1
|
Xu J, Shi Z, Xu L, Zheng X, Zong Y, Luo G, Zhang C, Liu M, Xie L. Recovery capability of anaerobic digestion from ammonia stress: Metabolic activity, energy generation, and genome-centric metagenomics. BIORESOURCE TECHNOLOGY 2024; 394:130203. [PMID: 38109977 DOI: 10.1016/j.biortech.2023.130203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/06/2023] [Accepted: 12/11/2023] [Indexed: 12/20/2023]
Abstract
Excessive ammonia stresses anaerobic digestion (AD) significantly. Although there has been progress in understanding AD under ammonia exposure, investigations on AD liberated from ammonia exposure are limited. Here, the recovery capability of AD from ammonia stress was evaluated, by examining specific methanogenic activity, energy-conserving capability, microbial community succession, and metabolic pathway reconstruction. The findings demonstrated that ammonia stress relief resulted in < 50% methane recovery, with propionate conversion identified as the critical impediment to AD reactivation. Energy generation could not recovered either. Efforts to mitigate ammonia stress failed to restore acetoclastic methanogens, e.g., Methanothrix soehngenii, and proved futile in awakening propionate oxidizers, e.g., Desulfobulbus. Interestingly, a symbiotic metabolism emerged, prevailing in stress-relieved AD due to its energy-conserving advantage. This study underscores the importance of targeted interventions, including stimulating acetoclastic methanogenesis, propionate oxidation, and energy generation, as priorities for AD recovery following ammonia stress, rather than focusing solely on ammonia level management.
Collapse
Affiliation(s)
- Jun Xu
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
| | - Zhijian Shi
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, PR China; Shanghai Technical Service Platform for Pollution Control and Resource Utilization of Organic Wastes, Shanghai 200438, PR China
| | - Ling Xu
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
| | - Xiaomei Zheng
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
| | - Yang Zong
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
| | - Gang Luo
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, PR China; Shanghai Technical Service Platform for Pollution Control and Resource Utilization of Organic Wastes, Shanghai 200438, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China
| | - Chen Zhang
- Shanghai Municipal Engineering Design Institute (Group) Co., LTD., Shanghai 200092, PR China
| | - Mingxian Liu
- Shanghai Key Lab of Chemical Assessment and Sustainability, School of Chemical Science and Engineering, Tongji University, Shanghai 200092, PR China
| | - Li Xie
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China.
| |
Collapse
|
2
|
Guo W, Qiu W, Zhu J, Shih CJ, Wu YC, Lai SJ, Zhou J, Zhu Z, You YT, Li Y, Chen SC. The complete genome sequence of Kineothrix sp. MB12-C1, isolated from the feces of black soldier fly larvae. Microbiol Resour Announc 2024; 13:e0100523. [PMID: 38112478 DOI: 10.1128/mra.01005-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 11/18/2023] [Indexed: 12/21/2023] Open
Abstract
Here, we present the complete genome sequence of Kineothrix sp. MB12-C1 (= BCRC 81406), isolated from the feces of black soldier fly (Hermetia illucens) larvae. The genome of strain MB12-C1 was chosen for further species classification and comparative genomic analysis.
Collapse
Affiliation(s)
- Wenjie Guo
- College of Environment and Resources, Fujian Normal University , Fuzhou, Fujian, China
- College of Carbon Neutral and Modern Industry, Fujian Normal University , Fuzhou, Fujian, China
- School of Resources and Chemical Engineering, Sanming University , Sanming, Fujian, China
- Fujian Provincial Key Laboratory of Resources and Environmental Monitoring and Sustainable Management and Utilization, Sanming University , Sanming, Fujian, China
| | - Wanling Qiu
- School of Resources and Chemical Engineering, Sanming University , Sanming, Fujian, China
| | - Junyu Zhu
- College of Environment and Safety Engineering, Fuzhou University , Fuzhou, Fujian, China
| | - Chao-Jen Shih
- Bioresource Collection and Research Center, Food Industry Research and Development Institute , Hsinchu, Taiwan, China
| | - Yen-Chi Wu
- Bioresource Collection and Research Center, Food Industry Research and Development Institute , Hsinchu, Taiwan, China
| | - Shu-Jung Lai
- Graduate Institute of Biomedical Sciences, China Medical University , Taichung City, Taiwan, China
- Research Center for Cancer Biology, China Medical University , Taichung City, Taiwan, China
| | - Jiahui Zhou
- School of Resources and Chemical Engineering, Sanming University , Sanming, Fujian, China
| | - Zetao Zhu
- School of Resources and Chemical Engineering, Sanming University , Sanming, Fujian, China
| | - Yi-Ting You
- Department of Life Sciences, National Chung Hsing University , Taichung City, Taiwan, China
| | - Yin Li
- College of Environment and Resources, Fujian Normal University , Fuzhou, Fujian, China
- School of Resources and Chemical Engineering, Sanming University , Sanming, Fujian, China
- Fujian Provincial Key Laboratory of Resources and Environmental Monitoring and Sustainable Management and Utilization, Sanming University , Sanming, Fujian, China
| | - Sheng-Chung Chen
- School of Resources and Chemical Engineering, Sanming University , Sanming, Fujian, China
- Fujian Provincial Key Laboratory of Resources and Environmental Monitoring and Sustainable Management and Utilization, Sanming University , Sanming, Fujian, China
| |
Collapse
|
3
|
Qiu W, Zhu J, Shih CJ, Wu YC, Lai SJ, You YT, Wu CH, Liao CH, Lin H, Li S, Yan Y, Luo X, Li Y, Chen SC. Complete genome sequence of Proteiniborus sp. MB09-C3, isolated from the feces of the black soldier fly larvae. Microbiol Resour Announc 2023; 12:e0060823. [PMID: 37847038 PMCID: PMC10652958 DOI: 10.1128/mra.00608-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 09/12/2023] [Indexed: 10/18/2023] Open
Abstract
Here, we report the complete genome sequence of Proteiniborus sp. MB09-C3 (= BCRC 81405), isolated from the feces of black soldier fly (Hermetia illucens) larvae. The genome of strain MB09-C3 was selected for further species delineation and comparative genomic analysis.
Collapse
Grants
- CA220255, 202311311022 Sanming University (SMU)
- 2020J01379 Fujian Provincial Department of Science and Technology ()
- 2020Y0090, 2022Y0075, 2022L3027, 2018J01516, 2023J011018 Fujian Provincial Department of Science and Technology ()
- JAT190706, B201919 Department of Education, Fujian Province ()
- 2020-G-60, 2021-G-3, 2021-G-4 Sanming University (SMU)
- 20YG08, 20YG09, 22YG13 | Distinguished Young Scientific Research Talents Plan in Universities of Fujian Province
- MOST110-2320-B-039-058 Ministry of Science and Technology, Taiwan (MOST)
- Min Jiao Ke [2018] No. 47, KC180079, Yuanke [2022] No. 22 | Distinguished Young Scientific Research Talents Plan in Universities of Fujian Province
- Fujian Provincial Department of Science and Technology (福建省科技厅)
- Department of Education, Fujian Province (福建省教育厅)
- 福建省教育厅 | Distinguished Young Scientific Research Talents Plan in Universities of Fujian Province
Collapse
Affiliation(s)
- Wanling Qiu
- School of Resources and Chemical Engineering, Sanming University, Sanming City, Fujian, China
| | - Junyu Zhu
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou, Fujian, China
| | - Chao-Jen Shih
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan, Republic of China
| | - Yen-Chi Wu
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan, Republic of China
| | - Shu-Jung Lai
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung City, Taiwan, Republic of China
- Research Center for Cancer Biology, China Medical University, Taichung City, Taiwan, Republic of China
| | - Yi-Ting You
- Department of Life Sciences, National Chung Hsing University, Taichung City, Taiwan, Republic of China
| | - Chih-Hung Wu
- School of Resources and Chemical Engineering, Sanming University, Sanming City, Fujian, China
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou, Fujian, China
- Fujian Provincial Key Laboratory of Resources and Environmental Monitoring and Sustainable Management and Utilization, Sanming University, Sanming, Fujian, China
| | - Ching-Hua Liao
- School of Resources and Chemical Engineering, Sanming University, Sanming City, Fujian, China
- Fujian Provincial Key Laboratory of Resources and Environmental Monitoring and Sustainable Management and Utilization, Sanming University, Sanming, Fujian, China
| | - Haozhe Lin
- School of Resources and Chemical Engineering, Sanming University, Sanming City, Fujian, China
| | - Shilong Li
- School of Resources and Chemical Engineering, Sanming University, Sanming City, Fujian, China
| | - Yujia Yan
- School of Resources and Chemical Engineering, Sanming University, Sanming City, Fujian, China
| | - Xuming Luo
- School of Resources and Chemical Engineering, Sanming University, Sanming City, Fujian, China
| | - Yin Li
- School of Resources and Chemical Engineering, Sanming University, Sanming City, Fujian, China
- Fujian Provincial Key Laboratory of Resources and Environmental Monitoring and Sustainable Management and Utilization, Sanming University, Sanming, Fujian, China
| | - Sheng-Chung Chen
- School of Resources and Chemical Engineering, Sanming University, Sanming City, Fujian, China
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou, Fujian, China
- Fujian Provincial Key Laboratory of Resources and Environmental Monitoring and Sustainable Management and Utilization, Sanming University, Sanming, Fujian, China
| |
Collapse
|
4
|
Bojanova DP, De Anda VY, Haghnegahdar MA, Teske AP, Ash JL, Young ED, Baker BJ, LaRowe DE, Amend JP. Well-hidden methanogenesis in deep, organic-rich sediments of Guaymas Basin. THE ISME JOURNAL 2023; 17:1828-1838. [PMID: 37596411 PMCID: PMC10579335 DOI: 10.1038/s41396-023-01485-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 07/06/2023] [Accepted: 07/24/2023] [Indexed: 08/20/2023]
Abstract
Deep marine sediments (>1mbsf) harbor ~26% of microbial biomass and are the largest reservoir of methane on Earth. Yet, the deep subsurface biosphere and controls on its contribution to methane production remain underexplored. Here, we use a multidisciplinary approach to examine methanogenesis in sediments (down to 295 mbsf) from sites with varying degrees of thermal alteration (none, past, current) at Guaymas Basin (Gulf of California) for the first time. Traditional (13C/12C and D/H) and multiply substituted (13CH3D and 12CH2D2) methane isotope measurements reveal significant proportions of microbial methane at all sites, with the largest signal at the site with past alteration. With depth, relative microbial methane decreases at differing rates between sites. Gibbs energy calculations confirm methanogenesis is exergonic in Guaymas sediments, with methylotrophic pathways consistently yielding more energy than the canonical hydrogenotrophic and acetoclastic pathways. Yet, metagenomic sequencing and cultivation attempts indicate that methanogens are present in low abundance. We find only one methyl-coenzyme M (mcrA) sequence within the entire sequencing dataset. Also, we identify a wide diversity of methyltransferases (mtaB, mttB), but only a few sequences phylogenetically cluster with methylotrophic methanogens. Our results suggest that the microbial methane in the Guaymas subsurface was produced over geologic time by relatively small methanogen populations, which have been variably influenced by thermal sediment alteration. Higher resolution metagenomic sampling may clarify the modern methanogen community. This study highlights the importance of using a multidisciplinary approach to capture microbial influences in dynamic, deep subsurface settings like Guaymas Basin.
Collapse
Affiliation(s)
- Diana P Bojanova
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
| | - Valerie Y De Anda
- Department of Marine Science, University of Texas at Austin, Austin, TX, USA
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | | | - Andreas P Teske
- Department of Earth, Marine, and Environmental Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Jeanine L Ash
- Earth, Environmental, and Planetary Sciences, Rice University, Houston, TX, USA
| | - Edward D Young
- Earth, Planetary, and Space Sciences, University of California - Los Angeles, Los Angeles, CA, USA
| | - Brett J Baker
- Department of Marine Science, University of Texas at Austin, Austin, TX, USA
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Douglas E LaRowe
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
| | - Jan P Amend
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA.
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.
| |
Collapse
|
5
|
Complete Genome Sequence of Methanofollis aquaemaris BCRC 16166
T
, Isolated from a Marine Aquaculture Fishpond. Microbiol Resour Announc 2022; 11:e0074322. [PMID: 36094213 PMCID: PMC9583781 DOI: 10.1128/mra.00743-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The hydrogenotrophic methanogen Methanofollis aquaemaris BCRC 16166T (= N2F9704T = DSM 14661T) was isolated from a marine aquaculture fishpond near Wang-gong (Taiwan, Republic of China). The genome of strain BCRC 16166T was selected for sequencing in order to provide further information about the species delineation and its infected virus.
Collapse
|
6
|
Dengler L, Meier J, Grünberger F, Bellack A, Rachel R, Grohmann D, Huber H. Methanofollis propanolicus sp. nov., a novel archaeal isolate from a Costa Rican oil well that uses propanol for methane production. Arch Microbiol 2022; 204:554. [PMID: 35962867 PMCID: PMC9375759 DOI: 10.1007/s00203-022-03152-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/28/2022] [Accepted: 07/27/2022] [Indexed: 11/29/2022]
Abstract
A novel methanogenic strain, CaP3V-MF-L2AT, was isolated from an exploratory oil well from Cahuita National Park, Costa Rica. The cells were irregular cocci, 0.8–1.8 μm in diameter, stained Gram-negative and were motile. The strain utilized H2/CO2, formate and the primary and secondary alcohols 1-propanol and 2-propanol for methanogenesis, but not acetate, methanol, ethanol, 1-butanol or 2-butanol. Acetate was required as carbon source. The novel isolate grew at 25–40 °C, pH 6.0–7.5 and 0–2.5% (w/v) NaCl. 16S rRNA gene sequence analysis revealed that the strain is affiliated to the genus Methanofollis. It shows 98.8% sequence similarity to its closest relative Methanofollis ethanolicus. The G + C content is 60.1 mol%. Based on the data presented here type strain CaP3V-MF-L2AT (= DSM 113321T = JCM 39176T) represents a novel species, Methanofollis propanolicus sp. nov.
Collapse
Affiliation(s)
- Linda Dengler
- Institute of Microbiology and Archaea Centre, University of Regensburg, Universitaetsstrasse 31, 93053, Regensburg, Germany
| | - Julia Meier
- Institute of Microbiology and Archaea Centre, University of Regensburg, Universitaetsstrasse 31, 93053, Regensburg, Germany
| | - Felix Grünberger
- Institute of Microbiology and Archaea Centre, University of Regensburg, Universitaetsstrasse 31, 93053, Regensburg, Germany
| | - Annett Bellack
- Institute of Microbiology and Archaea Centre, University of Regensburg, Universitaetsstrasse 31, 93053, Regensburg, Germany
| | - Reinhard Rachel
- Electron Microscopy Center, University of Regensburg, Universitaetsstrasse 31, 93053, Regensburg, Germany
| | - Dina Grohmann
- Institute of Microbiology and Archaea Centre, University of Regensburg, Universitaetsstrasse 31, 93053, Regensburg, Germany
| | - Harald Huber
- Institute of Microbiology and Archaea Centre, University of Regensburg, Universitaetsstrasse 31, 93053, Regensburg, Germany.
| |
Collapse
|
7
|
Chen SC, Wu CH, You YT, Wu SY, Liao CH, Wang X, Li H, Guo Y, You J, Qiu W. Complete Genome Sequence of Methanofollis formosanus DSM 15483 T, Isolated from an Aquaculture Fish Pond. Microbiol Resour Announc 2022; 11:e0006822. [PMID: 35481773 PMCID: PMC9119062 DOI: 10.1128/mra.00068-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/14/2022] [Indexed: 11/20/2022] Open
Abstract
The hydrogenotrophic strain Methanofollis formosanus DSM 15483T (= ML15T = OCM 798T) was isolated from an aquaculture fish pond near Wang-gong, Taiwan. The genome of strain DSM 15483T was selected for sequencing in order to provide further information about the species delineation and its unique habitat.
Collapse
Affiliation(s)
- Sheng-Chung Chen
- School of Resources and Chemical Engineering, Sanming University, Sanming, Fujian, People’s Republic of China
- Fujian Provincial Key Laboratory of Resources and Environmental Monitoring and Sustainable Management and Utilization, Sanming University, Sanming, Fujian, People’s Republic of China
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan, Republic of China
| | - Chih-Hung Wu
- School of Resources and Chemical Engineering, Sanming University, Sanming, Fujian, People’s Republic of China
- Fujian Provincial Key Laboratory of Resources and Environmental Monitoring and Sustainable Management and Utilization, Sanming University, Sanming, Fujian, People’s Republic of China
- College of Environment & Safety Engineering, Fuzhou University, Fuzhou, Fujian, People’s Republic of China
| | - Yi-Ting You
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan, Republic of China
| | - Sue-Yao Wu
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan, Republic of China
| | - Ching-Hua Liao
- School of Resources and Chemical Engineering, Sanming University, Sanming, Fujian, People’s Republic of China
| | - Xiang Wang
- College of Environment & Safety Engineering, Fuzhou University, Fuzhou, Fujian, People’s Republic of China
| | - Hongduo Li
- College of Environment & Safety Engineering, Fuzhou University, Fuzhou, Fujian, People’s Republic of China
| | - Yun Guo
- College of Environment & Safety Engineering, Fuzhou University, Fuzhou, Fujian, People’s Republic of China
| | - Jinhui You
- School of Resources and Chemical Engineering, Sanming University, Sanming, Fujian, People’s Republic of China
| | - Wanling Qiu
- School of Resources and Chemical Engineering, Sanming University, Sanming, Fujian, People’s Republic of China
| |
Collapse
|