H91 TK33, Ireland
| | - Bang Du
- Civil Engineering, School of Engineering, College of Science and Engineering, University of Galway, Galway H91 TK33, Ireland
| | - Kai He
- School of Civil Engineering, Sun Yat-Sen University, Guangzhou 51000, Guangdong, China
| | - Qidong Yin
- School of Civil Engineering, Sun Yat-Sen University, Guangzhou 51000, Guangdong, China
| | - Guangxue Wu
- Civil Engineering, School of Engineering, College of Science and Engineering, University of Galway, Galway H91 TK33, Ireland.
| |
Collapse
|
5
|
Yin L, Zhou A, Wei Y, Varrone C, Li D, Luo J, He Z, Liu W, Yue X. Deep insights into the roles and microbial ecological mechanisms behind waste activated sludge digestion triggered by persulfate oxidation activated through multiple modes. ENVIRONMENTAL RESEARCH 2024; 252:118905. [PMID: 38604480 DOI: 10.1016/j.envres.2024.118905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/23/2024] [Accepted: 04/08/2024] [Indexed: 04/13/2024]
Abstract
Persulfate oxidation (PS) is widely employed as a promising alternative for waste activated sludge pretreatment due to the capability of generating free radicals. The product differences and microbiological mechanisms by which PS activation triggers WAS digestion through multiple modes need to be further investigated. This study comprehensively investigated the effects of persulfate oxidation activated through multiple modes, i.e., ferrous, zero-valent iron (ZVI), ultraviolet (UV) and heat, on the performance of sludge digestion. Results showed that PS_ZVI significantly accelerated the methane production rate to 12.02 mL/g VSS. By contrast, PS_Heat promoted the sludge acidification and gained the maximum short-chain fatty acids (SCFAs) yield (277.11 ± 7.81 mg COD/g VSS), which was 3.41-fold compared to that in PS_ZVI. Moreover, ferrous and ZVI activated PS achieved the oriented conversion of acetate, the proportions of which took 73% and 78%, respectively. MiSeq sequencing results revealed that PS_Heat and PS_UV evidently enriched anaerobic fermentation bacteria (AFB) (i.e., Macellibacteroides and Clostridium XlVa). However, PS_Ferrous and PS_ZVI facilitated the enrichment of Woesearchaeota and methanogens. Furthermore, molecular ecological network and mantel test revealed the intrinsic interactions among the multiple functional microbes and environmental variables. The homo-acetogens and sulfate-reducing bacterial had potential cooperative and symbiotic relationships with AFB, while the nitrate-reducing bacteria displayed distinguishing ecological niches. Suitable activation modes for PS pretreatments resulted in an upregulation of genes expression responsible for digestion. This study established a scientific foundation for the application of sulfate radical-based oxidation on energy or high value-added chemicals recovery from waste residues.
Collapse
Affiliation(s)
- Lijiao Yin
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan, 030024, China
| | - Aijuan Zhou
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan, 030024, China; Shanxi-Zheda Institute of Advanced Materials and Chemical Engineering, Taiyuan, 030000, China.
| | - Yaoli Wei
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan, 030024, China
| | - Cristiano Varrone
- Department of Chemistry and BioScience, Aalborg University, Copenhagen, Denmark
| | - Dengfei Li
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan, 030024, China
| | - Jingyang Luo
- College of Environment, Hohai University, Nanjing, 210098, China
| | - Zhangwei He
- Shaanxi Key Laboratory of Environmental Engineering, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, China
| | - Wenzong Liu
- School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, 518005, China
| | - Xiuping Yue
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan, 030024, China; Shanxi-Zheda Institute of Advanced Materials and Chemical Engineering, Taiyuan, 030000, China; Shanxi Engineer Research Institute of Sludge Disposition and Resources, Taiyuan University of Technology, Taiyuan, 030024, China
| |
Collapse
|
6
|
Santos MVA, Morais JC, Veras STS, Leite WRM, Florencio L, Kato MT. Partial nitrification and simultaneous denitrification in sequential anaerobic and aerobic reactors: performance and microbial community dynamics. ENVIRONMENTAL TECHNOLOGY 2024:1-14. [PMID: 38830114 DOI: 10.1080/09593330.2024.2361930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 05/16/2024] [Indexed: 06/05/2024]
Abstract
ABSTRACTThe removal of organic matter and nitrogen from domestic sewage was evaluated using a system composed of two sequential reactors: an anaerobic reactor (ANR) with suspended sludge and an aerobic (AER) reactor with suspended and adhered sludge to polyurethane foams. Nitrogen removal consisted of AER operating at low dissolved oxygen (DO) concentrations; this favoured the simultaneous nitrification and denitrification (SND) process. The concentration of COD and N were 440 mgO2.L-1 and 37 mgTN.L-1, respectively. The operation was divided into three phases (P), lasting 51, 53, and 46 days, respectively. The initial DO concentrations applied in the AER were: 3.0 (PI) and 1.5 mg.L-1 (PII and PIII). In PIII, the AER effluent was recirculated to the ANR at a ratio of 0.25. Kinetic assays were performed to determine the nitrification and denitrification rates of the biomasses (ANR and AER in PIII). Changes in the microbial community were evaluated throughout phases PI to PIII by massive sequencing. In PIII, the best results obtained for chemical oxygen demand (COD) and total nitrogen (TN-N) removal efficiencies, were close to 94% and 65%, respectively. Under these conditions, system effluent concentrations below 30 mg COD.L-1 and 15 mg TN-N.L-1 were verified. The nitritation and nitration rates were 10.5 and 6.5 mg N.g VSS-1.h-1, while the denitrification via nitrite and nitrate were 6.8 and 5.8 mg N.g VSS-1.h-1, respectively. A mixotrophic community was prevalent, with Rhodococcus, Nitrosomonas, Pseudomnas, and Porphyromonas being dominant or co-dominant in most of the samples, confirming the SND process in the AER sludge.
Collapse
Affiliation(s)
- Marcus V A Santos
- Department of Civil and Environmental Engineering, Laboratory of Environmental Sanitation, Federal University of Pernambuco, Recife, Brazil
| | - Juliana C Morais
- Department of Infrastructure and Civil Construction, Federal Institute of Pernambuco, Recife, Brazil
| | - Shyrlane T S Veras
- Department of Civil and Environmental Engineering, Laboratory of Environmental Sanitation, Federal University of Pernambuco, Recife, Brazil
| | - Wanderli R M Leite
- Department of Civil and Environmental Engineering, Laboratory of Environmental Sanitation, Federal University of Pernambuco, Recife, Brazil
| | - Lourdinha Florencio
- Department of Civil and Environmental Engineering, Laboratory of Environmental Sanitation, Federal University of Pernambuco, Recife, Brazil
| | - Mario T Kato
- Department of Civil and Environmental Engineering, Laboratory of Environmental Sanitation, Federal University of Pernambuco, Recife, Brazil
| |
Collapse
|
7
|
Ma Y, Qu Y, Yao X, Xia C, Lv M, Lin X, Zhang L, Zhang M, Hu B. Unveiling the unique role of iron in the metabolism of methanogens: A review. ENVIRONMENTAL RESEARCH 2024; 250:118495. [PMID: 38367837 DOI: 10.1016/j.envres.2024.118495] [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: 12/26/2023] [Revised: 02/06/2024] [Accepted: 02/13/2024] [Indexed: 02/19/2024]
Abstract
Methanogens are the main participants in the carbon cycle, catalyzing five methanogenic pathways. Methanogens utilize different iron-containing functional enzymes in different methanogenic processes. Iron is a vital element in methanogens, which can serve as a carrier or reactant in electron transfer. Therefore, iron plays an important role in the growth and metabolism of methanogens. In this paper, we cast light on the types and functions of iron-containing functional enzymes involved in different methanogenic pathways, and the roles iron play in energy/substance metabolism of methanogenesis. Furthermore, this review provides certain guiding significance for lowering CH4 emissions, boosting the carbon sink capacity of ecosystems and promoting green and low-carbon development in the future.
Collapse
Affiliation(s)
- Yuxin Ma
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China; Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ying Qu
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiangwu Yao
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, Zhejiang, China; Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Chujun Xia
- Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Mengjie Lv
- Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiao Lin
- Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Lili Zhang
- Beijing Enterprises Water Group Limited, Beijing, China
| | - Meng Zhang
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, Zhejiang, China; Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Baolan Hu
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, Zhejiang, China; Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China.
| |
Collapse
|
8
|
Dzofou Ngoumelah D, Heggeset TMB, Haugen T, Sulheim S, Wentzel A, Harnisch F, Kretzschmar J. Effect of model methanogens on the electrochemical activity, stability, and microbial community structure of Geobacter spp. dominated biofilm anodes. NPJ Biofilms Microbiomes 2024; 10:17. [PMID: 38443373 PMCID: PMC10915144 DOI: 10.1038/s41522-024-00490-z] [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: 03/09/2023] [Accepted: 02/20/2024] [Indexed: 03/07/2024] Open
Abstract
Combining anaerobic digestion (AD) and microbial electrochemical technologies (MET) in AD-MET holds great potential. Methanogens have been identified as one cause of decreased electrochemical activity and deterioration of Geobacter spp. biofilm anodes. A better understanding of the different interactions between methanogenic genera/species and Geobacter spp. biofilms is needed to shed light on the observed reduction in electrochemical activity and stability of Geobacter spp. dominated biofilms as well as observed changes in microbial communities of AD-MET. Here, we have analyzed electrochemical parameters and changes in the microbial community of Geobacter spp. biofilm anodes when exposed to three representative methanogens with different metabolic pathways, i.e., Methanosarcina barkeri, Methanobacterium formicicum, and Methanothrix soehngenii. M. barkeri negatively affected the performance and stability of Geobacter spp. biofilm anodes only in the initial batches. In contrast, M. formicicum did not affect the stability of Geobacter spp. biofilm anodes but caused a decrease in maximum current density of ~37%. M. soehngenii induced a coloration change of Geobacter spp. biofilm anodes and a decrease in the total transferred charge by ~40%. Characterization of biofilm samples after each experiment by 16S rRNA metabarcoding, whole metagenome nanopore sequencing, and shotgun sequencing showed a higher relative abundance of Geobacter spp. after exposure to M. barkeri as opposed to M. formicicum or M. soehngenii, despite the massive biofilm dispersal observed during initial exposure to M. barkeri.
Collapse
Affiliation(s)
- Daniel Dzofou Ngoumelah
- DBFZ Deutsches Biomasseforschungszentrum gemeinnützige GmbH (German Biomass Research Centre), Department of Biochemical Conversion, 04347, Leipzig, Germany
| | | | - Tone Haugen
- SINTEF Industry, Department of Biotechnology and Nanomedicine, 7034, Trondheim, Norway
| | - Snorre Sulheim
- SINTEF Industry, Department of Biotechnology and Nanomedicine, 7034, Trondheim, Norway
| | - Alexander Wentzel
- SINTEF Industry, Department of Biotechnology and Nanomedicine, 7034, Trondheim, Norway
| | - Falk Harnisch
- Helmholtz Centre for Environmental Research - UFZ, Department of Microbial Biotechnology, 04318, Leipzig, Germany
| | - Jörg Kretzschmar
- DBFZ Deutsches Biomasseforschungszentrum gemeinnützige GmbH (German Biomass Research Centre), Department of Biochemical Conversion, 04347, Leipzig, Germany.
- Zittau/Görlitz University of Applied Sciences, Faculty of Natural and Environmental Sciences, 02763, Zittau, Germany.
| |
Collapse
|
9
|
Lu J, Hou R, Peng W, Guan F, Yuan Y. Responses of methane production and methanogenic pathways to polystyrene nanoplastics exposure in paddy soil. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133197. [PMID: 38113731 DOI: 10.1016/j.jhazmat.2023.133197] [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: 09/20/2023] [Revised: 12/03/2023] [Accepted: 12/05/2023] [Indexed: 12/21/2023]
Abstract
Nanoplastics (NPs) have attracted increasing attention within terrestrial ecosystems. However, our understanding of their impacts on the intricate anaerobic methanogenesis processes occurring in paddy soils microbial communities remains limited with respect to nanoplastics shape, function, and metabolic effects. Herein, we explored the effects of polystyrene nanoplastics (PS-NPs) and microplastics (PS-MPs) on anaerobic methanogenesis in a typical paddy soil. The results show that PS-NPs delayed methane production and the time to reach peak acetate content in incubation process of paddy soils, and the methanogenic rate increased rapidly after 13 days, with a maximum increase of 87.97%. However, PS-MPs had no marked effect on CH4, CO2 and acetate production. In addition, PS-NPs affected soil physicochemical properties by reducing pH and increasing electrical conductivity. Acetoclastic methanogens were enriched and the relative abundance of the genes ackA, pta, ACSS, cdhC, cdhD and cdhE in the acetoclastic pathways were significantly increased under PS-NPs exposure. In addition, PS-MPs had significant effect on the microbial community structure but no effect on methanogenic pathways of the paddy soils. This study provides important insights into the response of key microorganisms, functional genes and methanogenesis pathways to NPs during anaerobic methanogenesis in paddy soils.
Collapse
Affiliation(s)
- Jinrong Lu
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China
| | - Rui Hou
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Weijie Peng
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China
| | - Fengyi Guan
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China
| | - Yong Yuan
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China.
| |
Collapse
|
10
|
Li X, Bei Q, Rabiei Nematabad M, Peng J, Liesack W. Time-shifted expression of acetoclastic and methylotrophic methanogenesis by a single Methanosarcina genomospecies predominates the methanogen dynamics in Philippine rice field soil. MICROBIOME 2024; 12:39. [PMID: 38409166 PMCID: PMC10895765 DOI: 10.1186/s40168-023-01739-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 12/18/2023] [Indexed: 02/28/2024]
Abstract
BACKGROUND The final step in the anaerobic decomposition of biopolymers is methanogenesis. Rice field soils are a major anthropogenic source of methane, with straw commonly used as a fertilizer in rice farming. Here, we aimed to decipher the structural and functional responses of the methanogenic community to rice straw addition during an extended anoxic incubation (120 days) of Philippine paddy soil. The research combined process measurements, quantitative real-time PCR and RT-PCR of particular biomarkers (16S rRNA, mcrA), and meta-omics (environmental genomics and transcriptomics). RESULTS The analysis methods collectively revealed two major bacterial and methanogenic activity phases: early (days 7 to 21) and late (days 28 to 60) community responses, separated by a significant transient decline in microbial gene and transcript abundances and CH4 production rate. The two methanogenic activity phases corresponded to the greatest rRNA and mRNA abundances of the Methanosarcinaceae but differed in the methanogenic pathways expressed. While three genetically distinct Methanosarcina populations contributed to acetoclastic methanogenesis during the early activity phase, the late activity phase was defined by methylotrophic methanogenesis performed by a single Methanosarcina genomospecies. Closely related to Methanosarcina sp. MSH10X1, mapping of environmental transcripts onto metagenome-assembled genomes (MAGs) and population-specific reference genomes revealed this genomospecies as the key player in acetoclastic and methylotrophic methanogenesis. The anaerobic food web was driven by a complex bacterial community, with Geobacteraceae and Peptococcaceae being putative candidates for a functional interplay with Methanosarcina. Members of the Methanocellaceae were the key players in hydrogenotrophic methanogenesis, while the acetoclastic activity of Methanotrichaceae members was detectable only during the very late community response. CONCLUSIONS The predominant but time-shifted expression of acetoclastic and methylotrophic methanogenesis by a single Methanosarcina genomospecies represents a novel finding that expands our hitherto knowledge of the methanogenic pathways being highly expressed in paddy soils. Video Abstract.
Collapse
Affiliation(s)
- Xin Li
- Research group "Methanotrophic Bacteria and Environmental Genomics/Transcriptomics", Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, D-35043, Marburg, Germany
- Present address: Institute of Agricultural and Nutritional Sciences, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Strasse 5, Halle (Saale), Germany
| | - Qicheng Bei
- Research group "Methanotrophic Bacteria and Environmental Genomics/Transcriptomics", Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, D-35043, Marburg, Germany
- Present address: Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Theodor-Lieser-Strasse 4, Halle (Saale), Germany
| | - Mehrdad Rabiei Nematabad
- Research group "Methanotrophic Bacteria and Environmental Genomics/Transcriptomics", Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, D-35043, Marburg, Germany
| | - Jingjing Peng
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, Key Laboratory of Plant-Soil Interactions, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China.
| | - Werner Liesack
- Research group "Methanotrophic Bacteria and Environmental Genomics/Transcriptomics", Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, D-35043, Marburg, Germany.
| |
Collapse
|
11
|
Richter M, Sattler C, Schöne C, Rother M. Pyruvate-dependent growth of Methanosarcina acetivorans. J Bacteriol 2024; 206:e0036323. [PMID: 38305193 PMCID: PMC10882976 DOI: 10.1128/jb.00363-23] [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: 11/02/2023] [Accepted: 01/11/2024] [Indexed: 02/03/2024] Open
Abstract
Methanogenesis is a key step during anaerobic biomass degradation. Methanogenic archaea (methanogens) are the only organisms coupling methanogenic substrate conversion to energy conservation. The range of substrates utilized by methanogens is limited, with acetate and H2+CO2 being the ecologically most relevant. The only single methanogenic energy substrate containing more carbon-carbon bonds than acetate is pyruvate. Only the aggregate-forming, freshwater methanogen Methanosarcina barkeri Fusaro was shown to grow on this compound. Here, the pyruvate-utilizing capabilities of the single-celled, marine Methanosarcina acetivorans were addressed. Robust pyruvate-dependent, methanogenic, growth could be established by omitting CO2 from the growth medium. Growth rates which were independent of the pyruvate concentration indicated that M. acetivorans actively translocates pyruvate across the cytoplasmic membrane. When 2-bromoethanesulfonate (BES) inhibited methanogenesis to more than 99%, pyruvate-dependent growth was acetogenic and sustained. However, when methanogenesis was completely inhibited M. acetivorans did not grow on pyruvate. Analysis of metabolites showed that acetogenesis is used by BES-inhibited M. acetivorans as a sink for electrons derived from pyruvate oxidation and that other, thus far unidentified, metabolites are produced.IMPORTANCEThe known range of methanogenic growth substrates is very limited and M. acetivorans is only the second methanogenic species for which growth on pyruvate is demonstrated. Besides some commonalities, analysis of M. acetivorans highlights differences in pyruvate metabolism among Methanosarcina species. The observation that M. acetivorans probably imports pyruvate actively indicates that the capabilities for heterotrophic catabolism in methanogens may be underestimated. The mostly acetogenic growth of M. acetivorans on pyruvate with concomitant inhibition of methanogenesis confirms that energy conservation of methanogenic archaea can be independent of methane formation.
Collapse
Affiliation(s)
- Marcus Richter
- Fakultät Biologie, Technische Universität Dresden, Dresden, Germany
| | | | - Christian Schöne
- Fakultät Biologie, Technische Universität Dresden, Dresden, Germany
| | - Michael Rother
- Fakultät Biologie, Technische Universität Dresden, Dresden, Germany
| |
Collapse
|
12
|
Chin KJ, Ünal B, Sanderson M, Aboderin F, Nüsslein K. Selective trace elements significantly enhanced methane production in coal bed methane systems by stimulating microbial activity. Microbiol Spectr 2024; 12:e0350823. [PMID: 38236038 PMCID: PMC10846109 DOI: 10.1128/spectrum.03508-23] [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: 10/02/2023] [Accepted: 10/17/2023] [Indexed: 01/19/2024] Open
Abstract
Trace elements are associated with the microbial degradation of organic matter and methanogenesis, as enzymes in metabolic pathways often employ trace elements as essential cofactors. However, only a few studies investigated the effects of trace elements on the metabolic activity of microbial communities associated with biogenic coalbed methane production. We aimed to determine the effects of strategically selected trace elements on structure and function of active bacterial and methanogenic communities to stimulate methane production in subsurface coalbeds. Microcosms were established with produced water and coal from coalbed methane wells located in the Powder River Basin, Wyoming, USA. In initial pilot experiments with eight different trace elements, individual amendments of Co, Cu, and Mo lead to significantly higher methane production. Transcript levels of mcrA, the key marker gene for methanogenesis, positively correlated with increased methane production. Phylogenetic analysis of the mcrA cDNA library demonstrated compositional shifts of the active methanogenic community and increase of their diversity, particularly of hydrogenotrophic methanogens. High-throughput sequencing of cDNA obtained from 16S rRNA demonstrated active and abundant bacterial groups in response to trace element amendments. Active Acetobacterium members increased in response to Co, Cu, and Mo additions. The findings of this study yield new insights into the importance of essential trace elements on the metabolic activity of microbial communities involved in subsurface coalbed methane and provide a better understanding of how microbial community composition is shaped by trace elements.IMPORTANCEMicrobial life in the deep subsurface of coal beds is limited by nutrient replenishment. While coal bed microbial communities are surrounded by carbon sources, we hypothesized that other nutrients such as trace elements needed as cofactors for enzymes are missing. Amendment of selected trace elements resulted in compositional shifts of the active methanogenic and bacterial communities and correlated with higher transcript levels of mcrA. The findings of this study yield new insights to not only identify possible limitations of microbes by replenishment of trace elements within their specific hydrological placement but also into the importance of essential trace elements for the metabolic activity of microbial communities involved in subsurface coalbed methane production and provides a better understanding of how microbial community composition is shaped by trace elements. Furthermore, this finding might help to revive already spent coal bed methane well systems with the ultimate goal to stimulate methane production.
Collapse
Affiliation(s)
- Kuk-Jeong Chin
- Department of Biology, Georgia State University, Atlanta, Georgia, USA
| | - Burcu Ünal
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
- Department of Environmental Engineering, RheinMain University of Applied Sciences, Wiesbaden, Germany
| | - Michael Sanderson
- Department of Biology, Georgia State University, Atlanta, Georgia, USA
| | - Feranmi Aboderin
- Department of Biology, Georgia State University, Atlanta, Georgia, USA
| | - Klaus Nüsslein
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
| |
Collapse
|
13
|
Hao Z, Zhao L, Liu J, Pu Q, Chen J, Meng B, Feng X. Relative importance of aceticlastic methanogens and hydrogenotrophic methanogens on mercury methylation and methylmercury demethylation in paddy soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167601. [PMID: 37832685 DOI: 10.1016/j.scitotenv.2023.167601] [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: 08/22/2023] [Revised: 09/28/2023] [Accepted: 10/03/2023] [Indexed: 10/15/2023]
Abstract
The accumulation of methylmercury (MeHg) in paddy soil results from a subtle balance between inorganic mercury (e.g., HgII) methylation and MeHg demethylation. Methanogens not only act as Hg methylators but may also facilitate MeHg demethylation. However, the diverse methanogen flora (e.g., aceticlastic and hydrogenotrophic types) that exists under ambient conditions has not previously been considered. Accordingly, the roles of different types of methanogens in HgII methylation and MeHg degradation in paddy soils were studied using the Hg isotope tracing technique combined with the application of methanogen inhibitors/stimulants. It was found that the response of HgII methylation to methanogen inhibitors or stimulants was site-dependent. Specifically, aceticlastic methanogens were suggested as the potential HgII methylators at the low Hg level background site, whereas hydrogenotrophic methanogens were potentially involved in MeHg production as Hg levels increased. In contrast, both aceticlastic and hydrogenotrophic methanogens facilitated MeHg degradation across the sampling sites. Additionally, competition between hydrogenotrophic and aceticlastic methanogens was observed in Hg-polluted paddy soils, implying that net MeHg production could be alleviated by promoting aceticlastic methanogens or inhibiting hydrogenotrophic methanogens. The findings gained from this study improve the understanding of the role of methanogens in net MeHg formation and link carbon turnover to Hg biogeochemistry in rice paddy ecosystems.
Collapse
Affiliation(s)
- Zhengdong Hao
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Zhao
- School of Management Science, Guizhou University of Finance and Economics, Guiyang 550025, China; Guizhou Key Laboratory of Big Data Statistical Analysis (No. [2019]5103), Guiyang 550025, China.
| | - Jiang Liu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
| | - Qiang Pu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
| | - Ji Chen
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
| | - Bo Meng
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China.
| | - Xinbin Feng
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
14
|
Meier D, van Grinsven S, Michel A, Eickenbusch P, Glombitza C, Han X, Fiskal A, Bernasconi S, Schubert CJ, Lever MA. Hydrogen-independent CO 2 reduction dominates methanogenesis in five temperate lakes that differ in trophic states. ISME COMMUNICATIONS 2024; 4:ycae089. [PMID: 38988698 PMCID: PMC11235125 DOI: 10.1093/ismeco/ycae089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 05/20/2024] [Accepted: 06/20/2024] [Indexed: 07/12/2024]
Abstract
Emissions of microbially produced methane (CH4) from lake sediments are a major source of this potent greenhouse gas to the atmosphere. The rates of CH4 production and emission are believed to be influenced by electron acceptor distributions and organic carbon contents, which in turn are affected by anthropogenic inputs of nutrients leading to eutrophication. Here, we investigate how eutrophication influences the abundance and community structure of CH4 producing Archaea and methanogenesis pathways across time-resolved sedimentary records of five Swiss lakes with well-characterized trophic histories. Despite higher CH4 concentrations which suggest higher methanogenic activity in sediments of eutrophic lakes, abundances of methanogens were highest in oligotrophic lake sediments. Moreover, while the methanogenic community composition differed significantly at the lowest taxonomic levels (OTU), depending on whether sediment layers had been deposited under oligotrophic or eutrophic conditions, it showed no clear trend in relation to in situ distributions of electron acceptors. Remarkably, even though methanogenesis from CO2-reduction was the dominant pathway in all sediments based on carbon isotope fractionation values, taxonomic identities, and genomes of resident methanogens, CO2-reduction with hydrogen (H2) was thermodynamically unfavorable based on measured reactant and product concentrations. Instead, strong correlations between genomic abundances of CO2-reducing methanogens and anaerobic bacteria with potential for extracellular electron transfer suggest that methanogenic CO2-reduction in lake sediments is largely powered by direct electron transfer from syntrophic bacteria without involvement of H2 as an electron shuttle.
Collapse
Affiliation(s)
- Dimitri Meier
- Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, 8092 Zurich, Switzerland
- Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research, University of Bayreuth, Dr. Hans-Frisch-Straße 1-3, 95448 Bayreuth, Germany
| | - Sigrid van Grinsven
- Department of Surface Waters-Research and Management, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Seestrasse 79, 6047 Kastanienbaum, Switzerland
- Geomicrobiology, Department of Geosciences, Eberhard Karls Universität Tübingen (Tübingen University), Schnarrenbergstraße 94-96, 72076 Tübingen, Germany
| | - Anja Michel
- Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, 8092 Zurich, Switzerland
| | - Philip Eickenbusch
- Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, 8092 Zurich, Switzerland
| | - Clemens Glombitza
- Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, 8092 Zurich, Switzerland
| | - Xingguo Han
- Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, 8092 Zurich, Switzerland
| | - Annika Fiskal
- Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, 8092 Zurich, Switzerland
| | - Stefano Bernasconi
- Department of Earth Sciences, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Geological Institute, Sonneggstrasse 5, 8092 Zurich, Switzerland
| | - Carsten J Schubert
- Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, 8092 Zurich, Switzerland
- Department of Surface Waters-Research and Management, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Seestrasse 79, 6047 Kastanienbaum, Switzerland
| | - Mark A Lever
- Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, 8092 Zurich, Switzerland
- Marine Science Institute, Department of Marine Sciences, University of Texas at Austin, 750 Channel View Drive, Port Aransas, TX 78373, United States
| |
Collapse
|
15
|
Zhang Y, O'Loughlin EJ, Park SY, Kwon MJ. Effects of Fe(III) (hydr)oxide mineralogy on the development of microbial communities originating from soil, surface water, groundwater, and aerosols. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:166993. [PMID: 37717756 DOI: 10.1016/j.scitotenv.2023.166993] [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: 07/03/2023] [Revised: 09/09/2023] [Accepted: 09/09/2023] [Indexed: 09/19/2023]
Abstract
Microbial Fe(III) reduction is a key component of the iron cycle in natural environments. However, the susceptibility of Fe(III) (hydr)oxides to microbial reduction varies depending on the mineral's crystallinity, and the type of Fe(III) (hydr)oxide in turn will affect the composition of the microbial community. We created microcosm reactors with microbial communities from four different sources (soil, surface water, groundwater, and aerosols), three Fe(III) (hydr)oxides (lepidocrocite, goethite, and hematite) as electron acceptors, and acetate as an electron donor to investigate the shaping effect of Fe(III) mineral type on the development of microbial communities. During a 10-month incubation, changes in microbial community composition, Fe(III) reduction, and acetate utilization were monitored. Overall, there was greater reduction of lepidocrocite than of goethite and hematite, and the development of microbial communities originating from the same source diverged when supplied with different Fe(III) (hydr)oxides. Furthermore, each Fe(III) mineral was associated with unique taxa that emerged from different sources. This study illustrates the taxonomic diversity of Fe(III)-reducing microbes from a broad range of natural environments.
Collapse
Affiliation(s)
- Yidan Zhang
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, South Korea
| | - Edward J O'Loughlin
- Biosciences Division, Argonne National Laboratory, Lemont, IL 60439, United States
| | - Su-Young Park
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, South Korea
| | - Man Jae Kwon
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, South Korea.
| |
Collapse
|
16
|
Wang X, Xiang B, Li J, Zhang M, Frostegard A, Bakken L, Zhang X. Using adaptive and aggressive N 2O-reducing bacteria to augment digestate fertilizer for mitigating N 2O emissions from agricultural soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 903:166284. [PMID: 37586512 DOI: 10.1016/j.scitotenv.2023.166284] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/09/2023] [Accepted: 08/11/2023] [Indexed: 08/18/2023]
Abstract
Nitrous oxide (N2O) emitted from agricultural soils destroys stratospheric ozone and contributes to global warming. A promising approach to reduce emissions is fertilizing the soil using organic wastes augmented by non-denitrifying N2O-reducing bacteria (NNRB). To realize this potential, we need a suite of NNRB strains that fulfill several criteria: efficient reduction of N2O, ability to grow in organic waste, and ability to survive in farmland soil. In this study, we enriched such organisms by sequential anaerobic batch incubations with N2O and reciprocating inoculation between the sterilized substrates of anaerobic manure digestate and soils. 16S rDNA amplicon sequencing and metagenomics analysis showed that a cluster of bacteria containing nosZ genes encoding N2O-reductase, was enriched during the incubation process. Strains of several dominant members were then isolated and characterized, and three of them were found to harbor the nosZ gene but none of the other denitrifying genes, thus qualifying as NNRB. The selected isolates were tested for their capacities to reduce N2O emissions from three different typical Chinese farmland soils. The results indicated the significant mitigation effect of these isolates, even in very acidic red soil. In conclusion, this study demonstrated a strategy to engineer the soil microbiome with promising NNRB with high adaptability to livestock manure digestate as well as different agricultural soils, which would be suitable for developing novel fertilizer for farmland application to efficiently mitigate the N2O emissions from agricultural soils.
Collapse
Affiliation(s)
- Xinhui Wang
- State Key Laboratory of Microbial Metabolism, and Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Baoyu Xiang
- State Key Laboratory of Microbial Metabolism, and Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ji Li
- State Key Laboratory of Microbial Metabolism, and Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Menghui Zhang
- State Key Laboratory of Microbial Metabolism, and Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Asa Frostegard
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, N-1432 Aas, Norway
| | - Lars Bakken
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, N-1432 Aas, Norway
| | - Xiaojun Zhang
- State Key Laboratory of Microbial Metabolism, and Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| |
Collapse
|
17
|
McDaniel EA, Scarborough M, Mulat DG, Lin X, Sampara PS, Olson HM, Young RP, Eder EK, Attah IK, Markillie LM, Hoyt DW, Lipton MS, Hallam SJ, Ziels RM. Diverse electron carriers drive syntrophic interactions in an enriched anaerobic acetate-oxidizing consortium. THE ISME JOURNAL 2023; 17:2326-2339. [PMID: 37880541 PMCID: PMC10689502 DOI: 10.1038/s41396-023-01542-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 10/09/2023] [Accepted: 10/11/2023] [Indexed: 10/27/2023]
Abstract
In many anoxic environments, syntrophic acetate oxidation (SAO) is a key pathway mediating the conversion of acetate into methane through obligate cross-feeding interactions between SAO bacteria (SAOB) and methanogenic archaea. The SAO pathway is particularly important in engineered environments such as anaerobic digestion (AD) systems operating at thermophilic temperatures and/or with high ammonia. Despite the widespread importance of SAOB to the stability of the AD process, little is known about their in situ physiologies due to typically low biomass yields and resistance to isolation. Here, we performed a long-term (300-day) continuous enrichment of a thermophilic (55 °C) SAO community from a municipal AD system using acetate as the sole carbon source. Over 80% of the enriched bioreactor metagenome belonged to a three-member consortium, including an acetate-oxidizing bacterium affiliated with DTU068 encoding for carbon dioxide, hydrogen, and formate production, along with two methanogenic archaea affiliated with Methanothermobacter_A. Stable isotope probing was coupled with metaproteogenomics to quantify carbon flux into each community member during acetate conversion and inform metabolic reconstruction and genome-scale modeling. This effort revealed that the two Methanothermobacter_A species differed in their preferred electron donors, with one possessing the ability to grow on formate and the other only consuming hydrogen. A thermodynamic analysis suggested that the presence of the formate-consuming methanogen broadened the environmental conditions where ATP production from SAO was favorable. Collectively, these results highlight how flexibility in electron partitioning during SAO likely governs community structure and fitness through thermodynamic-driven mutualism, shedding valuable insights into the metabolic underpinnings of this key functional group within methanogenic ecosystems.
Collapse
Affiliation(s)
- Elizabeth A McDaniel
- Department of Civil Engineering, The University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada
| | - Matthew Scarborough
- Department of Civil and Environmental Engineering, University of Vermont, Burlington, VT, USA
| | - Daniel Girma Mulat
- Department of Civil Engineering, The University of British Columbia, Vancouver, BC, Canada
| | - Xuan Lin
- Department of Civil Engineering, The University of British Columbia, Vancouver, BC, Canada
| | - Pranav S Sampara
- Department of Civil Engineering, The University of British Columbia, Vancouver, BC, Canada
| | - Heather M Olson
- Environmental and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Robert P Young
- Environmental and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Elizabeth K Eder
- Environmental and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Isaac K Attah
- Environmental and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Lye Meng Markillie
- Environmental and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - David W Hoyt
- Environmental and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Mary S Lipton
- Environmental and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Steven J Hallam
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada
- ECOSCOPE Training Program, The University of British Columbia, Vancouver, BC, Canada
- Graduate Program in Bioinformatics, The University of British Columbia, Vancouver, BC, Canada
- Genome Science and Technology Program, The University of British Columbia, Vancouver, BC, Canada
- Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada
| | - Ryan M Ziels
- Department of Civil Engineering, The University of British Columbia, Vancouver, BC, Canada.
- Genome Science and Technology Program, The University of British Columbia, Vancouver, BC, Canada.
| |
Collapse
|
18
|
Li W, Chen J, Pang L, Lu Y, Yang P. Dosage effect of micron zero-valent iron during thermophilic anaerobic digestion of waste activated sludge: Performance and functional community. ENVIRONMENTAL RESEARCH 2023; 237:116997. [PMID: 37634689 DOI: 10.1016/j.envres.2023.116997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/09/2023] [Accepted: 08/25/2023] [Indexed: 08/29/2023]
Abstract
This work examined the performance and microbial traits in a thermophilic anaerobic digestion (TAD) of waste activated sludge that was impacted by micron zero valent iron (mZVI). Results showed that methane production was promoted by 0.8, 11.9, and 12.0 times, respectively, when mZVI was at dosages of 25, 100, and 250 mg/g total solid (TS). Also, the consumption of volatile fatty acids was increased by mZVI at higher dosages (100 and 250 mg/g TS). Furthermore, 16S rRNA sequencing demonstrated that microbial community stabilized after day 18 regardless of the dosage of mZVI, and that different dosages of mZVI induced different shifts in the functional community of the archaea rather than the bacteria involved in TAD. As a result, mZVI at 100 mg/g TS could increase the relative abundance of archaeal genera Methanothermobacter the most, increasing by 22.8% at the end of TAD compared to CK. Besides, redundancy analysis revealed that the physicochemical properties explained 79.65% and 89.10% of the variations of bacterial and archaeal abundance, respectively. Also, the findings of the correlation analysis revealed that total dissolved iron, ferrous iron, pH, and ammonium nitrogen, may be the key divers of altering functional communities, particularly archaea. Moreover, mZVI at 100 and 250 mg/g TS boosted the metabolic pathways of environmental information processing (ABC transporters) in bacteria and carbon metabolism and methane metabolism for archaea, as well as relative abundances of enzymes and their activities involved in various methanogenic pathways. This study provides new perspectives on the application of mZVI in solid wastes treatments.
Collapse
Affiliation(s)
- Wenqian Li
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, PR China
| | - Jianglin Chen
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, PR China
| | - Lina Pang
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, PR China.
| | - Yuanyuan Lu
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, PR China
| | - Ping Yang
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, PR China
| |
Collapse
|
19
|
Cheng Y, Shi Z, Shi Y, Zhang Y, Zhang S, Luo G. Biochar promoted microbial iron reduction in competition with methanogenesis in anaerobic digestion. BIORESOURCE TECHNOLOGY 2023; 387:129561. [PMID: 37506931 DOI: 10.1016/j.biortech.2023.129561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 07/23/2023] [Accepted: 07/25/2023] [Indexed: 07/30/2023]
Abstract
Microbial Fe (III) reduction generally could outcompete methanogenesis due to its thermodynamic advantage, while the low bioavailability of Fe (III) compounds limits this process in the anaerobic digestion system, which could result in the low recovery of vivianite. Therefore, this study investigated the competition between Fe (III) reduction and methanogenesis in the presence of different biochar (pyrochar and hydrochar). The results showed that pyrochar obtained at 500 °C (P5) resulted in the highest Fe (III) reduction (80.3%) compared to the control experiment (29.1%). P5 also decreased methane production by 9.4%. Both conductivity and surface oxygen-containing functional groups contributed to the promotion of direct electron transfer for Fe (III) reduction. Genomic-centric metatranscriptomics analysis showed that P5 led to the highest enrichment of Geobacter soli A19 and induced the significant expression of out membrane cytochrome c and pilA in Geobacter soli A19, which was related to higher Fe (III) reduction.
Collapse
Affiliation(s)
- Yafei Cheng
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
| | - Zhijian Shi
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
| | - Yan Shi
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
| | - Yalei Zhang
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai, China; State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, China
| | - Shicheng Zhang
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China; Shanghai Technical Service Platform for Pollution Control and Resource Utilization of Organic Wastes, Shanghai 200438, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, China
| | - Gang Luo
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China; Shanghai Technical Service Platform for Pollution Control and Resource Utilization of Organic Wastes, Shanghai 200438, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, China.
| |
Collapse
|
20
|
Zhou J, Smith JA, Li M, Holmes DE. Methane production by Methanothrix thermoacetophila via direct interspecies electron transfer with Geobacter metallireducens. mBio 2023; 14:e0036023. [PMID: 37306514 PMCID: PMC10470525 DOI: 10.1128/mbio.00360-23] [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: 02/10/2023] [Accepted: 04/13/2023] [Indexed: 06/13/2023] Open
Abstract
Methanothrix is widely distributed in natural and artificial anoxic environments and plays a major role in global methane emissions. It is one of only two genera that can form methane from acetate dismutation and through participation in direct interspecies electron transfer (DIET) with exoelectrogens. Although Methanothrix is a significant member of many methanogenic communities, little is known about its physiology. In this study, transcriptomics helped to identify potential routes of electron transfer during DIET between Geobacter metallireducens and Methanothrix thermoacetophila. Additions of magnetite to cultures significantly enhanced growth by acetoclastic methanogenesis and by DIET, while granular activated carbon (GAC) amendments impaired growth. Transcriptomics suggested that the OmaF-OmbF-OmcF porin complex and the octaheme outer membrane c-type cytochrome encoded by Gmet_0930, were important for electron transport across the outer membrane of G. metallireducens during DIET with Mx. thermoacetophila. Clear differences in the metabolism of Mx. thermoacetophila when grown via DIET or acetate dismutation were not apparent. However, genes coding for proteins involved in carbon fixation, the sheath fiber protein MspA, and a surface-associated quinoprotein, SqpA, were highly expressed in all conditions. Expression of gas vesicle genes was significantly lower in DIET- than acetate-grown cells, possibly to facilitate better contact between membrane-associated redox proteins during DIET. These studies reveal potential electron transfer mechanisms utilized by both Geobacter and Methanothrix during DIET and provide important insights into the physiology of Methanothrix in anoxic environments. IMPORTANCE Methanothrix is a significant methane producer in a variety of methanogenic environments including soils and sediments as well as anaerobic digesters. Its abundance in these anoxic environments has mostly been attributed to its high affinity for acetate and its ability to grow by acetoclastic methanogenesis. However, Methanothrix species can also generate methane by directly accepting electrons from exoelectrogenic bacteria through direct interspecies electron transfer (DIET). Methane production through DIET is likely to further increase their contribution to methane production in natural and artificial environments. Therefore, acquiring a better understanding of DIET with Methanothrix will help shed light on ways to (i) minimize microbial methane production in natural terrestrial environments and (ii) maximize biogas formation by anaerobic digesters treating waste.
Collapse
Affiliation(s)
- Jinjie Zhou
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
- Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, China
- Department of Microbiology, University of Massachusetts‐Amherst, Amherst, Massachusetts, USA
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Jessica A. Smith
- Department of Microbiology, University of Massachusetts‐Amherst, Amherst, Massachusetts, USA
- Department of Biomolecular Sciences, Central Connecticut State University, New Britain, Connecticut, USA
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Dawn E. Holmes
- Department of Microbiology, University of Massachusetts‐Amherst, Amherst, Massachusetts, USA
- Department of Physical and Biological Science, Western New England University, Springfield, Massachusetts, USA
| |
Collapse
|
21
|
Vigderovich H, Eckert W, Elvert M, Gafni A, Rubin-Blum M, Bergman O, Sivan O. Aerobic methanotrophy increases the net iron reduction in methanogenic lake sediments. Front Microbiol 2023; 14:1206414. [PMID: 37577416 PMCID: PMC10415106 DOI: 10.3389/fmicb.2023.1206414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 07/10/2023] [Indexed: 08/15/2023] Open
Abstract
In methane (CH4) generating sediments, methane oxidation coupled with iron reduction was suggested to be catalyzed by archaea and bacterial methanotrophs of the order Methylococcales. However, the co-existence of these aerobic and anaerobic microbes, the link between the processes, and the oxygen requirement for the bacterial methanotrophs have remained unclear. Here, we show how stimulation of aerobic methane oxidation at an energetically low experimental environment influences net iron reduction, accompanied by distinct microbial community changes and lipid biomarker patterns. We performed incubation experiments (between 30 and 120 days long) with methane generating lake sediments amended with 13C-labeled methane, following the additions of hematite and different oxygen levels in nitrogen headspace, and monitored methane turnover by 13C-DIC measurements. Increasing oxygen exposure (up to 1%) promoted aerobic methanotrophy, considerable net iron reduction, and the increase of microbes, such as Methylomonas, Geobacter, and Desulfuromonas, with the latter two being likely candidates for iron recycling. Amendments of 13C-labeled methanol as a potential substrate for the methanotrophs under hypoxia instead of methane indicate that this substrate primarily fuels methylotrophic methanogenesis, identified by high methane concentrations, strongly positive δ13CDIC values, and archaeal lipid stable isotope data. In contrast, the inhibition of methanogenesis by 2-bromoethanesulfonate (BES) led to increased methanol turnover, as suggested by similar 13C enrichment in DIC and high amounts of newly produced bacterial fatty acids, probably derived from heterotrophic bacteria. Our experiments show a complex link between aerobic methanotrophy and iron reduction, which indicates iron recycling as a survival mechanism for microbes under hypoxia.
Collapse
Affiliation(s)
- Hanni Vigderovich
- Department of Earth and Environmental Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Werner Eckert
- The Yigal Allon Kinneret Limnological Laboratory, Israel Oceanographic and Limnological Research, Migdal, Israel
| | - Marcus Elvert
- MARUM—Center for Marine Environmental Sciences and Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Almog Gafni
- Department of Earth and Environmental Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Maxim Rubin-Blum
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa, Israel
| | - Oded Bergman
- Department of Earth and Environmental Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- The Yigal Allon Kinneret Limnological Laboratory, Israel Oceanographic and Limnological Research, Migdal, Israel
| | - Orit Sivan
- Department of Earth and Environmental Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| |
Collapse
|
22
|
Schöne C, Poehlein A, Rother M. Genetic and Physiological Probing of Cytoplasmic Bypasses for the Energy-Converting Methyltransferase Mtr in Methanosarcina acetivorans. Appl Environ Microbiol 2023; 89:e0216122. [PMID: 37347168 PMCID: PMC10370330 DOI: 10.1128/aem.02161-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 06/01/2023] [Indexed: 06/23/2023] Open
Abstract
Methanogenesis is a unique energy metabolism carried out by members of the domain Archaea. Unlike most other methanogens, which reduce CO2 to methane with hydrogen as the electron donor, Methanosarcina acetivorans is able to grow on methylated compounds, on acetate, and on carbon monoxide (CO). These substrates are metabolized via distinct yet overlapping pathways. For the use of any single methanogenic substrate, the membrane-integral, energy-converting N5-methyl-tetrahydrosarcinapterin (H4SPT):coenzyme M (HS-CoM) methyltransferase (Mtr) is required. It was proposed that M. acetivorans can bypass the methyl transfer catalyzed by Mtr via cytoplasmic activities. To address this issue, conversion of different energy substrates by an mtr deletion mutant was analyzed. No significant methyl transfer from H4SPT to HS-CoM could be detected with CO as the electron donor. In contrast, formation of methane and CO2 in the presence of methanol or trimethylamine was indicative of an Mtr bypass in the oxidative direction. As methane thiol and dimethyl sulfide were transiently produced during methylotrophic methanogenesis in the mtr mutant, involvement in this process of methyl sulfide-dependent methyltransferases (Mts) was analyzed in a strain lacking both the Mts system and Mtr. It could be unequivocally demonstrated that the Mts system is not involved in bypassing Mtr, thereby ruling out previous proposals. Conversion of [13C]methanol indicated that in the absence of Mtr M. acetivorans provides the reducing equivalents for methyl-S-CoM reduction to methane by oxidizing (an) intracellular compound(s) to CO2 rather than disproportioning the source of methyl groups. Thus, no in vivo Mtr bypass appears to exist in M. acetivorans. IMPORTANCE Methanogenic archaea possess only a limited number of chemiosmotic coupling sites in their respiratory chains. Among them, N5-methyl-H4SPT:HS-CoM methyltransferase (Mtr) is the most widely distributed. Previous observations led to the conclusion that Methanosarcina acetivorans is able to bypass this reaction via methyl sulfide-dependent methyltransferases (Mts). However, strains lacking Mtr are not able to produce methane from CO. Also, these strains are unable to oxidize methylated substrates to CO2, in contrast to observations in the close relative Methanosarcina barkeri. The results also highlight the sole function of the Mts system in methyl sulfide metabolism. Thus, no in vivo Mtr bypass appears to exist in M. acetivorans.
Collapse
Affiliation(s)
- Christian Schöne
- Fakultät Biologie, Technische Universität Dresden, Dresden, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Michael Rother
- Fakultät Biologie, Technische Universität Dresden, Dresden, Germany
| |
Collapse
|
23
|
Conrad R. Complexity of temperature dependence in methanogenic microbial environments. Front Microbiol 2023; 14:1232946. [PMID: 37485527 PMCID: PMC10359720 DOI: 10.3389/fmicb.2023.1232946] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 06/20/2023] [Indexed: 07/25/2023] Open
Abstract
There is virtually no environmental process that is not dependent on temperature. This includes the microbial processes that result in the production of CH4, an important greenhouse gas. Microbial CH4 production is the result of a combination of many different microorganisms and microbial processes, which together achieve the mineralization of organic matter to CO2 and CH4. Temperature dependence applies to each individual step and each individual microbe. This review will discuss the different aspects of temperature dependence including temperature affecting the kinetics and thermodynamics of the various microbial processes, affecting the pathways of organic matter degradation and CH4 production, and affecting the composition of the microbial communities involved. For example, it was found that increasing temperature results in a change of the methanogenic pathway with increasing contribution from mainly acetate to mainly H2/CO2 as immediate CH4 precursor, and with replacement of aceticlastic methanogenic archaea by thermophilic syntrophic acetate-oxidizing bacteria plus thermophilic hydrogenotrophic methanogenic archaea. This shift is consistent with reaction energetics, but it is not obligatory, since high temperature environments exist in which acetate is consumed by thermophilic aceticlastic archaea. Many studies have shown that CH4 production rates increase with temperature displaying a temperature optimum and a characteristic apparent activation energy (Ea). Interestingly, CH4 release from defined microbial cultures, from environmental samples and from wetland field sites all show similar Ea values around 100 kJ mol-1 indicating that CH4 production rates are limited by the methanogenic archaea rather than by hydrolysis of organic matter. Hence, the final rather than the initial step controls the methanogenic degradation of organic matter, which apparently is rarely in steady state.
Collapse
|
24
|
Ouboter HT, Arshad A, Berger S, Saucedo Sanchez JG, Op den Camp HJM, Jetten MSM, Welte CU, Kurth JM. Acetate and Acetyl-CoA Metabolism of ANME-2 Anaerobic Archaeal Methanotrophs. Appl Environ Microbiol 2023; 89:e0036723. [PMID: 37272802 PMCID: PMC10304654 DOI: 10.1128/aem.00367-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/15/2023] [Indexed: 06/06/2023] Open
Abstract
Acetyl-CoA synthetase (ACS) and acetate ligase (ACD) are widespread among microorganisms, including archaea, and play an important role in their carbon metabolism, although only a few of these enzymes have been characterized. Anaerobic methanotrophs (ANMEs) have been reported to convert methane anaerobically into CO2, polyhydroxyalkanoate, and acetate. Furthermore, it has been suggested that they might be able to use acetate for anabolism or aceticlastic methanogenesis. To better understand the potential acetate metabolism of ANMEs, we characterized an ACS from ANME-2a as well as an ACS and an ACD from ANME-2d. The conversion of acetate into acetyl-CoA (Vmax of 8.4 μmol mg-1 min-1 and Km of 0.7 mM acetate) by the monomeric 73.8-kDa ACS enzyme from ANME-2a was more favorable than the formation of acetate from acetyl-CoA (Vmax of 0.4 μmol mg-1 min-1 and Km of 0.2 mM acetyl-CoA). The monomeric 73.4-kDa ACS enzyme from ANME-2d had similar Vmax values for both directions (Vmax,acetate of 0.9 μmol mg-1 min-1 versus Vmax,acetyl-CoA of 0.3 μmol mg-1 min-1). The heterotetrameric ACD enzyme from ANME-2d was active solely in the acetate-producing direction. Batch incubations of an enrichment culture dominated by ANME-2d fed with 13C2-labeled acetate produced 3 μmol of [13C]methane in 7 days, suggesting that this anaerobic methanotroph might have the potential to reverse its metabolism and perform aceticlastic methanogenesis using ACS to activate acetate albeit at low rates (2 nmol g [dry weight]-1 min-1). Together, these results show that ANMEs may have the potential to use acetate for assimilation as well as to use part of the surplus acetate for methane production. IMPORTANCE Acetyl-CoA plays a key role in carbon metabolism and is found at the junction of many anabolic and catabolic reactions. This work describes the biochemical properties of ACS and ACD enzymes from ANME-2 archaea. This adds to our knowledge of archaeal ACS and ACD enzymes, only a few of which have been characterized to date. Furthermore, we validated the in situ activity of ACS in ANME-2d, showing the conversion of acetate into methane by an enrichment culture dominated by ANME-2d.
Collapse
Affiliation(s)
- Heleen T. Ouboter
- Radboud Institute of Biological and Environmental Sciences, Microbiology Cluster, Radboud University, Nijmegen, Netherlands
- Soehngen Institute of Anaerobic Microbiology, Nijmegen, Netherlands
| | - Arslan Arshad
- Radboud Institute of Biological and Environmental Sciences, Microbiology Cluster, Radboud University, Nijmegen, Netherlands
| | - Stefanie Berger
- Radboud Institute of Biological and Environmental Sciences, Microbiology Cluster, Radboud University, Nijmegen, Netherlands
- Soehngen Institute of Anaerobic Microbiology, Nijmegen, Netherlands
| | - Jesus Gerardo Saucedo Sanchez
- Radboud Institute of Biological and Environmental Sciences, Microbiology Cluster, Radboud University, Nijmegen, Netherlands
| | - Huub J. M. Op den Camp
- Radboud Institute of Biological and Environmental Sciences, Microbiology Cluster, Radboud University, Nijmegen, Netherlands
| | - Mike S. M. Jetten
- Radboud Institute of Biological and Environmental Sciences, Microbiology Cluster, Radboud University, Nijmegen, Netherlands
- Soehngen Institute of Anaerobic Microbiology, Nijmegen, Netherlands
| | - Cornelia U. Welte
- Radboud Institute of Biological and Environmental Sciences, Microbiology Cluster, Radboud University, Nijmegen, Netherlands
- Soehngen Institute of Anaerobic Microbiology, Nijmegen, Netherlands
| | - Julia M. Kurth
- Radboud Institute of Biological and Environmental Sciences, Microbiology Cluster, Radboud University, Nijmegen, Netherlands
- Soehngen Institute of Anaerobic Microbiology, Nijmegen, Netherlands
- Microcosm Earth Center, Philipps-Universität Marburg and Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| |
Collapse
|
25
|
de Carvalho JC, de Souza Vandenberghe LP, Sydney EB, Karp SG, Magalhães AI, Martinez-Burgos WJ, Medeiros ABP, Thomaz-Soccol V, Vieira S, Letti LAJ, Rodrigues C, Woiciechowski AL, Soccol CR. Biomethane Production from Sugarcane Vinasse in a Circular Economy: Developments and Innovations. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9040349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
Sugarcane ethanol production generates about 360 billion liters of vinasse, a liquid effluent with an average chemical oxygen demand of 46,000 mg/L. Vinasse still contains about 11% of the original energy from sugarcane juice, but this chemical energy is diluted. This residue, usually discarded or applied in fertigation, is a suitable substrate for anaerobic digestion (AD). Although the technology is not yet widespread—only 3% of bioethanol plants used it in Brazil in the past, most discontinuing the process—the research continues. With a biomethane potential ranging from 215 to 324 L of methane produced by kilogram of organic matter in vinasse, AD could improve the energy output of sugarcane biorefineries. At the same time, the residual digestate could still be used as an agricultural amendment or for microalgal production for further stream valorization. This review presents the current technology for ethanol production from sugarcane and describes the state of the art in vinasse AD, including technological trends, through a recent patent evaluation. It also appraises the integration of vinasse AD in an ideal sugarcane biorefinery approach. It finally discusses bottlenecks and presents possible directions for technology development and widespread adoption of this simple yet powerful approach for bioresource recovery.
Collapse
Affiliation(s)
- Júlio Cesar de Carvalho
- Department of Bioprocess Engineering and Biotechnology, Centro Politécnico, Federal University of Paraná, Curitiba 81531-990, PR, Brazil
| | | | - Eduardo Bittencourt Sydney
- Department of Bioprocess Engineering and Biotechnology, Federal University of Technology—Paraná, Ponta Grossa 84016-210, PR, Brazil
| | - Susan Grace Karp
- Department of Bioprocess Engineering and Biotechnology, Centro Politécnico, Federal University of Paraná, Curitiba 81531-990, PR, Brazil
| | - Antonio Irineudo Magalhães
- Department of Bioprocess Engineering and Biotechnology, Centro Politécnico, Federal University of Paraná, Curitiba 81531-990, PR, Brazil
| | - Walter José Martinez-Burgos
- Department of Bioprocess Engineering and Biotechnology, Centro Politécnico, Federal University of Paraná, Curitiba 81531-990, PR, Brazil
| | - Adriane Bianchi Pedroni Medeiros
- Department of Bioprocess Engineering and Biotechnology, Centro Politécnico, Federal University of Paraná, Curitiba 81531-990, PR, Brazil
| | - Vanete Thomaz-Soccol
- Department of Bioprocess Engineering and Biotechnology, Centro Politécnico, Federal University of Paraná, Curitiba 81531-990, PR, Brazil
| | - Sabrina Vieira
- Department of Bioprocess Engineering and Biotechnology, Federal University of Technology—Paraná, Ponta Grossa 84016-210, PR, Brazil
| | - Luiz Alberto Junior Letti
- Department of Bioprocess Engineering and Biotechnology, Centro Politécnico, Federal University of Paraná, Curitiba 81531-990, PR, Brazil
| | - Cristine Rodrigues
- Department of Bioprocess Engineering and Biotechnology, Centro Politécnico, Federal University of Paraná, Curitiba 81531-990, PR, Brazil
| | - Adenise Lorenci Woiciechowski
- Department of Bioprocess Engineering and Biotechnology, Centro Politécnico, Federal University of Paraná, Curitiba 81531-990, PR, Brazil
| | - Carlos Ricardo Soccol
- Department of Bioprocess Engineering and Biotechnology, Centro Politécnico, Federal University of Paraná, Curitiba 81531-990, PR, Brazil
| |
Collapse
|
26
|
Huang X, Miao X, Chu X, Luo L, Zhang H, Sun Y. Enhancement effect of biochar addition on anaerobic co-digestion of pig manure and corn straw under biogas slurry circulation. BIORESOURCE TECHNOLOGY 2023; 372:128654. [PMID: 36682475 DOI: 10.1016/j.biortech.2023.128654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 06/17/2023]
Abstract
Based on the semi-continuous anaerobic co-digestion (AcoD) reactor, the effects of biochar addition on the internal environmental changes and gas production characteristics were studied under the condition of biogas slurry recirculation. The results showed that the addition of biochar enhanced the degradation and metabolic pathways of acetate and propionate, thereby reducing the concentrations of volatile fatty acids (VFAs), total ammonia and chemical oxygen demand by 55 %, 41 % and 61 %, respectively. The buffer system formed by the combination of NH4+ and VFAs of C2-C5 was also enhanced, thereby improving the stability of the system. The addition of biochar effectively increased the relative abundance of Bacteroidetes, Chloroflexi, Spirochaetota and Synergistota, and enhanced three methanogenic metabolic pathways. This study provides scientific support for the application of biochar to solve the system inhibition in mixed substrate semi-continuous AcoD process and provides technical support for the stable operation of biogas project.
Collapse
Affiliation(s)
- Xinning Huang
- Northeast Agriculture University, Harbin 15000, China; Key Laboratory of Agricultural Renewable Resources Utilization Technology and Equipment in Cold Areas of Heilongjiang Province, Harbin 150030, China; Key Laboratory of Pig-breeding Facilities Engineering, Ministry of Agriculture, Harbin 15000, China
| | - Xinying Miao
- Northeast Agriculture University, Harbin 15000, China; Key Laboratory of Agricultural Renewable Resources Utilization Technology and Equipment in Cold Areas of Heilongjiang Province, Harbin 150030, China; Key Laboratory of Pig-breeding Facilities Engineering, Ministry of Agriculture, Harbin 15000, China
| | - Xiaodong Chu
- Northeast Agriculture University, Harbin 15000, China; Key Laboratory of Agricultural Renewable Resources Utilization Technology and Equipment in Cold Areas of Heilongjiang Province, Harbin 150030, China; Key Laboratory of Pig-breeding Facilities Engineering, Ministry of Agriculture, Harbin 15000, China
| | - Lina Luo
- Northeast Agriculture University, Harbin 15000, China; Key Laboratory of Agricultural Renewable Resources Utilization Technology and Equipment in Cold Areas of Heilongjiang Province, Harbin 150030, China; Key Laboratory of Pig-breeding Facilities Engineering, Ministry of Agriculture, Harbin 15000, China
| | - Hongqiong Zhang
- Northeast Agriculture University, Harbin 15000, China; Key Laboratory of Agricultural Renewable Resources Utilization Technology and Equipment in Cold Areas of Heilongjiang Province, Harbin 150030, China; Key Laboratory of Pig-breeding Facilities Engineering, Ministry of Agriculture, Harbin 15000, China
| | - Yong Sun
- Northeast Agriculture University, Harbin 15000, China; Key Laboratory of Agricultural Renewable Resources Utilization Technology and Equipment in Cold Areas of Heilongjiang Province, Harbin 150030, China; Key Laboratory of Pig-breeding Facilities Engineering, Ministry of Agriculture, Harbin 15000, China.
| |
Collapse
|
27
|
Lee M, Yoo K, Kim H, Song KG, Kim D, Tiedje JM, Lee PH, Park J. Metatranscriptional characterization of metabolic dynamics in anaerobic membrane bioreactor producing methane from low-strength wastewater. BIORESOURCE TECHNOLOGY 2023; 370:128532. [PMID: 36574886 DOI: 10.1016/j.biortech.2022.128532] [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: 11/04/2022] [Revised: 12/19/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
An anaerobic membrane bioreactor (AnMBR) with media is an emerging carbon-neutral biotechnology for low-strength wastewater (LSWW) treatment and methane recovery. Understanding metabolic dynamics among methanogens and syntrophic bacteria is important in optimizing the design and operation of AnMBR. However, little is known about it, especially in media-attached microbial communities. This study explored metabolic dynamics to compare media-attached and suspended conditions. Accordingly, metagenomes and metatranscriptomes from AnMBRs with polymeric media and fed with different influent concentrations (350 and 700 mg-COD/L) were analyzed. Metabolic dynamics were profoundly influenced by the different growth habitats and influent conditions, although the applied influent concentrations are within the range of typical LSWW. Metabolic dynamics prediction results suggest that media-attached-growth habitats may have provided a more favorable microenvironment for methanogens to grow and produce methane, especially under low influent conditions. These findings provide significant implications for optimizing floating media design and operation of AnMBR-producing methane from LSWW.
Collapse
Affiliation(s)
- Minjoo Lee
- School of Civil and Environmental Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-Gu, Seoul 03722, Republic of Korea
| | - Keunje Yoo
- Department of Environmental Engineering, Korea Maritime & Ocean University, 727 Taejong-ro, Yeongdo-Gu, Busan 49112, Republic of Korea
| | - Hyemin Kim
- School of Civil and Environmental Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-Gu, Seoul 03722, Republic of Korea; Center for Water Cycle Research, Korea Institute of Science and Technology (KIST), 5 Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Kyung Guen Song
- Center for Water Cycle Research, Korea Institute of Science and Technology (KIST), 5 Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Dajung Kim
- School of Civil and Environmental Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-Gu, Seoul 03722, Republic of Korea
| | - James M Tiedje
- Center for Microbial Ecology, Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Po-Heng Lee
- Department of Civil and Environmental Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Joonhong Park
- School of Civil and Environmental Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-Gu, Seoul 03722, Republic of Korea.
| |
Collapse
|
28
|
Wang J, Wang X, Zheng X, Yang Y, He Z, Zhang L, Liao Q. Effects of florfenicol on methane accumulation and changes in the structure of the prokaryotic community in a water-sediment system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 847:157444. [PMID: 35868376 DOI: 10.1016/j.scitotenv.2022.157444] [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: 01/12/2022] [Revised: 07/13/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
Florfenicol has been widely used in the veterinary and aquaculture to control bacterial diseases because of its high efficacy, quick effect, and low cost. The water-sediment system has become an important sink for florfenicol, and the anaerobic environment of lake sediments is favorable for methane (CH4) production. Although antibiotics may impact methanogenesis under anaerobic conditions, the influence of florfenicol on CH4 accumulation in anaerobic water-sediment system remains uncertain. This study evaluated how florfenicol affects CH4 accumulation and the structure of the prokaryotic community in a water-sediment system. Anaerobic systems with different florfenicol concentrations (0, 0.2, 1, 5 and 10 mg/L) were incubated and CH4 accumulation, pH, total organic carbon content, degradation ratio of florfenicol, and structure of the prokaryotic community were monitored. It was found that CH4 accumulation raised in low florfenicol (0.2 and 1 mg/L) systems during the growth period, while CH4 accumulation declined in high florfenicol (5 and 10 mg/L) systems. In the first 13 d, 83.67-99.30 % of florfenicol degraded in different treatments. The addition of florfenicol also influenced the structure of the prokaryotic community of the sediments. Proteobacteria and Chloroflexi were dominant at the phylum level. The dominant taxa at the order level gradually changed from Methanomicrobiales to Methanobacteriales, and finally to Methanosarcinales, indicating the dynamic transformation of methanogens in the reactor. This study reveals the effects of florfenicol on CH4 production under anaerobic conditions and provides a theoretical basis for further research on the underlying mechanisms. The findings also provide some basic data on the impact of new pollutants on the global carbon cycle and greenhouse gas emission.
Collapse
Affiliation(s)
- Jinling Wang
- Department of Environmental Science, China Pharmaceutical University, Nanjing 211198, China
| | - Xinyu Wang
- Department of Environmental Science, China Pharmaceutical University, Nanjing 211198, China
| | - Xiaolan Zheng
- Department of Environmental Science, China Pharmaceutical University, Nanjing 211198, China
| | - Ye Yang
- Department of Environmental Science, China Pharmaceutical University, Nanjing 211198, China
| | - Zhenkai He
- Department of Environmental Science, China Pharmaceutical University, Nanjing 211198, China
| | - Lei Zhang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Qianjiahua Liao
- Department of Environmental Science, China Pharmaceutical University, Nanjing 211198, China.
| |
Collapse
|
29
|
Ou YF, Dong HP, McIlroy SJ, Crowe SA, Hallam SJ, Han P, Kallmeyer J, Simister RL, Vuillemin A, Leu AO, Liu Z, Zheng YL, Sun QL, Liu M, Tyson GW, Hou LJ. Expanding the phylogenetic distribution of cytochrome b-containing methanogenic archaea sheds light on the evolution of methanogenesis. THE ISME JOURNAL 2022; 16:2373-2387. [PMID: 35810262 PMCID: PMC9478090 DOI: 10.1038/s41396-022-01281-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 05/28/2023]
Abstract
Methane produced by methanogenic archaea has an important influence on Earth's changing climate. Methanogenic archaea are phylogenetically diverse and widespread in anoxic environments. These microorganisms can be divided into two subgroups based on whether or not they use b-type cytochromes for energy conservation. Methanogens with b-type cytochromes have a wider substrate range and higher growth yields than those without them. To date, methanogens with b-type cytochromes were found exclusively in the phylum "Ca. Halobacteriota" (formerly part of the phylum Euryarchaeota). Here, we present the discovery of metagenome-assembled genomes harboring methyl-coenzyme M reductase genes reconstructed from mesophilic anoxic sediments, together with the previously reported thermophilic "Ca. Methylarchaeum tengchongensis", representing a novel archaeal order, designated the "Ca. Methylarchaeales", of the phylum Thermoproteota (formerly the TACK superphylum). These microorganisms contain genes required for methyl-reducing methanogenesis and the Wood-Ljundahl pathway. Importantly, the genus "Ca. Methanotowutia" of the "Ca. Methylarchaeales" encode a cytochrome b-containing heterodisulfide reductase (HdrDE) and methanophenazine-reducing hydrogenase complex that have similar gene arrangements to those found in methanogenic Methanosarcinales. Our results indicate that members of the "Ca. Methylarchaeales" are methanogens with cytochromes and can conserve energy via membrane-bound electron transport chains. Phylogenetic and amalgamated likelihood estimation analyses indicate that methanogens with cytochrome b-containing electron transfer complexes likely evolved before diversification of Thermoproteota or "Ca. Halobacteriota" in the early Archean Eon. Surveys of public sequence databases suggest that members of the lineage are globally distributed in anoxic sediments and may be important players in the methane cycle.
Collapse
Affiliation(s)
- Ya-Fei Ou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China
| | - Hong-Po Dong
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China.
| | - Simon J McIlroy
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, QLD, 4102, Australia
| | - Sean A Crowe
- Ecosystem Services, Commercialization Platforms, and Entrepreneurship (ECOSCOPE) Training Program, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Ping Han
- Key Laboratory of Geographic Information Science, Ministry of Education, East China Normal University, Shanghai, 200241, China
| | - Jens Kallmeyer
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
| | - Rachel L Simister
- Ecosystem Services, Commercialization Platforms, and Entrepreneurship (ECOSCOPE) Training Program, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Aurele Vuillemin
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
| | - Andy O Leu
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, QLD, 4102, Australia
| | - Zhanfei Liu
- Marine Science Institute, The University of Texas at Austin, Port Aransas, TX, 78373, USA
| | - Yan-Ling Zheng
- Key Laboratory of Geographic Information Science, Ministry of Education, East China Normal University, Shanghai, 200241, China
| | - Qian-Li Sun
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China
| | - Min Liu
- Key Laboratory of Geographic Information Science, Ministry of Education, East China Normal University, Shanghai, 200241, China
| | - Gene W Tyson
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, QLD, 4102, Australia
| | - Li-Jun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China.
| |
Collapse
|
30
|
Lu Y, Liu Q, Fu L, Hu Y, Zhong L, Zhang S, Liu Q, Xie Q. The effect of modified biochar on methane emission and succession of methanogenic archaeal community in paddy soil. CHEMOSPHERE 2022; 304:135288. [PMID: 35691388 DOI: 10.1016/j.chemosphere.2022.135288] [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: 03/18/2022] [Revised: 05/24/2022] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
Modified biochars have been widely applied in ameliorating environmental problems. However, the effect of modified biochar on suppressing CH4 emission in rice paddy soil is not fully understood. In order to further study CH4 regulation in paddy soil via the modification of biochar and explore its influence on key archaeal communities, two modified biochars were generated with the pre-treatment of nitric acid (NBC) and hydrogen peroxide (OBC), respectively, and a control group was setup with water-washed biochar (WBC). Results showed that NBC significantly suppressed CH4 emission, followed by OBC and WBC, while NBC promoted the CO2 emission. Besides, the addition of biochars inhibited the accumulation of acetate and H2 in rice paddy soil, especially in the NBC treatment. 16S rRNA gene sequencing revealed that biochars amendment increased α-diversity of archaeal community and the modified biochars could mitigate the loss of α-diversity in the early stage of anaerobic incubation. Additionally, NBC amendment largely declined the relative abundance of methanogens (especially Methanosarcina) in archaeal community, while OBC and NBC promoted the relative abundance of Candidatus_Methanoperedens. Via Spearman's correlation coefficient analysis, NBC had positive correlations with Methanosaeta, and OBC showed a negative correlation with Methanocella. Overall, this study provided a practical way to regulate the CH4 emission and associated methanogenic archaea via the amendment of different modified biochars in rice paddy soil.
Collapse
Affiliation(s)
- Yue Lu
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, Hunan, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, Hunan, China.
| | - Qian Liu
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, Hunan, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, Hunan, China
| | - Leiling Fu
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, Hunan, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, Hunan, China
| | - Yingju Hu
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, Hunan, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, Hunan, China
| | - Linrui Zhong
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, Hunan, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, Hunan, China
| | - Shoujuan Zhang
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, Hunan, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, Hunan, China
| | - Qi Liu
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, Hunan, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, Hunan, China
| | - Qingqing Xie
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, Hunan, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, Hunan, China
| |
Collapse
|
31
|
Jeong SY, Kim TG. Determination of methanogenesis by nutrient availability via regulating the relative fitness of methanogens in anaerobic digestion. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156002. [PMID: 35588829 DOI: 10.1016/j.scitotenv.2022.156002] [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: 03/09/2022] [Revised: 04/25/2022] [Accepted: 05/12/2022] [Indexed: 05/16/2023]
Abstract
Response of microbial community to nutrient availability in anaerobic digestion (AD) remains elusive. Prokaryotic communities in AD batch cultures with 0, 1, 3, 5, 7, 11, 15, 20, and 25 g/L peptone were monitored using massive parallel sequencing and quantitative PCR over a 34-day experimental period. Methane production displayed a hump-shaped response to the nutrient gradient (peaking at 15 g/L peptone). Moreover, total and acetoclastic methanogens showed hump-shaped responses (both peaking at 11 g/L peptone). However, prokaryotic population increased with nutrient concentration (linear regression, R2 = 0.86) while diversity decreased (R2 = 0.94), and ordination analysis showed a gradual succession of community structure along the first axis. Network analysis revealed that extent of interspecific interactions (e.g., edge number and clustering coefficient) exhibited a hump-shaped response. The combined results indicate that abundant species became more dominated with increasing nutrient, which can result in a gain or loss of interspecific interaction within the community. Network module analysis showed that one module dominated the network at each nutrient level (comprising 41%-65% of the nodes), indicating that AD community formed a core microbial guild. The most abundant phylotypes, Macellibacteroides and Butyricicoccaceae, were consistently negative with acetoclastic methanogens in the dominant modules. Their predominance at ≥15 g/L peptone can explain the hump-shaped responses of methanogenesis and methanogens. Collectively, methanogenesis and microbial network exhibited hump-shaped responses, although microbial community exhibited monotonic responses. Therefore, nutrient availability can determine the methanogenesis through regulating the relative fitness of methanogens within the community.
Collapse
Affiliation(s)
- So-Yeon Jeong
- Department of Microbiology, Pusan National University, Pusan 46241, Republic of Korea
| | - Tae Gwan Kim
- Department of Microbiology, Pusan National University, Pusan 46241, Republic of Korea.
| |
Collapse
|
32
|
Li R, Liu D, Zhang Y, Tommaso G, Si B, Liu Z, Duan N. Enhanced anaerobic digestion of post-hydrothermal liquefaction wastewater: Bio-methane production, carbon distribution and microbial metabolism. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 837:155659. [PMID: 35513144 DOI: 10.1016/j.scitotenv.2022.155659] [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: 12/28/2021] [Revised: 04/28/2022] [Accepted: 04/28/2022] [Indexed: 06/14/2023]
Abstract
Hydrothermal liquefaction (HTL) is a cost-effective and environment-friendly technology for using biomass to produce bio-crude oil. The critical challenge of HTL is its complicated aqueous product containing high concentrations of organics and diverse toxicants. This paper reports the continuous anaerobic digestion of raw and zeolite-adsorbed Chlorella HTL wastewater using up-flow anaerobic sludge bed reactors. The bio-methane production capacity, total carbon distribution and microbial response were investigated. The anaerobic process was severely suppressed when more than 20% raw wastewater was fed; while it showed essentially improved performance till 60% pre-treated wastewater was added. Produced methane contained 17.3% of the total carbon in feedstock, which was comparable with the value (16.7%) when 25% of raw wastewater was added. The metagenomic analysis revealed distinct microbial community structures in different stages and feedstock shifts. The abundance of functional genes was consistent with anaerobic digester performance.
Collapse
Affiliation(s)
- Ruirui Li
- Laboratory of Environment-Enhancing Energy (E2E) and Key Laboratory of Agricultural Engineering in Structure and Environment, Ministry of Agriculture, College of Water Resources and Civil Engineering, China Agricultural University, Beijing 100083, China; Department of Chemical Engineering, Institute of Biochemical Engineering, Tsinghua University, Beijing, China
| | - Dianlei Liu
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Yuanhui Zhang
- Department of Agricultural and Biological Engineering, Univeristy of Illinois at Urbana-Champaign, 1304 W Pennsylvania Ave, Urbana, IL 61801, USA
| | - Giovana Tommaso
- Laboratory of Environmental Biotechnology, Faculty of Animal Science and Food Engineering (FZEA), University of São Paulo (USP), 225 N Duque de Caxias. Ave., Jardim Elite, Pirassununga, SP, Brazil
| | - Buchun Si
- Laboratory of Environment-Enhancing Energy (E2E) and Key Laboratory of Agricultural Engineering in Structure and Environment, Ministry of Agriculture, College of Water Resources and Civil Engineering, China Agricultural University, Beijing 100083, China
| | - Zhidan Liu
- Laboratory of Environment-Enhancing Energy (E2E) and Key Laboratory of Agricultural Engineering in Structure and Environment, Ministry of Agriculture, College of Water Resources and Civil Engineering, China Agricultural University, Beijing 100083, China
| | - Na Duan
- Laboratory of Environment-Enhancing Energy (E2E) and Key Laboratory of Agricultural Engineering in Structure and Environment, Ministry of Agriculture, College of Water Resources and Civil Engineering, China Agricultural University, Beijing 100083, China.
| |
Collapse
|
33
|
Hua B, Cai Y, Cui Z, Wang X. Bioaugmentation with methanogens cultured in a micro-aerobic microbial community for overloaded anaerobic digestion recovery. Anaerobe 2022; 76:102603. [PMID: 35709936 DOI: 10.1016/j.anaerobe.2022.102603] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 06/03/2022] [Accepted: 06/06/2022] [Indexed: 11/15/2022]
Abstract
Anaerobic digestion (AD) is widely used for conversion of waste materials into biogas, but inhibition of methane production caused by overloading can be a major problem. The micro-aerobic microbial community MC1 was used to successfully culture methanogens, Methanosarcina acetivorans C2A and Methanosaeta thermophila NBRC 101360. The maximum 16S rRNA gene concentrations of Methanosarcina acetivorans C2A and Methanosaeta thermophila NBRC101360 were 1.06 × 106 and 1.35 × 103 copies/mL, respectively. The five key bacteria in MC1 were quantified to assess the effect of inoculation on the abundances of the bacteria in the mixed culture. The original MC1 total 16S rRNA gene concentration was 1.93 × 108 copies/mL, and the total 16S rRNA gene concentration had increased to 4.79 × 109 copies/mL on day 9 (p < 0.05). The proportions of the key strains in MC1+MST had changed by day 9. Cells were harvested and used to bioaugment and increase the pH values of the high- and medium-temperature anaerobic systems. After bioaugmentation, thermophilic AD recovered well. The cumulative amounts of gas produced were 44.78% and 28.28% higher in the MC1+MST and MC1 groups, respectively, than the sterilized control. The MC1+MST group gave better results than the chemical addition control group (CaCO3). There was no clear effect of bioaugmentation in mesophilic AD. When compared with traditional pure culture of methanogens as inoculants, methanogen cultivation in MC1 was simple and there was no need to separate and purify the target strains. This simplified methanogenic bioaugmentation agent was useful to study the mechanism of bioaugmentation for the recovery from low pH inhibition, showing the potential for practical application.
Collapse
Affiliation(s)
- Binbin Hua
- National & Local Joint Engineering Research Center on Biomass Resource Utilization, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China
| | - Yafan Cai
- School of Chemical Engineering, Zhengzhou University, Kexue Dadao 100, 450001, Zhengzhou, China
| | - Zongjun Cui
- Center of Biomass Engineering, College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, PR China
| | - Xiaofen Wang
- Center of Biomass Engineering, College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, PR China.
| |
Collapse
|
34
|
Tang T, Liu M, Chen Y, Du Y, Feng J, Feng H. Influence of sulfamethoxazole on anaerobic digestion: Methanogenesis, degradation mechanism and toxicity evolution. JOURNAL OF HAZARDOUS MATERIALS 2022; 431:128540. [PMID: 35220120 DOI: 10.1016/j.jhazmat.2022.128540] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/04/2022] [Accepted: 02/20/2022] [Indexed: 06/14/2023]
Abstract
Sulfamethoxazole (SMX), one of the most widely used sulfonamides antibiotics, is frequently detected in the livestock wastewater. Currently, the focus needs to shift from performance effects to understanding of mechanisms and intermediate toxicity analysis. Our study found that SMX (0.5, 1, and 2 mg/L) stimulated methane production by promoting the process of acetogenesis and homo-acetogenesis. Since 1 mg/L SMX could inhibit the transformation of butyric acid, thus, the stimulation of methane was weak under this condition. Under anaerobic conditions, acetate kinase (AK) and cytochrome P450 enzymes (CYP450) continued to participate in SMX degradation. The increase in SMX concentration affected the release of metabolic enzymes, causing changes in SMX degradation pathways. Based on the main biotransformation products, five biotransformation pathways were proposed, the major transformation reactions including hydroxylation, hydrogenation, acetylation, deamination, oxidation, the elimination of oxygen atoms on sulfonyl, isoxazole ring and NS bond cleavage. Toxicity prediction analysis showed that the toxicities of most SMX transformation products were lower than that of SMX.
Collapse
Affiliation(s)
- Taotao Tang
- College of Architecture and Environment, Sichuan University, Chengdu 610065, PR China
| | - Min Liu
- College of Architecture and Environment, Sichuan University, Chengdu 610065, PR China
| | - Ying Chen
- College of Architecture and Environment, Sichuan University, Chengdu 610065, PR China.
| | - Ye Du
- College of Architecture and Environment, Sichuan University, Chengdu 610065, PR China
| | - Jieling Feng
- College of Architecture and Environment, Sichuan University, Chengdu 610065, PR China
| | - Haoran Feng
- College of Architecture and Environment, Sichuan University, Chengdu 610065, PR China
| |
Collapse
|
35
|
Huang W, Zhou J, Hu Q, Qiu B, Huang M, Murugadoss V, Guo Z. Improved methanogenesis in anaerobic wastewater treatment by magnetite@polyaniline (Fe 3O 4@PANI) composites. CHEMOSPHERE 2022; 296:133953. [PMID: 35157884 DOI: 10.1016/j.chemosphere.2022.133953] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 06/14/2023]
Abstract
The magnetite@polyaniline (Fe3O4@PANI) composites with different Fe3O4 loadings were prepared, and their effect on methane production in anaerobic systems was investigated. The Fe3O4@PANI composite with a 40% loading of Fe3O4 showed a better performance on accelerating methane production rate than other composites. The methane production rate was increased by 26.98% at the Fe3O4@PANI dosage of 0.6 g L-1. The results of the contact angle and CLSM revealed that Fe3O4@PANI had a good bio-affinity and contact directly with bacteria and archaea. Then the mechanisms related to the enhancement of methane production by the composites were explored by the species annotation and enzyme activity. It showed that Fe3O4@PANI promoted the enrichment of DIET-related functional bacteria and archaea and improved the enzyme activity related to the acetoclastic methanogenic pathway.
Collapse
Affiliation(s)
- Wen Huang
- Beijing Key Laboratory for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Jie Zhou
- Beijing Key Laboratory for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Qian Hu
- Beijing Key Laboratory for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Bin Qiu
- Beijing Key Laboratory for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China.
| | - Mina Huang
- Integrated Composites Laboratory (ICL), Department of Chemical and Biomolecular Engineering, University of Tennessee, 1512 Middle Dr, Knoxville, TN, 37996, USA
| | - Vignesh Murugadoss
- Advanced Materials Division, Engineered Multifunctional Composites (EMC) Nanotech LLC, Knoxville, TN, 37934, USA
| | - Zhanhu Guo
- Integrated Composites Laboratory (ICL), Department of Chemical and Biomolecular Engineering, University of Tennessee, 1512 Middle Dr, Knoxville, TN, 37996, USA.
| |
Collapse
|
36
|
High Salinity Wastewater Treatment Study Using an Automated Pilot Combining Anaerobic and Aerobic Biofilm Processes. Processes (Basel) 2022. [DOI: 10.3390/pr10040766] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
A 20-ft containerized biological pilot system consisting of both an anaerobic expended granular sludge bed (EGSB) and an aerobic biofilm continuous flow intermittent clean (CFIC®) system has been designed, constructed, and delivered onsite at a pharmaceutical wastewater producer for a wastewater treatment study. The pilot was operated for a total of 317 days, including 147 days of adaptive phase and 170 days of testing phase. A pilot adaptive phase feeding wastewater COD concentration from 2 to 50 g/L with salinity up to 16 g/L was carried out, achieving EGSB where COD removal reached over 80 to 95% at OLR up to 22 kg COD/m3·d. In the testing phase, with repressive practical wastewater, the EGSB can remove over 97% of feed COD (with up to 82% acetic acid) at an average 16.3 kg COD/m3·d. The high wastewater salinity at 20 g/L did not inhibit COD removal efficiency by the system. The complete system with EGSB and aerobic stage was very stable and removed over 90–97% of the total COD dependent on the wastewater composition. The pilot was demonstrated as a valuable tool because of its user-friendly nature with high automation level, as well as its high efficiency in treating specific wastewater under varying operational conditions. This study provides critical information for full-scale system design and offers training for the customer in handling a previously unfamiliar process in a confident manner.
Collapse
|
37
|
Min BR, Lee S, Jung H, Miller DN, Chen R. Enteric Methane Emissions and Animal Performance in Dairy and Beef Cattle Production: Strategies, Opportunities, and Impact of Reducing Emissions. Animals (Basel) 2022; 12:948. [PMID: 35454195 PMCID: PMC9030782 DOI: 10.3390/ani12080948] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/27/2022] [Accepted: 03/29/2022] [Indexed: 01/14/2023] Open
Abstract
Enteric methane (CH4) emissions produced by microbial fermentation in the rumen resulting in the emission of greenhouse gases (GHG) into the atmosphere. The GHG emissions reduction from the livestock industry can be attained by increasing production efficiency and improving feed efficiency, by lowering the emission intensity of production, or by combining the two. In this work, information was compiled from peer-reviewed studies to analyze CH4 emissions calculated per unit of milk production, energy-corrected milk (ECM), average daily gain (ADG), dry matter intake (DMI), and gross energy intake (GEI), and related emissions to rumen fermentation profiles (volatile fatty acids [VFA], hydrogen [H2]) and microflora activities in the rumen of beef and dairy cattle. For dairy cattle, there was a positive correlation (p < 0.001) between CH4 emissions and DMI (R2 = 0.44), milk production (R2 = 0.37; p < 0.001), ECM (R2 = 0.46), GEI (R2 = 0.50), and acetate/propionate (A/P) ratio (R2 = 0.45). For beef cattle, CH4 emissions were positively correlated (p < 0.05−0.001) with DMI (R2 = 0.37) and GEI (R2 = 0.74). Additionally, the ADG (R2 = 0.19; p < 0.01) and A/P ratio (R2 = 0.15; p < 0.05) were significantly associated with CH4 emission in beef steers. This information may lead to cost-effective methods to reduce enteric CH4 production from cattle. We conclude that enteric CH4 emissions per unit of ECM, GEI, and ADG, as well as rumen fermentation profiles, show great potential for estimating enteric CH4 emissions.
Collapse
Affiliation(s)
- Byeng-Ryel Min
- College of Agriculture, Environment and Nutrition Sciences, Tuskegee University, Tuskegee, AL 36088, USA;
| | - Seul Lee
- Animal Nutrition & Physiology Division, National Institute of Animal Science, Rural Development Administration, Wanju-gun 55365, Jeollabuk-do, Korea; (S.L.); (H.J.)
| | - Hyunjung Jung
- Animal Nutrition & Physiology Division, National Institute of Animal Science, Rural Development Administration, Wanju-gun 55365, Jeollabuk-do, Korea; (S.L.); (H.J.)
| | - Daniel N. Miller
- Agroecosystem Management Research Unit, USDA/ARS, 354 Filly Hall, Lincoln, NE 68583, USA;
| | - Rui Chen
- College of Agriculture, Environment and Nutrition Sciences, Tuskegee University, Tuskegee, AL 36088, USA;
| |
Collapse
|
38
|
Wu Q, Guthrie MJ, Jin Q. Physiological Acclimation Extrapolates the Kinetics and Thermodynamics of Methanogenesis From Laboratory Experiments to Natural Environments. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.838487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Chemotrophic microorganisms face the steep challenge of limited energy resources in natural environments. This observation has important implications for interpreting and modeling the kinetics and thermodynamics of microbial reactions. Current modeling frameworks treat microbes as autocatalysts, and simulate microbial energy conservation and growth with fixed kinetic and thermodynamic parameters. However, microbes are capable of acclimating to the environment and modulating their parameters in order to gain competitive fitness. Here we constructed an optimization model and described microbes as self-adapting catalysts by linking microbial parameters to intracellular metabolic resources. From the optimization results, we related microbial parameters to the substrate concentration and the energy available in the environment, and simplified the relationship between the kinetics and the thermodynamics of microbial reactions. We took as examples Methanosarcina and Methanosaeta – the methanogens that produce methane from acetate – and showed how the acclimation model extrapolated laboratory observations to natural environments and improved the simulation of methanogenesis and the dominance of Methanosaeta over Methanosarcina in lake sediments. These results highlight the importance of physiological acclimation in shaping the kinetics and thermodynamics of microbial reactions and in determining the outcome of microbial interactions.
Collapse
|
39
|
McKay LJ, Smith HJ, Barnhart EP, Schweitzer HD, Malmstrom RR, Goudeau D, Fields MW. Activity-based, genome-resolved metagenomics uncovers key populations and pathways involved in subsurface conversions of coal to methane. THE ISME JOURNAL 2022; 16:915-926. [PMID: 34689183 PMCID: PMC8941128 DOI: 10.1038/s41396-021-01139-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 09/28/2021] [Accepted: 10/04/2021] [Indexed: 11/08/2022]
Abstract
Microbial metabolisms and interactions that facilitate subsurface conversions of recalcitrant carbon to methane are poorly understood. We deployed an in situ enrichment device in a subsurface coal seam in the Powder River Basin (PRB), USA, and used BONCAT-FACS-Metagenomics to identify translationally active populations involved in methane generation from a variety of coal-derived aromatic hydrocarbons. From the active fraction, high-quality metagenome-assembled genomes (MAGs) were recovered for the acetoclastic methanogen, Methanothrix paradoxum, and a novel member of the Chlorobi with the potential to generate acetate via the Pta-Ack pathway. Members of the Bacteroides and Geobacter also encoded Pta-Ack and together, all four populations had the putative ability to degrade ethylbenzene, phenylphosphate, phenylethanol, toluene, xylene, and phenol. Metabolic reconstructions, gene analyses, and environmental parameters also indicated that redox fluctuations likely promote facultative energy metabolisms in the coal seam. The active "Chlorobi PRB" MAG encoded enzymes for fermentation, nitrate reduction, and multiple oxygenases with varying binding affinities for oxygen. "M. paradoxum PRB" encoded an extradiol dioxygenase for aerobic phenylacetate degradation, which was also present in previously published Methanothrix genomes. These observations outline underlying processes for bio-methane from subbituminous coal by translationally active populations and demonstrate activity-based metagenomics as a powerful strategy in next generation physiology to understand ecologically relevant microbial populations.
Collapse
Affiliation(s)
- Luke J McKay
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA.
- Thermal Biology Institute, Montana State University, Bozeman, MT, 59717, USA.
- Department of Land Resources & Environmental Sciences, Montana State University, Bozeman, MT, 59717, USA.
| | - Heidi J Smith
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA.
- Department of Microbiology & Cell Biology, Montana State University, Bozeman, MT, 59717, USA.
| | - Elliott P Barnhart
- U.S. Geological Survey, Wyoming-Montana Water Science Center, Helena, MT, 59601, USA
| | - Hannah D Schweitzer
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA
- Department of Microbiology & Cell Biology, Montana State University, Bozeman, MT, 59717, USA
- Arctic University of Norway, Tromsø, Norway
| | | | | | - Matthew W Fields
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA.
- Department of Microbiology & Cell Biology, Montana State University, Bozeman, MT, 59717, USA.
| |
Collapse
|
40
|
Aguilar-Muñoz P, Lavergne C, Chamy R, Cabrol L. The biotechnological potential of microbial communities from Antarctic soils and sediments: application to low temperature biogenic methane production. J Biotechnol 2022; 351:38-49. [DOI: 10.1016/j.jbiotec.2022.04.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/20/2022] [Accepted: 04/26/2022] [Indexed: 11/24/2022]
|
41
|
Gadol HJ, Elsherbini J, Kocar BD. Methanogen Productivity and Microbial Community Composition Varies With Iron Oxide Mineralogy. Front Microbiol 2022; 12:705501. [PMID: 35250895 PMCID: PMC8894893 DOI: 10.3389/fmicb.2021.705501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 12/27/2021] [Indexed: 01/04/2023] Open
Abstract
Quantifying the flux of methane from terrestrial environments remains challenging, owing to considerable spatial and temporal variability in emissions. Amongst a myriad of factors, variation in the composition of electron acceptors, including metal (oxyhydr)oxides, may impart controls on methane emission. The purpose of this research is to understand how iron (oxyhydr)oxide minerals with varied physicochemical properties influence microbial methane production and subsequent microbial community development. Incubation experiments, using lake sediment as an inoculum and acetate as a carbon source, were used to understand the influence of one poorly crystalline iron oxide mineral, ferrihydrite, and two well-crystalline minerals, hematite and goethite, on methane production. Iron speciation, headspace methane, and 16S-rRNA sequencing microbial community data were measured over time. Substantial iron reduction only occurred in the presence of ferrihydrite while hematite and goethite had little effect on methane production throughout the incubations. In ferrihydrite experiments the time taken to reach the maximum methane production rate was slower than under other conditions, but methane production, eventually occurred in the presence of ferrihydrite. We suggest that this is due to ferrihydrite transformation into more stable minerals like magnetite and goethite or surface passivation by Fe(II). While all experimental conditions enriched for Methanosarcina, only the presence of ferrihydrite enriched for iron reducing bacteria Geobacter. Additionally, the presence of ferrihydrite continued to influence microbial community development after the onset of methanogenesis, with the dissimilarity between communities growing in ferrihydrite compared to no-Fe-added controls increasing over time. This work improves our understanding of how the presence of different iron oxides influences microbial community composition and methane production in soils and sediments.
Collapse
Affiliation(s)
- Hayley J. Gadol
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- *Correspondence: Hayley J. Gadol,
| | - Joseph Elsherbini
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Graduate Program in Microbiology, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Benjamin D. Kocar
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Environmental Laboratory, U.S. Army Engineer Research and Development Center, Vicksburg, MS, United States
- Benjamin D. Kocar,
| |
Collapse
|
42
|
Meng X, Cao Q, Sun Y, Huang S, Liu X, Li D. 16S rRNA genes- and metagenome-based confirmation of syntrophic butyrate-oxidizing methanogenesis enriched in high butyrate loading. BIORESOURCE TECHNOLOGY 2022; 345:126483. [PMID: 34864185 DOI: 10.1016/j.biortech.2021.126483] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 11/27/2021] [Accepted: 11/29/2021] [Indexed: 06/13/2023]
Abstract
The understanding and enrichment of consortia formed by syntrophic butyrate-oxidizing bacteria and methanogens in the complex environment are crucial for effectively degrading butyrate and preventing acid inhibition. In this study, the better butyrate-tolerated and highly efficient microbial consortia were domesticated and enriched through adding butyric acid ranging from 0.2 to 4.4 g/(L·d). The volumetric biogas production continuously increased to 1.65 L/(L·d). Microbial community diversity showed that a dramatic shift of bacterial structure occurred at BAL of 1.6 g/(L·d) and the structure presented better stability at high BAL. The syntrophic consortia and the main metabolic pathways were revealed through combination of the 16S rDNA and metagenome sequencing analyses. Syntrophomonas was the major butyrate-oxidizing bacterium and oxidized butyrate mainly through β-oxidaiton. Synergistaceae and Mesotoga acted as the main acetate-oxidizing bacteria. IHT and methanogenesis pathways were strongly enhanced by DMER64 and Methanosarcina as the main H2 carrier and dominant methanogen, respectively.
Collapse
Affiliation(s)
- Xianghui Meng
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China; College of Engineering, Northeast Agriculture University, Harbin 150030, PR China
| | - Qin Cao
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Yong Sun
- College of Engineering, Northeast Agriculture University, Harbin 150030, PR China
| | - Siyuan Huang
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Xiaofeng Liu
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Dong Li
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China.
| |
Collapse
|
43
|
Wang Y, Mairinger W, Raj SJ, Yakubu H, Siesel C, Green J, Durry S, Joseph G, Rahman M, Amin N, Hassan MZ, Wicken J, Dourng D, Larbi E, Adomako LAB, Senayah AK, Doe B, Buamah R, Tetteh-Nortey JNN, Kang G, Karthikeyan A, Roy S, Brown J, Muneme B, Sene SO, Tuffuor B, Mugambe RK, Bateganya NL, Surridge T, Ndashe GM, Ndashe K, Ban R, Schrecongost A, Moe CL. Quantitative assessment of exposure to fecal contamination in urban environment across nine cities in low-income and lower-middle-income countries and a city in the United States. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 763:143007. [PMID: 34718001 DOI: 10.1016/j.scitotenv.2020.143007] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 10/08/2020] [Accepted: 10/08/2020] [Indexed: 05/23/2023]
Abstract
BACKGROUND During 2014 to 2019, the SaniPath Exposure Assessment Tool, a standardized set of methods to evaluate risk of exposure to fecal contamination in the urban environment through multiple exposure pathways, was deployed in 45 neighborhoods in ten cities, including Accra and Kumasi, Ghana; Vellore, India; Maputo, Mozambique; Siem Reap, Cambodia; Atlanta, United States; Dhaka, Bangladesh; Lusaka, Zambia; Kampala, Uganda; Dakar, Senegal. OBJECTIVE Assess and compare risk of exposure to fecal contamination via multiple pathways in ten cities. METHODS In total, 4053 environmental samples, 4586 household surveys, 128 community surveys, and 124 school surveys were collected. E. coli concentrations were measured in environmental samples as an indicator of fecal contamination magnitude. Bayesian methods were used to estimate the distributions of fecal contamination concentration and contact frequency. Exposure to fecal contamination was estimated by the Monte Carlo method. The contamination levels of ten environmental compartments, frequency of contact with those compartments for adults and children, and estimated exposure to fecal contamination through any of the surveyed environmental pathways were compared across cities and neighborhoods. RESULTS Distribution of fecal contamination in the environment and human contact behavior varied by city. Universally, food pathways were the most common dominant route of exposure to fecal contamination across cities in low-income and lower-middle-income countries. Risks of fecal exposure via water pathways, such as open drains, flood water, and municipal drinking water, were site-specific and often limited to smaller geographic areas (i.e., neighborhoods) instead of larger areas (i.e., cities). CONCLUSIONS Knowledge of the relative contribution to fecal exposure from multiple pathways, and the environmental contamination level and frequency of contact for those "dominant pathways" could provide guidance for Water, Sanitation, and Hygiene (WASH) programming and investments and enable local governments and municipalities to improve intervention strategies to reduce the risk of exposure to fecal contamination.
Collapse
Affiliation(s)
- Yuke Wang
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA.
| | - Wolfgang Mairinger
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Suraja J Raj
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Habib Yakubu
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Casey Siesel
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Jamie Green
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Sarah Durry
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - George Joseph
- Water Global Practice, The World Bank, Washington, DC, USA
| | - Mahbubur Rahman
- Environmental Interventions Unit, Infectious Disease Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Nuhu Amin
- Environmental Interventions Unit, Infectious Disease Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | | | | | | | - Eugene Larbi
- Training Research and Networking for Development (TREND), Accra, Ghana
| | | | | | - Benjamin Doe
- Training Research and Networking for Development (TREND), Accra, Ghana
| | - Richard Buamah
- Department of Civil Engineering, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Gagandeep Kang
- Wellcome Research Laboratory, Christian Medical College, Vellore, India
| | - Arun Karthikeyan
- Wellcome Research Laboratory, Christian Medical College, Vellore, India
| | - Sheela Roy
- Wellcome Research Laboratory, Christian Medical College, Vellore, India
| | - Joe Brown
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Bacelar Muneme
- Water Supply and Mapping, WE Consult, Maputo, Mozambique
| | - Seydina O Sene
- Initiative Prospective Agricole et Rurale (IPAR), Dakar, Senegal
| | - Benedict Tuffuor
- Training Research and Networking for Development (TREND), Accra, Ghana
| | - Richard K Mugambe
- Department of Disease Control and Environmental Health, Makerere University School of Public Health, Kampala, Uganda
| | - Najib Lukooya Bateganya
- Department of Environment and Public Health, Kampala Capital City Authority, Kampala, Uganda
| | - Trevor Surridge
- Deutsche Gesellschaft für Internationale Zusammenarbeit (GIZ) GmbH, Lusaka, Zambia
| | | | - Kunda Ndashe
- Department of Environmental Health, Faculty of Health Science, Lusaka Apex Medical University, Lusaka, Zambia
| | - Radu Ban
- Bill & Melinda Gates Foundation, Seattle, WA, USA
| | | | - Christine L Moe
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| |
Collapse
|
44
|
Cristiani L, Ferretti J, Majone M, Villano M, Zeppilli M. Autotrophic Acetate Production under Hydrogenophilic and Bioelectrochemical Conditions with a Thermally Treated Mixed Culture. MEMBRANES 2022; 12:membranes12020126. [PMID: 35207048 PMCID: PMC8876840 DOI: 10.3390/membranes12020126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 02/05/2023]
Abstract
Bioelectrochemical systems are emerging technologies for the reduction in CO2 in fuels and chemicals, in which anaerobic chemoautotrophic microorganisms such as methanogens and acetogens are typically used as biocatalysts. The anaerobic digestion digestate represents an abundant source of methanogens and acetogens microorganisms. In a mixed culture environment, methanogen’s inhibition is necessary to avoid acetate consumption by the presence of acetoclastic methanogens. In this study, a methanogenesis inhibition approach based on the thermal treatment of mixed cultures was adopted and evaluated in terms of acetate production under different tests consisting of hydrogenophilic and bioelectrochemical experiments. Batch experiments were carried out under hydrogenophilic and bioelectrochemical conditions, demonstrating the effectiveness of the thermal treatment and showing a 30 times higher acetate production with respect to the raw anaerobic digestate. Moreover, a continuous flow bioelectrochemical reactor equipped with an anion exchange membrane (AEM) successfully overcomes the methanogens reactivation, allowing for a continuous acetate production. The AEM membrane guaranteed the migration of the acetate from the biological compartment and its concentration in the abiotic chamber avoiding its consumption by acetoclastic methanogenesis. The system allowed an acetate concentration of 1745 ± 30 mg/L in the abiotic chamber, nearly five times the concentration measured in the cathodic chamber.
Collapse
|
45
|
Biological conversion of carbon monoxide and hydrogen by anaerobic culture: Prospect of anaerobic digestion and thermochemical processes combination. Biotechnol Adv 2021; 58:107886. [PMID: 34915147 DOI: 10.1016/j.biotechadv.2021.107886] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 11/26/2021] [Accepted: 12/08/2021] [Indexed: 01/04/2023]
Abstract
Waste biomass is considered a promising renewable energy feedstock that can be converted by anaerobic digestion. However, anaerobic digestion application can be challenging due to the structural complexity of several waste biomass kinds. Therefore, coupling anaerobic digestion with thermochemical processes can offset the limitations and convert the hardly biodegradable waste biomass, including digestate residue, into value-added products: syngas and pyrogas (gaseous mixtures consisting mainly of H2, CO, CO2), bio-oil, and biochar for further valorisation. In this review, the utilisation boundaries and benefits of the aforementioned products by anaerobic culture are discussed. First, thermochemical process parameters for an enhanced yield of desired products are summarised. Particularly, the microbiology of CO and H2 mixture biomethanation and fermentation in anaerobic digestion is presented. Finally, the state-of-the-art biological conversion of syngas and pyrogas to CH4 mediated by anaerobic culture is adequately described. Extensive research shows the successful selective biological conversion of CO and H2 to CH4, acetic acid, and alcohols. The main bottleneck is the gas-liquid mass transfer which can be enhanced appropriately by bioreactors' configurations. A few research groups focus on bio-oil and biochar addition into anaerobic digesters. However, according to the literature review, there has been no research for utilising all value-added products at once in anaerobic digestion published so far. Although synergic effects of such can be expected. In summary, the combination of anaerobic digestion and thermochemical processes is a promising alternative for wide-scale waste biomass utilisation in practice.
Collapse
|
46
|
Pelsma KAJ, In 't Zandt MH, Op den Camp HJM, Jetten MSM, Dean JF, Welte CU. Amsterdam urban canals contain novel niches for methane-cycling microorganisms. Environ Microbiol 2021; 24:82-97. [PMID: 34863018 PMCID: PMC9299808 DOI: 10.1111/1462-2920.15864] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 12/01/2021] [Accepted: 12/01/2021] [Indexed: 01/04/2023]
Abstract
Urbanised environments have been identified as hotspots of anthropogenic methane emissions. Especially urban aquatic ecosystems are increasingly recognised as important sources of methane. However, the microbiology behind these emissions remains unexplored. Here, we applied microcosm incubations and molecular analyses to investigate the methane‐cycling community of the Amsterdam canal system in the Netherlands. The sediment methanogenic communities were dominated by Methanoregulaceae and Methanosaetaceae, with co‐occurring methanotrophic Methanoperedenaceae and Methylomirabilaceae indicating the potential for anaerobic methane oxidation. Methane was readily produced after substrate amendment, suggesting an active but substrate‐limited methanogenic community. Bacterial 16S rRNA gene amplicon sequencing of the sediment revealed a high relative abundance of Thermodesulfovibrionia. Canal wall biofilms showed the highest initial methanotrophic potential under oxic conditions compared to the sediment. During prolonged incubations the maximum methanotrophic rate increased to 8.08 mmol gDW−1 d−1 that was concomitant with an enrichment of Methylomonadaceae bacteria. Metagenomic analysis of the canal wall biofilm lead to the recovery of a single methanotroph metagenome‐assembled genome. Taxonomic analysis showed that this methanotroph belongs to the genus Methyloglobulus. Our results underline the importance of previously unidentified and specialised environmental niches at the nexus of the natural and human‐impacted carbon cycle.
Collapse
Affiliation(s)
- Koen A J Pelsma
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands.,Netherlands Earth System Science Centre, Utrecht University, Heidelberglaan 2, Utrecht, 3584 CS, The Netherlands
| | - Michiel H In 't Zandt
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands.,Netherlands Earth System Science Centre, Utrecht University, Heidelberglaan 2, Utrecht, 3584 CS, The Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands.,Netherlands Earth System Science Centre, Utrecht University, Heidelberglaan 2, Utrecht, 3584 CS, The Netherlands.,Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
| | - Joshua F Dean
- School of Environmental Sciences, University of Liverpool, Liverpool, L69 3GP, UK
| | - Cornelia U Welte
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands.,Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
| |
Collapse
|
47
|
Hardy J, Bonin P, Lazuka A, Gonidec E, Guasco S, Valette C, Lacroix S, Cabrol L. Similar Methanogenic Shift but Divergent Syntrophic Partners in Anaerobic Digesters Exposed to Direct versus Successive Ammonium Additions. Microbiol Spectr 2021; 9:e0080521. [PMID: 34612672 PMCID: PMC8510171 DOI: 10.1128/spectrum.00805-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 08/02/2021] [Indexed: 01/04/2023] Open
Abstract
During anaerobic digestion (AD) of protein-rich wastewater, ammonium (NH4+) is released by amino acid degradation. High NH4+ concentrations disturb the AD microbiome balance, leading to process impairments. The sensitivity of the AD microbiome to NH4+ and the inhibition threshold depend on multiple parameters, especially the previous microbial acclimation to ammonium stress. However, little is known about the effect of different NH4+ acclimation strategies on the differential expression of key active microbial taxa. Here, we applied NH4+ inputs of increasing intensity (from 1.7 to 15.2 g N-NH4+ liters-1) in batch assays fed with synthetic wastewater, according to two different strategies: (i) direct independent inputs at a unique target concentration and (ii) successive inputs in a stepwise manner. In both strategies, along the NH4+ gradient, the active methanogens shifted from acetoclastic Methanosaeta to Methanosarcina and eventually hydrogenotrophic Methanoculleus. Despite shorter latency times, the successive input modality led to lower methane production rate, lower soluble chemical oxygen demand (sCOD) removal efficiency, and lower half maximal inhibitory concentration, together with higher volatile fatty acid (VFA) accumulation, compared to the independent input modality. These differential performances were associated with a drastically distinct succession pattern of the active bacterial partners in both experiments. In particular, the direct exposure modality was characterized by a progressive enrichment of VFA producers (mainly Tepidimicrobium) and syntrophic VFA oxidizers (mainly Syntrophaceticus) with increasing NH4+ concentration, while the successive exposure modality was characterized by a more dynamic succession of VFA producers (mainly Clostridium, Sporanaerobacter, Terrisporobacter) and syntrophic VFA oxidizers (mainly Tepidanaerobacter, Syntrophomonas). These results bring relevant insights for improved process management through inoculum adaptation, bioaugmentation, or community-driven optimization. IMPORTANCE Anaerobic digestion (AD) is an attractive biotechnological process for wastewater bioremediation and bioenergy production in the form of methane-rich biogas. However, AD can be inhibited by ammonium generated by protein-rich effluent, commonly found in agro-industrial activities. Insights in the microbial community composition and identification of AD key players are crucial for anticipating process impairments in response to ammonium stress. They can also help in defining an optimal microbiome adapted to high ammonium levels. Here, we compared two strategies for acclimation of AD microbiome to increasing ammonium concentration to better understand the effect of this stress on the methanogens and their bacterial partners. Our results suggest that long-term cumulative exposure to ammonia disrupted the AD microbiome more strongly than direct (independent) ammonium additions. We identified bioindicators with different NH4+ tolerance capacity among VFA producers and syntrophic VFA oxidizers.
Collapse
Affiliation(s)
- Julie Hardy
- MIO, Aix Marseille University, University of Toulon, CNRS, IRD, Marseille, France
- Scientific & Technological Expertise Department, Veolia, Maisons-Laffitte, France
| | - Patricia Bonin
- MIO, Aix Marseille University, University of Toulon, CNRS, IRD, Marseille, France
| | - Adele Lazuka
- Scientific & Technological Expertise Department, Veolia, Maisons-Laffitte, France
| | - Estelle Gonidec
- Scientific & Technological Expertise Department, Veolia, Maisons-Laffitte, France
| | - Sophie Guasco
- MIO, Aix Marseille University, University of Toulon, CNRS, IRD, Marseille, France
| | - Corinne Valette
- MIO, Aix Marseille University, University of Toulon, CNRS, IRD, Marseille, France
| | - Sébastien Lacroix
- Scientific & Technological Expertise Department, Veolia, Maisons-Laffitte, France
| | - Léa Cabrol
- MIO, Aix Marseille University, University of Toulon, CNRS, IRD, Marseille, France
- Instituto de Ecologia y Biodiversidad (IEB) Facultad de Ciencias, Universidad de Chile Las Palmeras, Nunoa, Santiago, Chile
| |
Collapse
|
48
|
Yan M, Zhu X, Treu L, Ravenni G, Campanaro S, Goonesekera EM, Ferrigno R, Jacobsen CS, Zervas A, Angelidaki I, Fotidis IA. Comprehensive evaluation of different strategies to recover methanogenic performance in ammonia-stressed reactors. BIORESOURCE TECHNOLOGY 2021; 336:125329. [PMID: 34052546 DOI: 10.1016/j.biortech.2021.125329] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 06/12/2023]
Abstract
In this study, strategies for recovery of ammonia-stressed AD reactors were attempted, by addition of preserved bioaugmentation consortium in gel (BioG), fresh consortium in liquid medium (BioL), woodchip biochar (BW), and straw biochar (BS). In comparison to control group with ammonia, effective treatments, i.e., BioG, BioL, BW and BS raised the maximum methane production rate by 77%, 23%, 35%, and 24%, respectively. BW possibly acted as interspecies electrical conduits for Direct Electron Transfer based on conductivity and SEM analysis. BioG facilitated slow release of bioaugmentation inocula from gel into the AD system, which protected them from a direct environmental shock. According to microbial analysis, both BioG, BioL and BW resulted in increased relative abundance of Methanothermobacter thermautotrophicus; and BS induced selective raise of Methanosarcina thermophila. The increase of methanogens via these strategies led to the faster recovery of the AD process.
Collapse
Affiliation(s)
- Miao Yan
- Department of Environmental Engineering, Technical University of Denmark, Building 115, Kgs. Lyngby DK-2800, Denmark
| | - Xinyu Zhu
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Building 227, Kgs. Lyngby DK-2800, Denmark
| | - Laura Treu
- Department of Biology, University of Padova, Via U. Bassi 58/b, Padova 35121, Italy
| | - Giulia Ravenni
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Building 313, Roskilde 4000, Denmark
| | - Stefano Campanaro
- Department of Biology, University of Padova, Via U. Bassi 58/b, Padova 35121, Italy
| | - Estelle Maria Goonesekera
- Department of Environmental Engineering, Technical University of Denmark, Building 115, Kgs. Lyngby DK-2800, Denmark
| | - Rosa Ferrigno
- Department of Environmental Engineering, Technical University of Denmark, Building 115, Kgs. Lyngby DK-2800, Denmark
| | - Carsten S Jacobsen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, Roskilde DK-4000, Denmark
| | - Athanasios Zervas
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, Roskilde DK-4000, Denmark
| | - Irini Angelidaki
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Building 227, Kgs. Lyngby DK-2800, Denmark
| | - Ioannis A Fotidis
- Department of Environmental Engineering, Technical University of Denmark, Building 115, Kgs. Lyngby DK-2800, Denmark; Faculty of Engineering and Natural Sciences, Tampere University, Tampere, Finland; School of Civil Engineering Southeast University Nanjing, 210096, China.
| |
Collapse
|
49
|
Lavergne C, Aguilar-Muñoz P, Calle N, Thalasso F, Astorga-España MS, Sepulveda-Jauregui A, Martinez-Cruz K, Gandois L, Mansilla A, Chamy R, Barret M, Cabrol L. Temperature differently affected methanogenic pathways and microbial communities in sub-Antarctic freshwater ecosystems. ENVIRONMENT INTERNATIONAL 2021; 154:106575. [PMID: 33901975 DOI: 10.1016/j.envint.2021.106575] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 06/12/2023]
Abstract
Freshwater ecosystems are responsible for an important part of the methane (CH4) emissions which are likely to change with global warming. This study aims to evaluate temperature-induced (from 5 to 20 °C) changes on microbial community structure and methanogenic pathways in five sub-Antarctic lake sediments from Magallanes strait to Cape Horn, Chile. We combined in situ CH4 flux measurements, CH4 production rates (MPRs), gene abundance quantification and microbial community structure analysis (metabarcoding of the 16S rRNA gene). Under unamended conditions, a temperature increase of 5 °C doubled MPR while microbial community structure was not affected. Stimulation of methanogenesis by methanogenic precursors as acetate and H2/CO2, resulted in an increase of MPRs up to 127-fold and 19-fold, respectively, as well as an enrichment of mcrA-carriers strikingly stronger under acetate amendment. At low temperatures, H2/CO2-derived MPRs were considerably lower (down to 160-fold lower) than the acetate-derived MPRs, but the contribution of hydrogenotrophic methanogenesis increased with temperature. Temperature dependence of MPRs was significantly higher in incubations spiked with H2/CO2 (c. 1.9 eV) compared to incubations spiked with acetate or unamended (c. 0.8 eV). Temperature was not found to shape the total microbial community structure, that rather exhibited a site-specific variability among the studied lakes. However, the methanogenic archaeal community structure was driven by amended methanogenic precursors with a dominance of Methanobacterium in H2/CO2-based incubations and Methanosarcina in acetate-based incubations. We also suggested the importance of acetogenic H2-production outcompeting hydrogenotrohic methanogenesis especially at low temperatures, further supported by homoacetogen proportion in the microcosm communities. The combination of in situ-, and laboratory-based measurements and molecular approaches indicates that the hydrogenotrophic pathway may become more important with increasing temperatures than the acetoclastic pathway. In a continuously warming environment driven by climate change, such issues are crucial and may receive more attention.
Collapse
Affiliation(s)
- Céline Lavergne
- HUB AMBIENTAL UPLA, Laboratory of Aquatic Environmental Research, Centro de Estudios Avanzados, Universidad de Playa Ancha, Valparaíso, Chile; Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Avenida Brasil 2085, 2340950 Valparaíso, Chile.
| | - Polette Aguilar-Muñoz
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Avenida Brasil 2085, 2340950 Valparaíso, Chile
| | - Natalia Calle
- Departamento de Química, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Frédéric Thalasso
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Departamento de Biotecnología y Bioingeniería, México, DF, Mexico
| | - Maria Soledad Astorga-España
- Departamento de Ciencias y Recursos Naturales, Universidad de Magallanes, Punta Arenas, Chile; ENBEELAB, University of Magallanes, Punta Arenas, Chile
| | - Armando Sepulveda-Jauregui
- ENBEELAB, University of Magallanes, Punta Arenas, Chile; Center for Climate and Resilience Research (CR)(2), Santiago, Chile
| | - Karla Martinez-Cruz
- Departamento de Ciencias y Recursos Naturales, Universidad de Magallanes, Punta Arenas, Chile; ENBEELAB, University of Magallanes, Punta Arenas, Chile
| | - Laure Gandois
- Laboratoire Écologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse, France
| | - Andrés Mansilla
- Departamento de Ciencias y Recursos Naturales, Universidad de Magallanes, Punta Arenas, Chile
| | - Rolando Chamy
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Avenida Brasil 2085, 2340950 Valparaíso, Chile
| | - Maialen Barret
- Laboratoire Écologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse, France
| | - Léa Cabrol
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Avenida Brasil 2085, 2340950 Valparaíso, Chile; Aix-Marseille University, Univ Toulon, CNRS, IRD, M.I.O. UM 110, Mediterranean Institute of Oceanography, Marseille, France; Institute of Ecology and Biodiversity IEB, Faculty of Sciences, Universidad de Chile, Santiago, Chile.
| |
Collapse
|
50
|
Wu D, Zhao C, Bai H, Feng F, Sui X, Sun G. Characteristics and metabolic patterns of soil methanogenic archaea communities in the high-latitude natural forested wetlands of China. Ecol Evol 2021; 11:10396-10408. [PMID: 34367583 PMCID: PMC8328403 DOI: 10.1002/ece3.7842] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 04/07/2021] [Accepted: 06/10/2021] [Indexed: 01/12/2023] Open
Abstract
Soil methanogenic microorganisms are one of the primary methane-producing microbes in wetlands. However, we still poorly understand the community characteristic and metabolic patterns of these microorganisms according to vegetation type and seasonal changes. Therefore, to better elucidate the effects of the vegetation type and seasonal factors on the methanogenic community structure and metabolic patterns, we detected the characteristics of the soil methanogenic mcrA gene from three types of natural wetlands in different seasons in the Xiaoxing'an Mountain region, China. The results indicated that the distribution of Methanobacteriaceae (hydrogenotrophic methanogens) was higher in winter, while Methanosarcinaceae and Methanosaetaceae accounted for a higher proportion in summer. Hydrogenotrophic methanogenesis was the dominant trophic pattern in each wetland. The results of principal coordinate analysis and cluster analysis showed that the vegetation type considerably influenced the methanogenic community composition. The methanogenic community structure in the Betula platyphylla-Larix gmelinii wetland was relatively different from the structure of the other two wetland types. Indicator species analysis further demonstrated that the corresponding species of indicator operational taxonomic units from the Alnus sibirica wetland and the Betula ovalifolia wetland were similar. Network analysis showed that cooperative and competitive relationships exist both within and between the same or different trophic methanogens. The core methanogens with higher abundance in each wetland were conducive to the adaptation to environmental disturbances. This information is crucial for the assessment of metabolic patterns of soil methanogenic archaea and future fluxes in the wetlands of the Xiaoxing'an Mountain region given their vulnerability.
Collapse
Affiliation(s)
- Di Wu
- Key Laboratory of Saline‐Alkali Vegetation Ecology Restoration (Northeast Forestry University)Ministry of EducationHarbinChina
- College of Life ScienceNortheast Forestry UniversityHarbinChina
| | - Caihong Zhao
- College of Life ScienceNortheast Forestry UniversityHarbinChina
| | - Hui Bai
- Key Laboratory of Fast‐Growing Tree Cultivating of Heilongjiang ProvinceForestry Science Research Institute of Heilongjiang ProvinceHarbinChina
| | - Fujuan Feng
- College of Life ScienceNortheast Forestry UniversityHarbinChina
| | - Xin Sui
- Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold RegionSchool of Life SciencesHeilongjiang UniversityHarbinChina
| | - Guangyu Sun
- Key Laboratory of Saline‐Alkali Vegetation Ecology Restoration (Northeast Forestry University)Ministry of EducationHarbinChina
- College of Life ScienceNortheast Forestry UniversityHarbinChina
| |
Collapse
|