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Li Q, Deng H, He R, Hu S, Sun L, Li M, Wu QL, Zeng J. Effects of different emergent macrophytes on methane flux and rhizosphere microbial communities in wetlands. Sci Total Environ 2024; 932:172565. [PMID: 38642750 DOI: 10.1016/j.scitotenv.2024.172565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 03/02/2024] [Accepted: 04/16/2024] [Indexed: 04/22/2024]
Abstract
Emergent macrophytes are of great importance for the structure and functioning of wetland ecosystems and play a significant role in environmental improvement, element cycling, and greenhouse gas (GHG) emissions. However, our understanding of how GHG fluxes differ among macrophyte species and its links with the microbial communities remain limited. In this study, we investigated the rhizosphere microbial communities (including total bacteria, methanotrophs, and methanogens) and the GHG fluxes associated with four emergent macrophytes-Phragmites australis, Thalia dealbata, Pontederia cordata, and Zizania latifolia-collected from Xuanwu Lake wetland, China. We observed the highest CH4 flux (FCH4) (9.35 ± 2.52 mg·m-2·h-1) from Z. latifolia zone, followed by P. australis, P. cordata, and T. dealbata zones (5.38 ± 1.63, 2.38 ± 2.91, and 2.02 ± 0.69 mg·m-2·h-1, respectively). Methanogenesis was methylotrophic at all sites, as the 13C-CH4 values were higher than -64 ‰ and the fractionation coefficients were lower than 1.055. We found a positive linear relationship between FCH4 and the methanogen community, in particular the relative abundances of Methanobacterium and Methanosarcina, indicating that the variations in FCH4 among the studied macrophyte-dominated zones might be attributed to the differences in rhizosphere microbial communities. The methane emissions in various macrophyte zones might be due to the higher capacity of methanogenesis compared to methane oxidation which was inhibited by nutrient-rich sediments. Our findings provide insights for selecting specific emergent macrophytes characterized by low FCH4 in wetland ecological restoration.
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Affiliation(s)
- Qisheng Li
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongyang Deng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rujia He
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210098, China
| | - Siwen Hu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210098, China
| | - Lijie Sun
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210098, China
| | - Mengyuan Li
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing 210044, China
| | - Qinglong L Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing 100039, China; Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Jin Zeng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing 100039, China; Poyang Lake Wetland Research Station, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Jiujiang 332899, China.
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Mahieux M, Richard C, Aemig Q, Delgenès JP, Juge M, Trably E, Escudié R. Archaeal community composition as key driver of H2 consumption rates at the start-up of the biomethanation process. Sci Total Environ 2024; 931:172922. [PMID: 38701927 DOI: 10.1016/j.scitotenv.2024.172922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/03/2024] [Accepted: 04/29/2024] [Indexed: 05/05/2024]
Abstract
The performance of hydrogen consumption by various inocula derived from mesophilic anaerobic digestion plants was evaluated under ex situ biomethanation. A panel of 11 mesophilic inocula was operated at a concentration of 15 gVS.L-1 at a temperature of 35 °C in batch system with two successive injections of H2:CO2 (4:1 mol:mol). Hydrogen consumption and methane production rates were monitored from 44 h to 72 h. Hydrogen consumption kinetics varies significantly based on the inoculum origin, with no accumulation of volatile fatty acids. Microbial community analyses revealed that microbial indicators such as the increase in Methanosarcina sp. abundance and the increase of the Archaea/Bacteria ratio were associated to high initial hydrogen consumption rates. The improvement in the hydrogen consumption rate between the two injections was correlated with the enrichment in hydrogenotrophic methanogens. This work provides new insights into the early response of microbial communities to hydrogen injection and on the microbial structures that may favor their adaptation to the biomethanation process.
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Affiliation(s)
- M Mahieux
- INRAE, Univ. Montpellier, LBE, 102 Avenue des étangs, F-11100 Narbonne, France; ENGIE, Lab CRIGEN, 4 Rue Joséphine Baker, 93240 Stains, France
| | - C Richard
- ENGIE, Lab CRIGEN, 4 Rue Joséphine Baker, 93240 Stains, France
| | - Q Aemig
- ENGIE, Lab CRIGEN, 4 Rue Joséphine Baker, 93240 Stains, France
| | - J-P Delgenès
- INRAE, Univ. Montpellier, LBE, 102 Avenue des étangs, F-11100 Narbonne, France
| | - M Juge
- ENGIE, Lab CRIGEN, 4 Rue Joséphine Baker, 93240 Stains, France
| | - E Trably
- INRAE, Univ. Montpellier, LBE, 102 Avenue des étangs, F-11100 Narbonne, France
| | - R Escudié
- INRAE, Univ. Montpellier, LBE, 102 Avenue des étangs, F-11100 Narbonne, France.
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Wang Q, Zheng G, Ni L, Wang H, Li W, Guo P, Wang Y, Zheng D, Wu J, Zhang D. Colonization characteristics and dynamic transition of archaea communities on polyethylene and polypropylene microplastics in the sediments of mangrove ecosystems. J Hazard Mater 2024; 471:134343. [PMID: 38640671 DOI: 10.1016/j.jhazmat.2024.134343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 02/28/2024] [Accepted: 04/16/2024] [Indexed: 04/21/2024]
Abstract
Microplastics are a growing concern in mangrove ecosystems; however, their effects on archaeal communities and related ecological processes remain unclear. We conducted in situ biofilm-enrichment experiments to investigate the ecological influence of polyethylene (PE) and polypropylene microplastics on archaeal communities in the sediments of mangrove ecosystems. The archaeal community present on microplastics was distinct from that of the surrounding sediments at an early stage but became increasingly similar over time. Bathyarchaeota, Thaumarchaeota, Euryarchaeota, and Asgardaeota were the most abundant phyla. Methanolobus, an archaeal biomarker, was enriched in PE biofilms, and significantly controlled by homogeneous selection in the plastisphere, indicating an increased potential risk of methane emission. The dominant archaeal assembly process in the sediments was deterministic (58.85%-70.47%), while that of the PE biofilm changed from stochastic to deterministic during the experiment. The network of PE plastispheres showed less complexity and competitive links, and higher modularity and stability than that of sediments. Functional prediction showed an increase in aerobic ammonia oxidation during the experiment, whereas methanogenesis and chemoheterotrophy were significantly higher in the plastisphere. This study provides novel insights into the impact of microplastic pollution on archaeal communities and their mediating ecological functions in mangrove ecosystems.
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Affiliation(s)
- Qiong Wang
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China; Donghai Laboratory, Zhoushan 316021, Zhejiang, China; Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan 430064, Hubei, China
| | - Gang Zheng
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China; Xianghu Laboratory, Hangzhou 311231, Zhejiang, China
| | - Lingfang Ni
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
| | - Heng Wang
- Key Laboratory of Health Risk Factors for Seafood of Zhejiang Province, Zhoushan 316021, Zhejiang, China
| | - Weiye Li
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
| | - Peng Guo
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan 430064, Hubei, China
| | - Yi Wang
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan 430064, Hubei, China
| | - Daoqiong Zheng
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China; Donghai Laboratory, Zhoushan 316021, Zhejiang, China
| | - Jiaping Wu
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
| | - Dongdong Zhang
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China; Donghai Laboratory, Zhoushan 316021, Zhejiang, China; Key Laboratory of Health Risk Factors for Seafood of Zhejiang Province, Zhoushan 316021, Zhejiang, China.
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Yang R, Ji M, Zhang X, He F, Yu Z, Zeng J, Zhao D. Methane emissions and microbial communities under differing flooding conditions and seasons in littoral wetlands of urban lake. Environ Res 2024; 250:118390. [PMID: 38331139 DOI: 10.1016/j.envres.2024.118390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/10/2024]
Abstract
Wetlands are the largest natural sources of methane (CH4) emissions worldwide. Littoral wetlands of urban lakes represent an ecotone between aquatic and terrestrial ecosystems and are strongly influenced by water levels, environmental conditions, and anthropogenic activities. Despite these littoral zones being potential "hotspots" of CH4 emissions, the status of CH4 emissions therein and the role of physicochemical properties and microbial communities regulating these emissions remain unclear. This study compared the CH4 fluxes, physicochemical properties, and CH4-cycling microbial communities (methanogens and methanotrophs) of three zones (a non-flooded supralittoral zone, a semi-flooded eulittoral zone, and a flooded infralittoral zone) in the littoral wetlands of Lake Pipa, Jiangsu Province, China, for two seasons (summer and winter). The eulittoral zone was a CH4 source (median: 11.49 and 0.02 mg m-2 h-1 in summer and winter, respectively), whereas the supralittoral zone acted as a CH4 sink (median: -0.78 and -0.09 mg m-2 h-1 in summer and winter, respectively). The infralittoral zone shifted from CH4 sink to source between the summer (median: -10.65 mg m-2 h-1) and winter (median: 0.11 mg m-2 h-1). The analysis of the functional genes of methanogenesis (mcrA) and methanotrophy (pmoA) and path analysis showed that CH4 fluxes were strongly regulated by biotic factors (abundance of the mcrA gene and alpha diversity of CH4-cycling microbial communities) and abiotic factors (ammonia nitrogen, moisture, and soil organic carbon). In particular, biotic factors had a major influence on the variation in the CH4 flux, whereas abiotic factors had a minor influence. Our findings provide novel insights into the spatial and seasonal variations in CH4-cycling microbial communities and identify the key factors influencing CH4 fluxes in littoral wetlands. These results are important for managing nutrient inputs and regulating the hydrological regimes of urban lakes.
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Affiliation(s)
- Runhan Yang
- Joint International Research Laboratory of Global Change and Water Cycle, the National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing, 210098, China
| | - Mengting Ji
- Joint International Research Laboratory of Global Change and Water Cycle, the National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing, 210098, China
| | - Xiaomin Zhang
- Joint International Research Laboratory of Global Change and Water Cycle, the National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing, 210098, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Fei He
- Joint International Research Laboratory of Global Change and Water Cycle, the National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing, 210098, China; Ministry of Ecology and Environment, Nanjing Institute of Environment Sciences, Nanjing, 210042, China
| | - Zhongbo Yu
- Joint International Research Laboratory of Global Change and Water Cycle, the National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing, 210098, China
| | - Jin Zeng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China; Poyang Lake Wetland Research Station, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Jiujiang, 332899, China
| | - Dayong Zhao
- Joint International Research Laboratory of Global Change and Water Cycle, the National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing, 210098, China.
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Cena JAD, Belmok A, Kyaw CM, Dame-Teixeira N. The Archaea domain: Exploring historical and contemporary perspectives with in silico primer coverage analysis for future research in Dentistry. Arch Oral Biol 2024; 161:105936. [PMID: 38422909 DOI: 10.1016/j.archoralbio.2024.105936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 02/07/2024] [Accepted: 02/21/2024] [Indexed: 03/02/2024]
Abstract
OBJECTIVE The complete picture of how the human microbiome interacts with its host is still largely unknown, particularly concerning microorganisms beyond bacteria. Although existing in very low abundance and not directly linked to causing diseases, archaea have been detected in various sites of the human body, including the gastrointestinal tract, oral cavity, skin, eyes, respiratory and urinary systems. But what exactly are these microorganisms? In the early 1990 s, archaea were classified as a distinct domain of life, sharing a more recent common ancestor with eukaryotes than with bacteria. While archaea's presence and potential significance in Dentistry remain under-recognized, there are concerns that they may contribute to oral dysbiosis. However, detecting archaea in oral samples presents challenges, including difficulties in culturing, the selection of DNA extraction methods, primer design, bioinformatic analysis, and databases. DESIGN This is a comprehensive review on the oral archaeome, presenting an in-depth in silico analysis of various primers commonly used for detecting archaea in human body sites. RESULTS Among several primer pairs used for detecting archaea in human samples across the literature, only one specifically designed for detecting methanogenic archaea in stool samples, exhibited exceptional coverage levels for the domain and various archaea phyla. CONCLUSIONS Our in silico analysis underscores the need for designing new primers targeting not only methanogenic archaea but also nanoarchaeal and thaumarchaeota groups to gain a comprehensive understanding of the archaeal oral community. By doing so, researchers can pave the way for further advancements in the field of oral archaeome research.
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Affiliation(s)
| | - Aline Belmok
- Institute of Biology, University of Brasilia, Brazil
| | | | - Naile Dame-Teixeira
- Department of Dentistry, School of Health Sciences, University of Brasilia, Brazil; Division of Oral Biology, School of Dentistry, University of Leeds, UK.
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Chen T, Zhang L, Guo W, Zhang W, Sajjad W, Ilahi N, Usman M, Faisal S, Bahadur A. Temperature drives microbial communities in anaerobic digestion during biogas production from food waste. Environ Sci Pollut Res Int 2024:10.1007/s11356-024-32698-z. [PMID: 38436844 DOI: 10.1007/s11356-024-32698-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 02/25/2024] [Indexed: 03/05/2024]
Abstract
Resource depletion and climate changes due to human activities and excessive burning of fossil fuels are the driving forces to explore alternatives clean energy resources. The objective of this study was to investigate the potential of potato peel waste (PPW) at various temperatures T15 (15 °C), T25 (25 °C), and T35 (35 °C) in anaerobic digestion (AD) for biogas generation. The highest biogas and CH4 production (117 mL VS-g and 74 mL VS-g) was observed by applying 35 °C (T35) as compared with T25 (65 mL VS-g and 22 mL VS-g) on day 6. Changes in microbial diversity associated with different temperatures were also explored. The Shannon index of bacterial community was not significantly affected, while there was a positive correlation of archaeal community with the applied temperatures. The bacterial phyla Firmicutes were strongly affected by T35 (39%), whereas Lactobacillus was the dominant genera at T15 (27%). Methanobacterium and Methanosarcina, as archaeal genera, dominated in T35 temperature reactors. In brief, at T35, Proteiniphilum and Methanosarcina were positively correlated with volatile fatty acids (VFAs) concentration. Spearman correlation revealed dynamic interspecies interactions among bacterial and archaeal genera; facilitating the AD system. This study revealed that temperature variations can enhance the microbial community of the AD system, leading to increased biogas production. It is recommended for optimizing the AD of food wastes.
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Affiliation(s)
- Tuo Chen
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Lu Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Wei Guo
- Lanzhou Xinrong Environmental Energy Engineering Technology Co., Ltd, Lanzhou, China
| | - Wei Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Wasim Sajjad
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Nikhat Ilahi
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Muhammad Usman
- State Key Laboratory of Grassland Agroecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, Gansu, China
| | - Shah Faisal
- Department of Environmental Engineering, School of Architecture and Civil Engineering, Chengdu University, Chengdu, 610106, People's Republic of China
| | - Ali Bahadur
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.
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Fang S, Geng Y, Wang L, Zeng J, Zhang S, Wu Y, Lin X. Coupling between 2, 2', 4, 4'-tetrabromodiphenyl ether (BDE-47) debromination and methanogenesis in anaerobic soil microcosms. Sci Total Environ 2024; 914:169831. [PMID: 38185166 DOI: 10.1016/j.scitotenv.2023.169831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/15/2023] [Accepted: 12/30/2023] [Indexed: 01/09/2024]
Abstract
Polybrominated diphenyl ethers (PBDEs) are persistent pollutants that may undergo microbial-mediated debromination in anoxic environments, where diverse anaerobic microbes such as methanogenic archaea co-exist. However, current understanding of the relations between PBDE pollution and methanogenic process is far from complete. To address this knowledge gap, a series of anaerobic soil microcosms were established. BDE-47 (2, 2', 4, 4'-tetrabromodiphenyl ether) was selected as a model pollutant, and electron donors were supplied to stimulate the activity of anaerobes. Debromination and methane production were monitored during the 12 weeks incubation, while obligate organohalide-respiring bacteria (OHRBs), methanogenic, and the total bacterial communities were examined at week 7 and 12. The results demonstrated slow debromination of BDE-47 in all microcosms, with considerable growth of Dehalococcoides and Dehalogenimonas over the incubation observed in most BDE-47 spiked treatments. In addition, the accumulation of intermediate metabolites positively correlated with the abundance of Dehalogenimonas at week 7, suggesting potential role of these OHRBs in debromination. Methanosarcinaceae were identified as the primary methanogenic archaea, and their abundance were correlated with the production of debrominated metabolites at week 7. Furthermore, it was observed for the first time that BDE-47 considerably enhanced methane production and increased the abundance of mcrA genes, highlighting the potential effects of PBDE pollution on climate change. This might be related to the inhibition of reductive N- and S-transforming microbes, as revealed by the quantitative microbial element cycling (QMEC) analysis. Overall, our findings shed light on the intricate interactions between PBDE and methanogenic processes, and contribute to a better understanding of the environmental fate and ecological implication of PBDE under anaerobic settings.
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Affiliation(s)
- Shasha Fang
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450046, China; Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yue Geng
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Lu Wang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Jun Zeng
- Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Shimin Zhang
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450046, China.
| | - Yucheng Wu
- Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Xiangui Lin
- Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
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Ma S, Yang M, Chen X, Wang F, Xia Y, Xu P, Ma J, Luo C, Zhou C, Xu T, Zhu Y. Microbial methanogenesis in aerobic water: A key driver of surface methane enrichment in a deep reservoir. J Environ Manage 2024; 355:120481. [PMID: 38447515 DOI: 10.1016/j.jenvman.2024.120481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/07/2024] [Accepted: 02/20/2024] [Indexed: 03/08/2024]
Abstract
Significant amounts of the greenhouse gas methane (CH4) are released into the atmosphere worldwide via freshwater sources. The surface methane maximum (SMM), where methane is supersaturated in surface water, has been observed in aquatic systems and contributes significantly to emissions. However, little is known about the temporal and spatial variability of SMM or the mechanisms underlying its development in artificial reservoirs. Here, the community composition of methanogens as major methane producers in the water column and the mcrA gene was investigated, and the cause of surface methane supersaturation was analyzed. In accordance with the findings, elevated methane concentration of SMM in the transition zone, with an annually methane emission flux 2.47 times higher than the reservoir average on a large and deep reservoir. In the transition zone, methanogens with mcrA gene abundances ranging from 0.5 × 103-1.45 × 104 copies/L were found. Methanobacterium, Methanoseata and Methanosarcina were the three dominate methanogens, using both acetic acid and H2/CO2 pathways. In summary, this study contributes to our comprehension of CH4 fluxes and their role in the atmospheric methane budget. Moreover, it offers biological proof of methane generation, which could aid in understanding the role of microbial methanogenesis in aerobic water.
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Affiliation(s)
- Shuwen Ma
- School of Environmental and Chemical Engineering, Shanghai University, 99 Shangda Road, Shanghai, 200444, China
| | - Meilin Yang
- School of Environmental and Chemical Engineering, Shanghai University, 99 Shangda Road, Shanghai, 200444, China
| | - Xueping Chen
- School of Environmental and Chemical Engineering, Shanghai University, 99 Shangda Road, Shanghai, 200444, China.
| | - Fushun Wang
- School of Environmental and Chemical Engineering, Shanghai University, 99 Shangda Road, Shanghai, 200444, China
| | - Yue Xia
- School of Environmental and Chemical Engineering, Shanghai University, 99 Shangda Road, Shanghai, 200444, China
| | - Peifan Xu
- School of Environmental and Chemical Engineering, Shanghai University, 99 Shangda Road, Shanghai, 200444, China
| | - Jing Ma
- School of Environmental and Chemical Engineering, Shanghai University, 99 Shangda Road, Shanghai, 200444, China
| | - Chai Luo
- School of Environmental and Chemical Engineering, Shanghai University, 99 Shangda Road, Shanghai, 200444, China
| | - Canran Zhou
- School of Environmental and Chemical Engineering, Shanghai University, 99 Shangda Road, Shanghai, 200444, China
| | - Tian Xu
- School of Environmental and Chemical Engineering, Shanghai University, 99 Shangda Road, Shanghai, 200444, China
| | - Yongguan Zhu
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China.
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Ruiz-Bastidas RC, Ochoa-Durán C, Sanabria J, Cadavid-Rodríguez LS. Effect of Ecuadorian natural zeolite on the performance of anaerobic digestion of swine waste in semicontinuous regime. Chemosphere 2024; 352:141517. [PMID: 38387656 DOI: 10.1016/j.chemosphere.2024.141517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 01/29/2024] [Accepted: 02/20/2024] [Indexed: 02/24/2024]
Abstract
This study explores the potential of zeolite as an amendment to mitigate ammonium inhibition in the anaerobic digestion of swine waste. Two 50 L reactors, one with and one without zeolite amendment were operated at an OLR of 3.0 g VS L-1d-1 for 130 days, and fed with swine waste from a full-scale pig farm. Under these conditions, zeolite doses of 4 g L-1 allowed total ammonia nitrogen (TAN) concentrations to be kept below 1000 mgNH3-N L-1. The zeolite-amended reactor not only showed an average increase of 8% in methane production under stable conditions but also exhibited 34% reduction in H2S concentrations in the biogas, compared to the reactor without zeolite. The community of archaea originating from the inoculum was conserved in the reactor with zeolite amendment, particularly the acetoclastic methanogens of the genus Methanosaeta. On the other hand, in the reactor without zeolite addition, the microbial community went from being dominated by the acetoclastic methanogen Methanosaeta to having a high relative abundance of hydrogenotrophic methanogens. The zeolite addition also favoured the reactor stability, prevented foaming, and produced an enriched natural zeolite with N, P and K. However, additional studies on the potential of enriched zeolite as a fertilizer are required, which could make the use of zeolite in Anaerobic Digestion of swine waste not only energetically favourable but also economically feasible.
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Affiliation(s)
- Rosa Cecilia Ruiz-Bastidas
- Universidad Nacional de Colombia - Sede Medellín, Facultad de Ciencias, Cra. 65 #59a-110, Medellín, 050034, Colombia.
| | - Camilo Ochoa-Durán
- Universidad Nacional de Colombia - Sede Palmira, Facultad de Ingeniería y Administración, Departamento de Ingeniería, Cra. 32 No 12-00, Palmira, 763533, Colombia
| | - Janeth Sanabria
- Universidad del Valle, Microbiology and Environmental Biotechnology Laboratory, Cali, 760042, Colombia
| | - Luz Stella Cadavid-Rodríguez
- Universidad Nacional de Colombia - Sede Palmira, Facultad de Ingeniería y Administración, Departamento de Ingeniería, Cra. 32 No 12-00, Palmira, 763533, Colombia.
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10
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Su Y, Liu W, Rahaman MH, Chen Z, Zhai J. Methane emission from water level fluctuation zone of the Three Gorges Reservoir: Seasonal variation and microbial mechanism. Sci Total Environ 2024; 912:168935. [PMID: 38042199 DOI: 10.1016/j.scitotenv.2023.168935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 11/22/2023] [Accepted: 11/25/2023] [Indexed: 12/04/2023]
Abstract
Periodic and significant water level fluctuations within the Three Gorges Reservoir (TGR) create a complex water level fluctuation zone (WLFZ) that can significantly influence greenhouse gas emissions. However, the scarcity of comprehensive studies investigating long-term monitoring and analysis of CH4 flux patterns and underlying mechanisms concerning water level variations, environmental characteristics, and microbial communities has limited our understanding. This study conducted a four-year monitoring campaign to examine in situ CH4 emissions from three representative sampling sites. Results indicated that the CH4 flux remained relatively stable at lower water levels, specifically at the control site (S1). However, water level fluctuations significantly influenced CH4 emissions at the sampling sites situated within the WLFZ. Notably, the highest CH4 flux of 0.252 ± 0.089 mg/(m2·h) was observed during the drying period (June to August), while the lowest CH4 flux of 0.048 ± 0.026 mg/(m2·h) was recorded during the flooding period. Moreover, CH4 emissions through the water-air interface surpassed those through the soil-air interface. The CH4 flux positively correlated with organic carbon, temperature, and soil moisture. The relative abundance of methane metabolism microorganisms peaked during the drying period and decreased during the impounding and flooding periods. The primary methanogenesis pathway was hydrogenotrophic, whereas methanotrophic processes were mainly aerobic, with Ca. Methylomirabilis governing the anaerobic methanotrophic process. Overall, the current findings serve as crucial theoretical references for understanding CH4 emissions and carbon metabolism processes within WLFZ environments.
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Affiliation(s)
- Yiming Su
- Key Laboratory of Three Gorges Reservoir Region's Eco-environment, Chongqing University, Chongqing 400045, China
| | - Wenbo Liu
- Institute for Smart City of Chongqing University in Liyang, Chongqing University, Jiangsu 213300, China
| | - Md Hasibur Rahaman
- Institute for Smart City of Chongqing University in Liyang, Chongqing University, Jiangsu 213300, China
| | - Zhongbing Chen
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 16500 Praha, Suchdol, Czech Republic
| | - Jun Zhai
- Key Laboratory of Three Gorges Reservoir Region's Eco-environment, Chongqing University, Chongqing 400045, China; Institute for Smart City of Chongqing University in Liyang, Chongqing University, Jiangsu 213300, China.
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11
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Ouyang C, Qin Y, Fang P, Liang Y. Methane flux at the water-gas interface is influenced by complex interactions among phytoplankton, phosphorus inputs and methane-functional bacteria: A microcosm systems study. Sci Total Environ 2024; 912:169373. [PMID: 38104802 DOI: 10.1016/j.scitotenv.2023.169373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/16/2023] [Accepted: 12/12/2023] [Indexed: 12/19/2023]
Abstract
Phytoplankton affect carbon cycling and emissions in eutrophic reservoirs dramatically, but our knowledge about carbon emissions response to phytoplankton bloom and phosphorus enrichment is rather limited. Here we performed a microcosm experiment with five treatments to investigate how phytoplankton blooms and phosphorus addition will impact the carbon emissions and the methane-functional bacterial community. During the 43-day incubation, the CH4 and CO2 flux at the water-air interface in the five water columns fluctuated between 7.536 and 16.689 μmol and between 2788.501 and 4142.726 μmol, respectively. The flux of CH4 and CO2 during phytoplankton decay was 1.542 to 10.397 times and 4.203 to 8.622 times higher, respectively, compared to that during phytoplankton growth. Furthermore, exogenous phosphorus increases bloom biomass of phytoplankton and subsequent CH4 production, even with low nitrogen concentrations. The addition of 1 mg KH2PO4 resulted in a conservative increase of 0.0715 μmol in CH4 emission and 11.911 μmol in CO2 emission in the water column, respectively, compared to the in-situ water column. High throughput sequencing determined that hydrogenotrophic Methanoregula dominated methanogens (MPB) and Methylocystaceae dominated methanotrophs (MOB) in the sediment. Phosphorus inhibited the relative abundance of Methanoregula after incubation, resulting in a significant decrease. Real-time quantitative polymerase chain reaction indicated that the absolute abundance of MPB and MOB (i.e., the mcrA gene and the pmoA gene) in the sediments ranged from 5.1354E+06 to 6.3176E+07 copies·g-1 and 1.1656E+06 to 9.5056E+06 copies·g-1, respectively. The mcrA gene showed a preference for sediments with high organic carbon content. The effect of eutrophication on CH4 emissions is closely related to nutrient load and distinct niche of methane-functional bacteria.
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Affiliation(s)
- Changyue Ouyang
- School of River and Ocean Engineering, Chongqing Jiaotong University, Chongqing 400074, China; Key Laboratory of Hydraulic and Waterway Engineering of the Ministry of Education, Chongqing Jiaotong University, 400074 Chongqing, China
| | - Yu Qin
- School of River and Ocean Engineering, Chongqing Jiaotong University, Chongqing 400074, China; Key Laboratory of Hydraulic and Waterway Engineering of the Ministry of Education, Chongqing Jiaotong University, 400074 Chongqing, China.
| | - Peng Fang
- Chongqing Aerospace Rocket Electronic Technology Co., Ltd, Chongqing 400039, China
| | - Yue Liang
- School of River and Ocean Engineering, Chongqing Jiaotong University, Chongqing 400074, China
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12
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Bouzid F, Gtif I, Charfeddine S, Abid L, Kharrat N. Polyphasic molecular approach to the characterization of methanogens in the saliva of Tunisian adults. Anaerobe 2024; 85:102820. [PMID: 38309618 DOI: 10.1016/j.anaerobe.2024.102820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 11/22/2023] [Accepted: 01/18/2024] [Indexed: 02/05/2024]
Abstract
OBJECTIVES Methanogenic archaea are a minor component of human oral microbiota. Due to their relatively low abundance, the detection of these neglected microorganisms is challenging. This study concerns the presence of methanogens in salivary samples collected from Tunisian adults to evaluate their prevalence and burden using a polyphasic molecular approach. METHODS A total of 43 saliva samples were included. Metagenomic and standard 16S rRNA sequencing were performed as an initial screening to detect the presence of methanogens in the oral microbiota of Tunisian adults. Further investigations were performed using specific quantitative real-time PCR targeting Methanobrevibacter oralis and Methanobrevibacter smithii. RESULTS Methanobrevibacter was detected in 5/43 (11.62 %) saliva samples after metagenomic 16S rRNA data analysis. The presence of M. oralis was confirmed in 6/43 samples by standard 16S rRNA sequencing. Using real-time PCR, methanogens were detected in 35/43 (81.39 %) samples, including 62.79 % positive for M. oralis and 76.74 % positive for M. smithii. These findings reflect the high prevalence of both methanogens, revealed by the high sensitivity of the real-time PCR approach. Interestingly, we also noted a significant statistical association between the detection of M. smithii and poor adherence to a Mediterranean diet, indicating the impact of diet on M. smithii prevalence. CONCLUSION Our study showed the presence of methanogens in the oral microbiota of Tunisian adults with an unprecedented relatively high prevalence. Choice of methodology is also central to picturing the real prevalence and diversity of such minor taxa in the oral microbiota.
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Affiliation(s)
- Fériel Bouzid
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia.
| | - Imen Gtif
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Salma Charfeddine
- Department of Cardiology, Hédi Chaker University Hospital, Faculty of Medicine of Sfax, University of Sfax, Tunisia
| | - Leila Abid
- Department of Cardiology, Hédi Chaker University Hospital, Faculty of Medicine of Sfax, University of Sfax, Tunisia
| | - Najla Kharrat
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
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Du B, Wang Z, Lens PNL, Zhan X, Wu G. New insights into syntrophic ethanol oxidation: Effects of operational modes and solids retention times. Environ Res 2024; 241:117607. [PMID: 37939810 DOI: 10.1016/j.envres.2023.117607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/21/2023] [Accepted: 11/04/2023] [Indexed: 11/10/2023]
Abstract
Anaerobic ethanol oxidation relies on syntrophic interactions among functional microorganisms to become thermodynamically feasible. Different operational modes (sequencing batch reactors, SBRs, and continuous flow reactors, CFRs) and solids retention times (SRT, 25 days and 10 days) were employed in four ethanol-fed reactors, named as SBR25d, SBR10d, CFR25d, and CFR10d, respectively. System performance, syntrophic relationships, microbial communities, and metabolic pathways were examined. During the long-term operation, 2002.7 ± 56.0 mg COD/L acetate was accumulated in CFR10d due to the washout of acetotrophic methanogens. Microorganisms with high half-saturation constants were enriched in reactors of 25-day SRT. Moreover, ethanol oxidizing bacteria and acetotrophic methanogens with high half-saturation constants could be acclimated in SBRs. In SBRs, Syner-01 and Methanothrix dominated, and the low SRT of 10 days increased the relative abundance of Geobacter to 38.0%. In CFRs, the low SRT of 10 days resulted in an increase of Desulfovibrio among syntrophic bacteria, and CFR10d could be employed in enriching hydrogenotrophic methanogens like Methanobrevibacter.
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Affiliation(s)
- Bang Du
- Civil Engineering, School of Engineering, College of Science and Engineering, University of Galway, Galway, H91 TK33, Ireland
| | - Zhongzhong Wang
- Civil Engineering, School of Engineering, College of Science and Engineering, University of Galway, Galway, H91 TK33, Ireland
| | - Piet N L Lens
- Microbiology, School of Biological and Chemical Sciences, College of Science and Engineering, University of Galway, Galway, H91 TK33, Ireland
| | - Xinmin Zhan
- Civil Engineering, School of Engineering, College of Science and Engineering, University of Galway, Galway, H91 TK33, Ireland
| | - Guangxue Wu
- Civil Engineering, School of Engineering, College of Science and Engineering, University of Galway, Galway, H91 TK33, Ireland.
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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. Sci Total Environ 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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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15
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Diaz GR, Gaire TN, Ferm P, Case L, Caixeta LS, Goldsmith TJ, Armstrong J, Noyes NR. Effect of castration timing and weaning strategy on the taxonomic and functional profile of ruminal bacteria and archaea of beef calves. Anim Microbiome 2023; 5:61. [PMID: 38041127 PMCID: PMC10691087 DOI: 10.1186/s42523-023-00284-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 11/28/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND Beef cattle experience several management challenges across their lifecycle. Castration and weaning, two major interventions in the early life of beef cattle, can have a substantial impact on animal performance. Despite the key role of the rumen microbiome on productive traits of beef cattle, the effect of castration timing and weaning strategy on this microbial community has not been formally described. We assessed the effect of four castration time windows (at birth, turnout, pre-weaning and weaning) and two weaning strategies (fence-line and truck transportation) on the rumen microbiome in a randomized controlled study with 32 male calves across 3 collection days (i.e., time points). Ruminal fluid samples were submitted to shotgun metagenomic sequencing and changes in the taxonomic (microbiota) and functional profile (metagenome) of the rumen microbiome were described. RESULTS Using a comprehensive yet stringent taxonomic classification approach, we identified 10,238 unique taxa classified under 40 bacterial and 7 archaeal phyla across all samples. Castration timing had a limited long-term impact on the rumen microbiota and was not associated with changes in alpha and beta diversity. The interaction of collection day and weaning strategy was associated with changes in the rumen microbiota, which experienced a significant decrease in alpha diversity and shifts in beta diversity within 48 h post-weaning, especially in calves abruptly weaned by truck transportation. Calves weaned using a fence-line weaning strategy had lower relative abundance of Bacteroides, Lachnospira, Fibrobacter and Ruminococcus genera compared to calves weaned by truck transportation. Some genes involved in the hydrogenotrophic methanogenesis pathway (fwdB and fwdF) had higher relative abundance in fence-line-weaned calves post-weaning. The antimicrobial resistance gene tetW consistently represented more than 50% of the resistome across time, weaning and castration groups, without significant changes in relative abundance. CONCLUSIONS Within the context of this study, castration timing had limited long-term effects on the rumen microbiota, while weaning strategy had short-term effects on the rumen microbiota and methane-associated metagenome, but not on the rumen resistome.
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Affiliation(s)
- Gerardo R Diaz
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Tara N Gaire
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Peter Ferm
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Lacey Case
- North Central Research and Outreach Center, Department of Animal Science, University of Minnesota, St. Paul, MN, 55108, USA
| | - Luciano S Caixeta
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Timothy J Goldsmith
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Joe Armstrong
- Agricultural and Natural Resource Systems, University of Minnesota Extension, University of Minnesota, St. Paul, MN, 55108, USA
| | - Noelle R Noyes
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA.
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Zhao Q, Lu Y. Anaerobic oxidation of methane in terrestrial wetlands: The rate, identity and metabolism. Sci Total Environ 2023; 902:166049. [PMID: 37543312 DOI: 10.1016/j.scitotenv.2023.166049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/19/2023] [Accepted: 08/02/2023] [Indexed: 08/07/2023]
Abstract
The recent discovery of anaerobic oxidation of methane (AOM) in freshwater ecosystems has caused a great interest in "cryptic methane cycle" in terrestrial ecosystems. Anaerobic methanotrophs appears widespread in wetland ecosystems, yet, the scope and mechanism of AOM in natural wetlands remain poorly understood. In this paper, we review the recent progress regarding the potential of AOM, the diversity and distribution, and the metabolism of anaerobic methanotrophs in wetland ecosystems. The potential of AOM determined through laboratory incubation or in situ isotopic labeling ranges from 1.4 to 704.0 nmol CH4·g-1 dry soil·d-1. It appears that the availability of electron acceptors is critical in driving different AOM in wetland soils. The environmental temperature and salinity exert a significant influence on AOM activity. Reversal methanogenesis and extracellular electron transfer are likely involved in the AOM process. In addition to anaerobic methanotrophic archaea, the direct involvement of methanogens in AOM is also probable. This review presented an overview of the rate, identity, and metabolisms to unravel the biogeochemical puzzle of AOM in wetland soils.
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Affiliation(s)
- Qingzhou Zhao
- College of Urban and Environmental Science, Peking University, Beijing 100871, PR China
| | - Yahai Lu
- College of Urban and Environmental Science, Peking University, Beijing 100871, PR China.
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17
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Wang T, Zhumabieke M, Zhang N, Liu C, Zhong J, Liao Q, Zhang L. Variable promotion of algae and macrophyte organic matter on methanogenesis in anaerobic lake sediment. Environ Res 2023; 237:116922. [PMID: 37598844 DOI: 10.1016/j.envres.2023.116922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/29/2023] [Accepted: 08/17/2023] [Indexed: 08/22/2023]
Abstract
Shallow lakes are an important natural source of atmospheric methane (CH4), and the input of autochthonous organic matter (OM) into their sediments encourages methanogenesis. Although algal- and macrophytic-originated OM in these lakes are expected to have different impacts on methanogenesis and methanogenic archaeal communities in lake sediments owing to their various properties, their specific influence and role in sediment remain unclear. In this study, a 148-day incubation was carried out by adding algal- and macrophytic-OM to the sediments of shallow eutrophic Lake Chaohu and Lake Taihu in China. CH4 was periodically monitored, while the methanogens were examined via qPCR and high-throughput sequencing at the end of incubation. Algal-OM stimulated CH4 production more than macrophytic-OM in both sediments, with the rates initially increasing and then decreasing before reaching a relative constant. Macrophytic-OM promoted CH4 production to a comparable extent in both lakes, while algal-OM promoted greater CH4 in Lake Chaohu than in Lake Taihu. However, algal-OM did not significantly increase mcrA gene copies, while macrophytic-OM did by 17.0-20.1-fold. Algal-OM potentially promoted the methylotrophic pathway in Lake Taihu but did not change the methanogenic structure in Lake Chaohu. Comparatively, macrophytic-OM promoted CH4 production mainly by acetoclastic methanogen proliferation in both lakes. More CH4 release with algal-OM compared to macrophytic-OM deserves further attention owing to the prevailing increasing algal blooms and the declining macrophyte population in lakes.
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Affiliation(s)
- Tong Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Maidina Zhumabieke
- Department of Environmental Science, China Pharmaceutical University, Nanjing, 211198, PR China
| | - Nan Zhang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, PR China; School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing, 210044, PR China
| | - Cheng Liu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, PR China
| | - Jicheng Zhong
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, PR China
| | - Qianjiahua Liao
- Department of Environmental Science, China Pharmaceutical University, Nanjing, 211198, PR China.
| | - Lei Zhang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, PR China.
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Romero P, Belanche A, Jiménez E, Hueso R, Ramos-Morales E, Salwen JK, Kebreab E, Yáñez-Ruiz DR. Rumen microbial degradation of bromoform from red seaweed (Asparagopsis taxiformis) and the impact on rumen fermentation and methanogenic archaea. J Anim Sci Biotechnol 2023; 14:133. [PMID: 37907951 PMCID: PMC10619242 DOI: 10.1186/s40104-023-00935-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 09/01/2023] [Indexed: 11/02/2023] Open
Abstract
BACKGROUND The red macroalgae Asparagopsis is an effective methanogenesis inhibitor due to the presence of halogenated methane (CH4) analogues, primarily bromoform (CHBr3). This study aimed to investigate the degradation process of CHBr3 from A. taxiformis in the rumen and whether this process is diet-dependent. An in vitro batch culture system was used according to a 2 × 2 factorial design, assessing two A. taxiformis inclusion rates [0 (CTL) and 2% DM diet (AT)] and two diets [high-concentrate (HC) and high-forage diet (HF)]. Incubations lasted for 72 h and samples of headspace and fermentation liquid were taken at 0, 0.5, 1, 3, 6, 8, 12, 16, 24, 48 and 72 h to assess the pattern of degradation of CHBr3 into dibromomethane (CH2Br2) and fermentation parameters. Additionally, an in vitro experiment with pure cultures of seven methanogens strains (Methanobrevibacter smithii, Methanobrevibacter ruminantium, Methanosphaera stadtmanae, Methanosarcina barkeri, Methanobrevibacter millerae, Methanothermobacter wolfei and Methanobacterium mobile) was conducted to test the effects of increasing concentrations of CHBr3 (0.4, 2, 10 and 50 µmol/L). RESULTS The addition of AT significantly decreased CH4 production (P = 0.002) and the acetate:propionate ratio (P = 0.003) during a 72-h incubation. The concentrations of CHBr3 showed a rapid decrease with nearly 90% degraded within the first 3 h of incubation. On the contrary, CH2Br2 concentration quickly increased during the first 6 h and then gradually decreased towards the end of the incubation. Neither CHBr3 degradation nor CH2Br2 synthesis were affected by the type of diet used as substrate, suggesting that the fermentation rate is not a driving factor involved in CHBr3 degradation. The in vitro culture of methanogens showed a dose-response effect of CHBr3 by inhibiting the growth of M. smithii, M. ruminantium, M. stadtmanae, M. barkeri, M. millerae, M. wolfei, and M. mobile. CONCLUSIONS The present work demonstrated that CHBr3 from A. taxiformis is quickly degraded to CH2Br2 in the rumen and that the fermentation rate promoted by different diets is not a driving factor involved in CHBr3 degradation.
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Affiliation(s)
- Pedro Romero
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Profesor Albareda 1, Granada, 18008, Spain
| | - Alejandro Belanche
- Department of Animal Production and Food Sciences, University of Zaragoza, Miguel Servet 177, Saragossa, 50013, Spain.
| | - Elisabeth Jiménez
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Profesor Albareda 1, Granada, 18008, Spain
| | - Rafael Hueso
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Profesor Albareda 1, Granada, 18008, Spain
| | - Eva Ramos-Morales
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Profesor Albareda 1, Granada, 18008, Spain
| | | | - Ermias Kebreab
- Department of Animal Science, University of California, Davis, CA, 95618, USA
| | - David R Yáñez-Ruiz
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Profesor Albareda 1, Granada, 18008, Spain.
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Ngo T, Khudur LS, Krohn C, Hassan S, Jansriphibul K, Hakeem IG, Shah K, Surapaneni A, Ball AS. Wood biochar enhances methanogenesis in the anaerobic digestion of chicken manure under ammonia inhibition conditions. Heliyon 2023; 9:e21100. [PMID: 37920507 PMCID: PMC10618790 DOI: 10.1016/j.heliyon.2023.e21100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/28/2023] [Accepted: 10/16/2023] [Indexed: 11/04/2023] Open
Abstract
The process of breaking down chicken manure through anaerobic digestion is an effective waste management technology. However, chicken manure can be a challenging feedstock, causing ammonia stress and digester instability. This study examined the impacts of adding wood biochar and acid-alkali-treated wood biochar to anaerobically digest chicken manure under conditions of ammonia inhibition. The results highlighted that only the addition of 5 % acid-alkali-treated wood biochar by volume can achieve cumulative methane production close to the typical methane potential range of chicken manure. The treated wood biochar also exhibited highest total ammonia nitrogen removal compared to the Control treatment. Scanning Electron Microscope revealed growing interactions between biochar and methanogens over time. Real-time polymerase chain reaction showed that treated wood biochar produced the highest number of bacterial biomass. In addition, 16S amplicon-based sequencing identified a more robust archaeal community from treated biochar addition. Overall, the acid-alkali treatment of biochar represents an effective method of modifying biochar to improve its performance in anaerobic digestion.
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Affiliation(s)
- Tien Ngo
- School of Science, RMIT University, Melbourne, VIC 3083, Australia
- ARC Training Centre for the Transformation of Australia's Biosolids Resource, RMIT University, Bundoora, VIC 3083, Australia
| | - Leadin S. Khudur
- School of Science, RMIT University, Melbourne, VIC 3083, Australia
- ARC Training Centre for the Transformation of Australia's Biosolids Resource, RMIT University, Bundoora, VIC 3083, Australia
| | - Christian Krohn
- School of Science, RMIT University, Melbourne, VIC 3083, Australia
- ARC Training Centre for the Transformation of Australia's Biosolids Resource, RMIT University, Bundoora, VIC 3083, Australia
| | - Soulayma Hassan
- School of Science, RMIT University, Melbourne, VIC 3083, Australia
- ARC Training Centre for the Transformation of Australia's Biosolids Resource, RMIT University, Bundoora, VIC 3083, Australia
| | - Kraiwut Jansriphibul
- School of Science, RMIT University, Melbourne, VIC 3083, Australia
- ARC Training Centre for the Transformation of Australia's Biosolids Resource, RMIT University, Bundoora, VIC 3083, Australia
| | - Ibrahim Gbolahan Hakeem
- ARC Training Centre for the Transformation of Australia's Biosolids Resource, RMIT University, Bundoora, VIC 3083, Australia
- School of Engineering, RMIT University, Melbourne, VIC 3000, Australia
| | - Kalpit Shah
- ARC Training Centre for the Transformation of Australia's Biosolids Resource, RMIT University, Bundoora, VIC 3083, Australia
- School of Engineering, RMIT University, Melbourne, VIC 3000, Australia
| | - Aravind Surapaneni
- ARC Training Centre for the Transformation of Australia's Biosolids Resource, RMIT University, Bundoora, VIC 3083, Australia
- South East Water, 101 Wells Street, Frankston, VIC 3199, Australia
| | - Andrew S. Ball
- School of Science, RMIT University, Melbourne, VIC 3083, Australia
- ARC Training Centre for the Transformation of Australia's Biosolids Resource, RMIT University, Bundoora, VIC 3083, Australia
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20
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Cheng X, Zeng Z, Liu X, Li L, Wang H, Zhao R, Bodelier PLE, Wang W, Wang Y, Tuovinen OH. Methanotrophs dominate methanogens and act as a methane sink in a subterranean karst cave. Sci Total Environ 2023:164562. [PMID: 37257612 DOI: 10.1016/j.scitotenv.2023.164562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/24/2023] [Accepted: 05/28/2023] [Indexed: 06/02/2023]
Abstract
Karst caves are potential sinks of atmospheric methane due to microbial consumption. However, knowledge gaps on methanogens (methane producing microorganisms) and their interaction with methane-oxidizing bacteria (MOB) hinder our further understanding about methane dynamics in karst caves. Here we reported methanogen community composition and their interaction with MOBs in the Heshang Cave to comprehensively understand methane cycling in subsurface biosphere. MOBs in karst cave were dominated by high-affinity MOB, upland soil cluster (USC), with USCγ pmoA gene abundance within the range of 1.34 × 104 to 1.8 × 107 copies·g-1 DW. In contrast, methanogens were dominated by Methanoregula and cluster ZC-I. The mcrA numbers were 7.21 × 103 to 8.31 × 104 copies·g-1 DW, 1-3 orders of magnitude lower than those of MOB. The inter-domain network analysis indicated that MOBs and methanogens cooperated more in the interior of the cave. Despite of the higher number of methanogenic nodes in the network, MOB dominated the keystone taxa, suggesting a leading functional role of MOB. MOB in caves showed a comparable with or higher potential methane oxidizing rate (PMOR, 0.63 ng CH4·g-1 DW·h-1 in sediment versus 11.02 ng CH4·g-1 DW·h-1 in weathered rock) than those in soils, whereas methane produced by methanogens was undetected. Collectively, high absolute abundances of MOB, high PMORs, the dominance of methanotrophic keystone taxa in the inter-domain network confirmed the superiority of MOB over methanogens in the oligotrophic karst cave, mounting new evidence on caves as important methane sink in terms of the interaction between methanogens and MOBs.
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Affiliation(s)
- Xiaoyu Cheng
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, China; Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, the Netherlands
| | - Zhilin Zeng
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Xiaoyan Liu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Lu Li
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Hongmei Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, China.
| | - Rui Zhao
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Paul L E Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, the Netherlands
| | - Weiqi Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Yiheng Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Olli H Tuovinen
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
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21
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Weil M, Wang H, Zak D, Urich T. Spatial and temporal niche separation of methanomassiliicoccales phylotypes in temperate fens. FEMS Microbiol Ecol 2023:7160450. [PMID: 37169886 DOI: 10.1093/femsec/fiad049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023] Open
Abstract
The hydrogen-dependent and methylotrophic order Methanomassiliicoccales consists of the families Methanomethylophilaceae and Methanomassiliicoccaceae. While Methanomethylophilaceae are comparatively well studied, there is a lack of knowledge on Methanomassiliicoccaceae. In this 16S rRNA gene amplicon sequencing based study we investigated the temporal and spatial dynamics of the Methanomassiliicoccales in drained and rewetted sites of three common temperate fen peatlands. A 2.5-year-monitoring of the fen microbiome composition in three peat depths revealed a dynamic methanogen and Methanomassiliicoccales composition across space and time. Four Methanomassiliicoccales phylotypes were found and they were differentially distributed between the fen types. The wetland cluster phylotype was omnipresent and dominant in abundance in all sites along all depths. The Methanomassiliicoccales phylotype was highly abundant in topsoil while the AB364942 phylotype was exclusively found in deeper regions of the rewetted percolation fen. The phylotype affiliated with Methanomassiliicoccales strain U3.2.1 was only detected in the rewetted percolation fen. We discussed the distribution of the four phylotypes with implications to their ecophysiology, where oxygen tolerance and substrate spectrum might play major roles. In conclusion, the Methanomassiliicoccales are widespread and do account for a significant proportion of methanogens, which might suggest their importance for methane emissions from peatlands.
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Affiliation(s)
- Micha Weil
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Str. 8, 17487 Greifswald, Germany
- Greifswald Mire Center, Soldmannstraße 15, 17487 Greifswald, Germany
| | - Haitao Wang
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Str. 8, 17487 Greifswald, Germany
| | - Dominik Zak
- Aarhus University, Department of Bioscience, F. Møllers Allé 3, 8000 Aarhus C, Denmark
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Department of Ecohydrology and Biogeochemistry, Müggelseedamm 301, 12587 Berlin, Germany
| | - Tim Urich
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Str. 8, 17487 Greifswald, Germany
- Greifswald Mire Center, Soldmannstraße 15, 17487 Greifswald, Germany
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22
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Kimisto A, Muia AW, Ong'ondo GO, Ndung'u K. Molecular characterization of microorganisms with industrial potential for methane production in sludge from Kangemi sewage treatment plant, Nyeri county-Kenya. Heliyon 2023; 9:e15715. [PMID: 37234610 PMCID: PMC10205513 DOI: 10.1016/j.heliyon.2023.e15715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 04/18/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023] Open
Abstract
Microbial consortia under anaerobic conditions are involved in oxidizing organic matter in the sludge to produce methane gas. However, in developing countries like Kenya, these microbes have not been fully identified to target them for the efficient harnessing of biofuel. This study collected wet sludge from two anaerobic digestion lagoons 1 and 2 that were operational during sampling at Kangemi Sewage Treatment Plant, in Nyeri County, Kenya. DNA was extracted from samples using commercially available ZymoBIOMICS™ DNA Miniprep Kit and sequenced using Shotgun metagenomics. Samples were analyzed using MG-RAST software (Project ID: mgp100988), which allowed for identifying microorganisms directly involved in various stages of methanogenesis pathways. The study found hydrogenotrophic methanogens, such as Methanospirillum (32%), Methanobacterium (27%), Methanobrevibacter (27%), and Methanosarcina (32%), being predominant in the lagoon communities, whereas acetoclastic microorganisms such as the Methanoregula (22%) and the acetate oxidazing bacteria such as Clostridia (68%) were the key microbes for that pathway in the sewage digester sludge. Furthermore, Methanothermobacter (18%), Methanosarcina (21%), Methanosaeta (15%), and Methanospirillum (13%) carried out the methylotrophic pathway. In contrast, Methanosarcina (23%),Methanoregula (14%), methanosaeta (13%), and methnanoprevibacter (13%) seemed to play an important role in the final step of methane release. This study concluded that the sludge produced from the Nyeri-Kangemi WWTP harbors microbes with significant potential for biogas production. The study recommends a pilot study to investigate the efficiency of the identified microbes for biogas production.
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Affiliation(s)
- Allan.K. Kimisto
- Department of Biological Sciences, Egerton University, P.O Box 536- 20115 Egerton, Kenya
| | - Anastasia W. Muia
- Department of Biological Sciences, Egerton University, P.O Box 536- 20115 Egerton, Kenya
| | - Geoffrey O. Ong'ondo
- Department of Biological Sciences, Egerton University, P.O Box 536- 20115 Egerton, Kenya
| | - Kimani.C. Ndung'u
- Kenya Agricultural and Livestock Research Organisation (KALRO), Njoro Station, Private Bag 20107 Njoro, Kenya
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23
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Wang J, Lou Y, Ma D, Feng K, Chen C, Zhao L, Xing D. Co-treatment with free nitrous acid and calcium peroxide regulates microbiome and metabolic functions of acidogenesis and methanogenesis in sludge anaerobic digestion. Sci Total Environ 2023; 870:161924. [PMID: 36736410 DOI: 10.1016/j.scitotenv.2023.161924] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 01/26/2023] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Wasted activated sludge (WAS) is a promising feedstock for carbon management because of its abundance and carbon-neutral features. Currently, the goal is to maximize the energy in WAS and avoid secondary toxic effects or accumulation of harmful substances in the environment. Chemical pretreatment is an effective strategy for enhancing WAS disintegration and production of short chain fatty acids (SCFAs). However, the role of pretreatment in shaping the core microbiome and functional metabolism of anaerobic microorganisms remains obscure. Here, the mechanisms of SCFA synthesis and microbiome response to free nitrous acid (FNA) and calcium peroxide (CaO2) co-treatment during sludge anaerobic digestion (AD) were investigated. The combination of FNA and CaO2 enriched acidogenic Macellibacteroides, Petrimonas, and Sedimentibacter to a relative abundance of 15.0%, 10.3%, and 7.3%, respectively, resulting in an apparent increase in SCFA production. Metagenome analysis indicated that FNA + CaO2 co-treatment facilitated glycolysis, phosphate acetyltransferase-acetate kinase pathway, amino acid metabolism, and acetate transport, but inhibited CO2 reduction and common pathway of methanogenesis compared with the untreated control. This work provides theoretical insights into the functional activity and interaction of microorganisms with ecological factors.
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Affiliation(s)
- Jing Wang
- State Key Lab of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Yu Lou
- State Key Lab of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Dongmei Ma
- State Key Lab of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Kun Feng
- State Key Lab of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Chuan Chen
- State Key Lab of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Lei Zhao
- State Key Lab of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Defeng Xing
- State Key Lab of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China.
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24
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Obregon D, Mafa-Attoye TG, Baskerville M, Mitter EK, de Souza LF, Oelbermann M, Thevathasan NV, Tsai SM, Dunfield KE. Functionality of methane cycling microbiome during methane flux hot moments from riparian buffer systems. Sci Total Environ 2023; 870:161921. [PMID: 36739023 DOI: 10.1016/j.scitotenv.2023.161921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/26/2023] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
Riparian buffer systems (RBS) are a common agroforestry practice that involves maintaining a forested boundary adjacent to water bodies to protect the aquatic ecosystems in agricultural landscapes. While RBS have potential for carbon sequestration, they also can be sources of methane emissions. Our study site at Washington Creek in Southern Ontario, includes a rehabilitated tree buffer (RH), a grassed buffer (GRB), an undisturbed deciduous forest (UNF), an undisturbed coniferous forest (CF), and an adjacent agricultural field (AGR). The objective of this study was to assess the diversity and activity of CH4 cycling microbial communities in soils sampled during hot moments of methane fluxes (July 04 and August 15). We used qPCR and high-throughput amplicon sequencing from both DNA and cDNA to target methanogen and methanotroph communities. Methanogens, including the archaeal genera Methanosaeta, Methanosarcina, Methanomassiliicoccus, and Methanoreggula, were abundant in all RBSs, but they were significantly more active in UNF soils, where CH4 emissions were highest. Methylocystis was the most prevalent taxon among methanotrophs in all the riparian sites, except for AGR soils where the methanotrophs community was composed primarily of members of rice paddy clusters (RPCs and RPC-1) and upland soil clusters (TUSC and USCα). The main factors influencing the composition and assembly of methane-cycling microbiomes were soil carbon and moisture content. We concluded that the differences in CH4 fluxes observed between RBSs were primarily caused by differences in the presence and activity of methanogens, which were influenced by total soil carbon and water content. Overall, this study emphasizes the importance of understanding the microbial drivers of CH4 fluxes in RBSs in order to maximize RBS environmental benefits.
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Affiliation(s)
- Dasiel Obregon
- School of Environmental Science, University of Guelph, 50 Stone Rd E, Guelph, ON N1H 2W1, Canada; Center for Nuclear Energy in Agriculture, University of São Paulo, Av. Centenário, 303 - São Dimas, Piracicaba, SP 13400-970, Brazil
| | - Tolulope G Mafa-Attoye
- School of Environmental Science, University of Guelph, 50 Stone Rd E, Guelph, ON N1H 2W1, Canada
| | - Megan Baskerville
- Environment and Climate Change Canada, 351, Boul. Saint-Joseph, Gatineau, Quebec, QC K1A 0H3, Canada
| | - Eduardo K Mitter
- School of Environmental Science, University of Guelph, 50 Stone Rd E, Guelph, ON N1H 2W1, Canada
| | - Leandro Fonseca de Souza
- Center for Nuclear Energy in Agriculture, University of São Paulo, Av. Centenário, 303 - São Dimas, Piracicaba, SP 13400-970, Brazil
| | - Maren Oelbermann
- School of Environment, Resources, and Sustainability, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
| | - Naresh V Thevathasan
- School of Environmental Science, University of Guelph, 50 Stone Rd E, Guelph, ON N1H 2W1, Canada
| | - Siu Mui Tsai
- Center for Nuclear Energy in Agriculture, University of São Paulo, Av. Centenário, 303 - São Dimas, Piracicaba, SP 13400-970, Brazil
| | - Kari E Dunfield
- School of Environmental Science, University of Guelph, 50 Stone Rd E, Guelph, ON N1H 2W1, Canada.
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25
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Dengler L, Meier J, Klingl A, Nißl L, Bellack A, Grohmann D, Rachel R, Huber H. A novel interdomain consortium from a Costa Rican oil well composed of Methanobacterium cahuitense sp. nov. and Desulfomicrobium aggregans sp. nov. Arch Microbiol 2023; 205:189. [PMID: 37055657 PMCID: PMC10102059 DOI: 10.1007/s00203-023-03533-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/20/2023] [Accepted: 03/31/2023] [Indexed: 04/15/2023]
Abstract
A novel interdomain consortium composed of a methanogenic Archaeon and a sulfate-reducing bacterium was isolated from a microbial biofilm in an oil well in Cahuita National Park, Costa Rica. Both organisms can be grown in pure culture or as stable co-culture. The methanogenic cells were non-motile rods producing CH4 exclusively from H2/CO2. Cells of the sulfate-reducing partner were motile rods forming cell aggregates. They utilized hydrogen, lactate, formate, and pyruvate as electron donors. Electron acceptors were sulfate, thiosulfate, and sulfite. 16S rRNA sequencing revealed 99% gene sequence similarity of strain CaP3V-M-L2AT to Methanobacterium subterraneum and 98.5% of strain CaP3V-S-L1AT to Desulfomicrobium baculatum. Both strains grew from 20 to 42 °C, pH 5.0-7.5, and 0-4% NaCl. Based on our data, type strains CaP3V-M-L2AT (= DSM 113354 T = JCM 39174 T) and CaP3V-S-L1AT (= DSM 113299 T = JCM 39179 T) represent novel species which we name Methanobacterium cahuitense sp. nov. and Desulfomicrobium aggregans sp. nov.
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Affiliation(s)
- Linda Dengler
- Institute of Microbiology and Archaea Centre, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany.
| | - Julia Meier
- Institute of Microbiology and Archaea Centre, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany
| | - Andreas Klingl
- Plant Development and Electron Microscopy, Biocenter LMU Munich, Planegg-Martinsried, Germany
| | - Laura Nißl
- Institute of Microbiology and Archaea Centre, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany
| | - Annett Bellack
- Institute of Microbiology and Archaea Centre, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany
| | - Dina Grohmann
- Institute of Microbiology and Archaea Centre, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany
| | - Reinhard Rachel
- Centre for Electron Microscopy, Faculty for Biology and Preclinical Medicine, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany
| | - Harald Huber
- Institute of Microbiology and Archaea Centre, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany.
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26
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Pilliol V, Guindo CO, Terrer E, Aboudharam G, Drancourt M, Grine G. Culturing clinical Methanobrevibacter smithii using GG medium in a minimal anaerobe atmosphere. J Microbiol Methods 2023; 207:106704. [PMID: 36907565 DOI: 10.1016/j.mimet.2023.106704] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/02/2023] [Accepted: 03/08/2023] [Indexed: 03/12/2023]
Abstract
Methanobrevibacter smithii (M. smithii), the most prevalent and abundant gut methanogen, detoxifies hydrogen into methane and is, therefore, of paramount importance for the equilibrium of the gut microbiota. The isolation by culture of M. smithii has routinely relied upon hydrogen‑carbon dioxide-enriched, oxygen-deprived atmospheres. In this study, we developed a medium referred to as "GG", which allowed for M. smithii growth and isolation by culture in an oxygen-deprived atmosphere, with no supply of either hydrogen or carbon dioxide, making it easier to detect M. smithii by culture in clinical microbiology laboratories.
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Affiliation(s)
- Virginie Pilliol
- Aix-Marseille Univ., IRD, MEPHI, AP-HM, IHU Méditerranée Infection, Marseille, France; Aix-Marseille Université, Ecole de Médecine Dentaire, Marseille, France
| | - Cheick Oumar Guindo
- Aix-Marseille Univ., IRD, MEPHI, AP-HM, IHU Méditerranée Infection, Marseille, France; IHU Méditerranée Infection, Marseille, France
| | - Elodie Terrer
- Aix-Marseille Univ., IRD, MEPHI, AP-HM, IHU Méditerranée Infection, Marseille, France; Aix-Marseille Université, Ecole de Médecine Dentaire, Marseille, France
| | - Gérard Aboudharam
- Aix-Marseille Univ., IRD, MEPHI, AP-HM, IHU Méditerranée Infection, Marseille, France; Aix-Marseille Université, Ecole de Médecine Dentaire, Marseille, France
| | - Michel Drancourt
- Aix-Marseille Univ., IRD, MEPHI, AP-HM, IHU Méditerranée Infection, Marseille, France; IHU Méditerranée Infection, Marseille, France
| | - Ghiles Grine
- Aix-Marseille Univ., IRD, MEPHI, AP-HM, IHU Méditerranée Infection, Marseille, France; IHU Méditerranée Infection, Marseille, France.
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27
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Sivabalasarma S, de Sousa Machado JN, Albers SV, Jarrell KF. Archaella Isolation. Methods Mol Biol 2023; 2646:183-195. [PMID: 36842116 DOI: 10.1007/978-1-0716-3060-0_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
Swimming archaea are propelled by a filamentous structure called the archaellum. The first step for the structural characterization of this filament is its isolation. Here we provide various methods that allow for the isolation of archaella filaments from well-studied archaeal model organisms. Archaella filaments have been successfully extracted from organisms belonging to different archaeal phyla, e.g., euryarchaeal methanogens such as Methanococcus voltae, and crenarchaeal hyperthermoacidophiles like Sulfolobus acidocaldarius. The filament isolation protocols that we provide in this chapter follow one of two strategies: either the filaments are sheared or extracted from whole cells by detergent extraction, prior to further final purification by centrifugation methods.
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Affiliation(s)
- Shamphavi Sivabalasarma
- Molecular Biology of Archaea, Faculty of Biology, Institute of Biology II, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
| | - João N de Sousa Machado
- Molecular Biology of Archaea, Faculty of Biology, Institute of Biology II, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Faculty of Biology, Institute of Biology II, University of Freiburg, Freiburg, Germany.
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany.
| | - Ken F Jarrell
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
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28
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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. Bioresour Technol 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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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.
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Ali SS, Zagklis D, Kornaros M, Sun J. Cobalt oxide nanoparticles as a new strategy for enhancing methane production from anaerobic digestion of noxious aquatic weeds. Bioresour Technol 2023; 368:128308. [PMID: 36370936 DOI: 10.1016/j.biortech.2022.128308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/04/2022] [Accepted: 11/05/2022] [Indexed: 06/16/2023]
Abstract
This study investigated the effect of cobalt oxide nanoparticles (Co3O4-NPs) supplementation on anaerobic microbial population changes and anaerobic digestion (AD) performance and production. Co3O4-NPs (3 mg/L) showed the maximum enhancement of biogas yield over the cow dung (CD) as control and the co-digestion process of CD with water hyacinth (WH) by 58.9 and 27.2 %, respectively. Furthermore, methane (CH4) yield was enhanced by 89.96 and 43.4 % over CD and co-digestion processes, respectively. Additionally, the microbiological assessment analysis using VIT® gene probe technology showed that Co3O4-NPs enhance the viability of total bacterial cells by 9 %. The techno-economic analysis reflects the revenue of this strategy on the highest net energy content of biogas, which was achieved with 3 mg/L Co3O4-NPs and was 428.05 kWh with a net profit of 67.66 USD/m3 of the substrate. Therefore, nanoparticle supplementation to the AD process can be considered a promising approach to enhance biogas and CH4.
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Affiliation(s)
- Sameh Samir Ali
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; Botany Department, Faculty of Science, Tanta University, Tanta 31527, Egypt
| | - Dimitris Zagklis
- Laboratory of Biochemical Engineering & Environmental Technology (LBEET), Department of Chemical Engineering, University of Patras, 26504 Patras, Greece
| | - Michael Kornaros
- Laboratory of Biochemical Engineering & Environmental Technology (LBEET), Department of Chemical Engineering, University of Patras, 26504 Patras, Greece
| | - Jianzhong Sun
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China.
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Oliveira JMS, Poulsen JS, Foresti E, Nielsen JL. Microbial communities and metabolic pathways involved in reductive decolorization of an azo dye in a two-stage AD system. Chemosphere 2023; 310:136731. [PMID: 36209855 DOI: 10.1016/j.chemosphere.2022.136731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/10/2022] [Accepted: 10/01/2022] [Indexed: 06/16/2023]
Abstract
Multiple stage anaerobic system was found to be an effective strategy for reductive decolorization of azo dyes in the presence of sulfate. Bulk color removal (56-90%) was achieved concomitant with acidogenic activity in the 1st-stage reactor (R1), while organic matter removal (≤100%) and sulfate reduction (≤100%) occurred predominantly in the 2nd-stage reactor (R2). However, azo dye reduction mechanism and metabolic routes involved remain unclear. The involved microbial communities and conditions affecting the azo dye removal in a two-stage anaerobic digestion (AD) system were elucidated using amplicon sequencing (16S rRNA, fhs, dsrB and mcrA) and correlation analysis. Reductive decolorization was found to be co-metabolic and mainly associated with hydrogen-producing pathways. We also found evidence of the involvement of an azoreductase from Lactococcus lactis. Bacterial community in R1 was sensitive and shifted in the presence of the azo dye, while microorganisms in R2 were more protected. Higher diversity of syntrophic-acetate oxidizers, sulfate reducers and methanogens in R2 highlights the role of the 2nd-stage in organic matter and sulfate removals, and these communities might be involved in further transformations of the azo dye reduction products. The results improve our understanding on the role of different microbial communities in anaerobic treatment of azo dyes and can help in the design of better solutions for the treatment of textile effluents.
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Affiliation(s)
- J M S Oliveira
- Biological Processes Laboratory (LPB), São Carlos School of Engineering (EESC), University of São Paulo (USP), 1100 João Dagnone Avenue, 13563-120, São Carlos, SP, Brazil; Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, DK-9220 Aalborg, Denmark
| | - J S Poulsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, DK-9220 Aalborg, Denmark
| | - E Foresti
- Biological Processes Laboratory (LPB), São Carlos School of Engineering (EESC), University of São Paulo (USP), 1100 João Dagnone Avenue, 13563-120, São Carlos, SP, Brazil
| | - J L Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, DK-9220 Aalborg, Denmark.
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31
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Chen Z, Chen H, Zhu X, Xia D, Chen Y, Geng M, Bai Z. Physical, chemical, and bio-pretreatments on microbial gas production in Baode Block coal. Environ Sci Pollut Res Int 2023; 30:5791-5798. [PMID: 35978250 DOI: 10.1007/s11356-022-22527-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 08/09/2022] [Indexed: 06/15/2023]
Abstract
Currently, the exploitation of Baode Block as a biogenic coal-bed gas field has been in the later stage of stable production; hence, exploration and activation of microbial gas production are of great practical significance for the enhancement and stabilization of block production. Pretreatment is the key process to improve anaerobic biodegradation performance and increase yield and production rate of gas. In this study, we examine physical, chemical, and biological pretreatment methods and compare their effectiveness toward microbial gas production in the coal seam. The obtained results indicate that: (1) grinding can enhance contact between the coal sample and bacteria liquid, and coal powder has greater gas-producing performance than the coal lump. (2) Chemical pretreatment of coal samples using acid and base can enhance gas production capacity. NaOH treatment has better gas-producing performance than HCl treatment, and the activity of microbial flora is higher after treatment. (3) Biological pretreatment can greatly enhance the microbial degradation of coal bed. The highest gas yield after white rot fungus pretreatment is 11.65 m3/t, and gas production cycle is shorter than before. This may be due to the white rot fungus effectively degrading macromolecules and, therefore, shortening the duration of methanogenic hydrolysis, which provides more organic matter for methanogens to decompose. During production, in addition to selecting a proper pretreatment method, the treatment cost and balance between energy input of pretreatment and gas energy output must also be considered. The joint pretreatment between different reagents and treatment methods is a possible solution to the problem and a current research trend to realize the large-scale degradation of coal. The simulated microbial methane production of coal seam is feasible for Baode Block in Ordos, where coal samples in this block have great gas-producing potential after treatment, and provides good references for further in-field tests.
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Affiliation(s)
- Zhenhong Chen
- Research Institute of Petroleum Exploration and Development, Beijing, 100083, China
| | - Hao Chen
- Research Institute of Petroleum Exploration and Development, Beijing, 100083, China.
| | - Xinfa Zhu
- CCDC Changqing Downhole Technology Company, Xi'an, 700021, China
| | - Daping Xia
- School of Energy Science and Engineering, Henan Polytechnic University, Jiaozuo, 454000, China
| | - Yanpeng Chen
- Research Institute of Petroleum Exploration and Development, Beijing, 100083, China
| | - Meng Geng
- Research Institute of Petroleum Exploration and Development, Beijing, 100083, China
| | - Zhihao Bai
- School of Geology and Mining Engineering, Xinjiang University, Urumchi, 830000, China
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Chen H, He J, Zhou D, Zhang Z, Yao J, Qiu Z, Shen D. Introduction of acid-neutralizing layer to facilitate the stabilization of municipal solid waste landfill. Waste Manag 2022; 154:245-251. [PMID: 36279592 DOI: 10.1016/j.wasman.2022.10.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 10/07/2022] [Accepted: 10/13/2022] [Indexed: 06/16/2023]
Abstract
Rapid stabilization is important for landfill operation and beneficial for treatment capacity recovery, biogas production, and pollution control. Acidification of municipal solid waste (MSW) landfill hinders the degradation of MSW. In this study, a leachate-recirculated landfill bioreactor with acid-neutralizing layer (reactor BL) and a control landfill bioreactor without the acid-neutralizing layer (CL) were operated for 509 days. The pH of the landfill was increased by the acid-neutralizing layer. The landfill gas production volume increased by 18.3 % in reactor BL compared with CL during the study period, and the CH4 concentration was also increased. A greater MSW mass reduction was observed in reactor BL than in CL. Microbial community analysis demonstrated that the presence of the acid-neutralizing layer promoted the abundance of methanogens. Based on these observations, it is believed that application of the acid-neutralizing layer accelerated the stabilization by mitigating the acidification of landfill, which promote the abundance of methanogens and enhance the MSW degradation. These results help to understand the influencing mechanism of acid-neutralizing layer on the landfill stabilization, and provide a new approach for the practical landfill to achieve fast stabilization.
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Affiliation(s)
- Hui Chen
- Engineering Technology Center for Pollution Prevention and Control of Taizhou, Taizhou University, Jiaojiang 318000, Zhejiang province, China
| | - Jian He
- Engineering Technology Center for Pollution Prevention and Control of Taizhou, Taizhou University, Jiaojiang 318000, Zhejiang province, China
| | - Dandan Zhou
- Engineering Technology Center for Pollution Prevention and Control of Taizhou, Taizhou University, Jiaojiang 318000, Zhejiang province, China
| | - Zhicheng Zhang
- Engineering Technology Center for Pollution Prevention and Control of Taizhou, Taizhou University, Jiaojiang 318000, Zhejiang province, China
| | - Jun Yao
- Engineering Technology Center for Pollution Prevention and Control of Taizhou, Taizhou University, Jiaojiang 318000, Zhejiang province, China.
| | - Zhanhong Qiu
- Engineering Technology Center for Pollution Prevention and Control of Taizhou, Taizhou University, Jiaojiang 318000, Zhejiang province, China
| | - Dongsheng Shen
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Zhejiang Gongshang University, Hangzhou 310018, China
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Singh AK, Nakhate SP, Gupta RK, Chavan AR, Poddar BJ, Prakash O, Shouche YS, Purohit HJ, Khardenavis AA. Mining the landfill soil metagenome for denitrifying methanotrophic taxa and validation of methane oxidation in microcosm. Environ Res 2022; 215:114199. [PMID: 36058281 DOI: 10.1016/j.envres.2022.114199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 05/21/2022] [Accepted: 08/20/2022] [Indexed: 06/15/2023]
Abstract
In the present study, the microbial community residing at different depths of the landfill was characterized to assess their roles in serving as a methane sink. Physico-chemical characterization revealed the characteristic signatures of anaerobic degradation of organic matter in the bottom soil (50-60 cm) and, active process of aerobic denitrification in the top soil (0-10 cm). This was also reflected from the higher abundance of bacterial domain in the top soil metagenome represented by dominant phyla Proteobacteria and Actinobacteria which are prime decomposers of organic matter in landfill soils. The multiple fold higher relative abundances of the two most abundant genera; Streptomyces and Intrasporangium in the top soil depicted greater denitrifying taxa in top soil than the bottom soil. Amongst the aerobic methanotrophs, the genera Methylomonas, Methylococcus, Methylocella, and Methylacidiphilum were abundantly found in the top soil metagenome that were essential for oxidizing methane generated in the landfill. On the other hand, the dominance of archaeal domain represented by Methanosarcina and Methanoculleus in the bottom soil highlighted the complete anaerobic digestion of organic components via acetoclasty, carboxydotrophy, hydrogenotrophy, methylotrophy. Functional characterization revealed a higher abundance of methane monooxygenase gene in the top soil and methyl coenzyme M reductase gene in the bottom soil that correlated with the higher relative abundance of aerobic methanotrophs in the top soil while methane generation being the active process in the highly anaerobic bottom soil in the landfill. The activity dependent abundance of endogenous microbial communities in the different zones of the landfill was further validated by microcosm studies in serum bottles which established the ability of the methanotrophic community for methane metabolism in the top soil and their potential to serve as sink for methane. The study provides a better understanding about the methanotrophs in correlation with their endogenous environment, so that these bacteria can be used in resolving the environmental issues related to methane and nitrogen management at landfill site.
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Affiliation(s)
- Ashish Kumar Singh
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Suraj Prabhakarrao Nakhate
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Rakesh Kumar Gupta
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Atul Rajkumar Chavan
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Bhagyashri Jagdishprasad Poddar
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Om Prakash
- National Centre for Microbial Resource, National Centre for Cell Sciences, Pune, Maharashtra, 411007, India
| | - Yogesh S Shouche
- National Centre for Microbial Resource, National Centre for Cell Sciences, Pune, Maharashtra, 411007, India
| | - Hemant J Purohit
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Anshuman Arun Khardenavis
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Changey F, Aissaoui G, Plain C, Ranger J, Legout A, Zeller B, Epron D, Lerch TZ. Prolonged Effect of Forest Soil Compaction on Methanogen and Methanotroph Seasonal Dynamics. Microb Ecol 2022:10.1007/s00248-022-02149-8. [PMID: 36409329 DOI: 10.1007/s00248-022-02149-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 11/14/2022] [Indexed: 06/16/2023]
Abstract
Methane (CH4) oxidation by methanotrophic bacteria in forest soils is the largest biological sink for this greenhouse gas on earth. However, the compaction of forest soils by logging traffic has previously been shown to reduce the potential rate of CH4 uptake. This change could be due to not only a decrease of methanotrophs but also an increase in methanogen activity. In this study, we investigated whether the decrease in CH4 uptake by forest soils, subjected to compaction by heavy machinery 7 years earlier, can be explained by quantitative and qualitative changes in methanogenic and methanotrophic communities. We measured the functional gene abundance and polymorphism of CH4 microbial oxidizers (pmoA) and producers (mcrA) at different depths and during different seasons. Our results revealed that the soil compaction effect on the abundance of both genes depended on season and soil depth, contrary to the effect on gene polymorphism. Bacterial pmoA abundance was significantly lower in the compacted soil than in the controls across all seasons, except in winter in the 0-10 cm depth interval and in summer in the 10-20 cm depth interval. In contrast, archaeal mcrA abundance was higher in compacted than control soil in winter and autumn in the two soil depths investigated. This study shows the usefulness of using pmoA and mcrA genes simultaneously in order to better understand the spatial and temporal variations of soil CH4 fluxes and the potential effect of physical disturbances.
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Affiliation(s)
- Frédérique Changey
- Institut d'Ecologie et des Sciences de l'Environnement de Paris, UMR 7618 (CNRS, SU, INRAe, UPEC, IRD, UPC), 94010, Créteil, France
- Laboratoire de Chimie Physique et Microbiologie pour les Matériaux et l'Environnement, UMR 7564, CNRS, Univ. Lorraine), 54600, Villers-Lès-Nancy, France
| | - Ghozlane Aissaoui
- Institut d'Ecologie et des Sciences de l'Environnement de Paris, UMR 7618 (CNRS, SU, INRAe, UPEC, IRD, UPC), 94010, Créteil, France
| | - Caroline Plain
- Ecologie et Ecophysiologie Forestières, UMR 1137 (INRAe, Univ. Lorraine), 54280, Champenoux, France
| | - Jacques Ranger
- Biogéochimie des Ecosystèmes Forestiers, 1138 INRAe, 54280, Champenoux, UR, France
| | - Arnaud Legout
- Biogéochimie des Ecosystèmes Forestiers, 1138 INRAe, 54280, Champenoux, UR, France
| | - Bernd Zeller
- Biogéochimie des Ecosystèmes Forestiers, 1138 INRAe, 54280, Champenoux, UR, France
| | - Daniel Epron
- Ecologie et Ecophysiologie Forestières, UMR 1137 (INRAe, Univ. Lorraine), 54280, Champenoux, France
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Thomas Z Lerch
- Institut d'Ecologie et des Sciences de l'Environnement de Paris, UMR 7618 (CNRS, SU, INRAe, UPEC, IRD, UPC), 94010, Créteil, France.
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Nijman TPA, Lemmens M, Lurling M, Kosten S, Welte C, Veraart AJ. Phosphorus control and dredging decrease methane emissions from shallow lakes. Sci Total Environ 2022; 847:157584. [PMID: 35882339 DOI: 10.1016/j.scitotenv.2022.157584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/17/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
Freshwater ecosystems are an important source of the greenhouse gas methane (CH4), and their emissions are expected to increase due to eutrophication. Two commonly applied management techniques to reduce eutrophication are the addition of phosphate-binding lanthanum modified bentonite (LMB, trademark Phoslock©) and dredging, but their effect on CH4 emissions is still poorly understood. Here, this study researched how LMB and dredging affected CH4 emissions using a full-factorial mesocosm design monitored for 18 months. The effect was tested by measuring diffusive and ebullitive CH4 fluxes, plant community composition, methanogen and methanotroph activity and community composition, and a range of physicochemical water and sediment variables. LMB addition decreased total CH4 emissions, while dredging showed a trend towards decreasing CH4 emissions. Total CH4 emissions in all mesocosms were much higher in the summer of the second year, likely because of higher algal decomposition and organic matter availability. First, LMB addition lowered CH4 emissions by decreasing P-availability, which reduced coverage of the floating fern Azolla filiculoides, and thereby prevented anoxia and decreased surface water NH4+ concentrations, lowering CH4 production rates. Second, dredging decreased CH4 emissions in the first summer, possibly it removed the methanogenic community, and in the second year by preventing autumn and winter die-off of the rooted macrophyte Potamogeton cripsus. Finally, methanogen community composition was related to surface water NH4+ and O2, and porewater total phosphorus, while methanotroph community composition was related to organic matter content. To conclude, LMB addition and dredging not only improve water quality, but also decrease CH4 emissions, mitigating climate change.
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Affiliation(s)
- Thomas P A Nijman
- Department of Aquatic Ecology and Environmental Biology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands.
| | - Maxime Lemmens
- Department of Aquatic Ecology and Environmental Biology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Miquel Lurling
- Aquatic Ecology & Water Quality Management Group, Department of Environmental Sciences, Wageningen University, Droevendaalsesteeg 3a, 6708 PB Wageningen, the Netherlands
| | - Sarian Kosten
- Department of Aquatic Ecology and Environmental Biology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Cornelia Welte
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Annelies J Veraart
- Department of Aquatic Ecology and Environmental Biology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
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36
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Birg A, Ritz N, Barton LL, Lin HC. Hydrogen Availability Is Dependent on the Actions of Both Hydrogen-Producing and Hydrogen-Consuming Microbes. Dig Dis Sci 2022; 68:1253-1259. [PMID: 36323965 DOI: 10.1007/s10620-022-07743-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 10/19/2022] [Indexed: 12/09/2022]
Abstract
Hydrogen gas (H2) is produced by H2-producing microbes in the gut during polysaccharide fermentation. Gut microbiome also includes H2-consuming microbes utilizing H2 for metabolism: methanogens producing methane, CH4, and sulfate-reducing bacteria producing hydrogen sulfide, H2S. H2S is not measured in the evaluation of gaseous byproducts of microbial fermentation. We hypothesize that the availability of measured H2 depends on both hydrogen producers and hydrogen consumers by measuring H2 in vitro and in vivo. In the in vitro study, groups were Bacteroides thetaiotaomicron (B. theta, H2 producers), Desulfovibrio vulgaris (D. vulgaris, H2 consumers), and D. vulgaris + B. theta combined. Gas samples were collected at 2 h and 24 h after incubation and assayed for H2, CH4, and H2S. In the in vivo study Sprague-Dawley rats were gavaged with suspended bacteria in four groups: B. theta, D. vulgaris, combined, and control. Gas was analyzed for H2 at 60 min. In the in vitro experiment, H2 concentration was higher in the combined group (188 ± 93.3 ppm) compared with D. vulgaris (27.17 ± 9.6 ppm) and B. theta groups (34.2 ± 29.8 ppm; P < 0.05); H2S concentration was statistically higher in the combined group (10.32 ± 1.5 ppm) compared with B. theta (0.19 ± 0.03 ppm) and D. vulgaris group (3.46 ± 0.28 ppm; P < 0.05). In the in vivo study, H2 concentrations were significantly higher in the B. theta group (44.3 ± 6.0 ppm) compared with control (31.8 ± 4.3) and the combined group (34.2 ± 8.7, P < 0.05). This study shows that sulfate-reducing bacteria could convert available H2 to H2S, leading to measured hydrogen levels that are dependent on the actions of both H2 producers and H2 consumers.
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Affiliation(s)
- Aleksandr Birg
- Division of Gastroenterology and Hepatology, University of New Mexico, Albuquerque, NM, 87106, USA
| | - Nathaniel Ritz
- Biomedical Research Institute of New Mexico, Albuquerque, NM, 87108, USA
| | - Larry L Barton
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Henry C Lin
- Division of Gastroenterology and Hepatology, University of New Mexico, Albuquerque, NM, 87106, USA.
- Medicine Service, New Mexico VA Health Care System, 1501 San Pedro St., Albuquerque, NM, 87108, USA.
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Kang H, Lee J, Zhou X, Kim J, Yang Y. The Effects of N Enrichment on Microbial Cycling of Non-CO 2 Greenhouse Gases in Soils-a Review and a Meta-analysis. Microb Ecol 2022; 84:945-957. [PMID: 34725713 DOI: 10.1007/s00248-021-01911-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 10/25/2021] [Indexed: 06/13/2023]
Abstract
Terrestrial ecosystems are typically nitrogen (N) limited, but recent years have witnessed N enrichment in various soil ecosystems caused by human activities such as fossil fuel combustion and fertilizer application. This enrichment may alter microbial processes in soils in a way that would increase the emissions of methane (CH4) and nitrous oxide (N2O), thereby aggravating global climate change. This review focuses on the effects of N enrichment on methanogens and methanotrophs, which play a central role in the dynamics of CH4 at the global scale. We also address the effects of N enrichment on N2O, which is produced in soils mainly by nitrification and denitrification. Overall, N enrichment inhibits methanogenesis in pure culture experiments, while its effects on CH4 oxidation are more complicated. The majority of previous studies reported that N enrichment, especially NH4+ enrichment, inhibits CH4 oxidation, resulting in higher CH4 emissions from soils. However, both activation and neutral responses have also been reported, particularly in rice paddies and landfill sites, which is well reflected in our meta-analysis. In contrast, N enrichment substantially increases N2O emission by both nitrification and denitrification, which increases proportionally to the amount of N amended. Future studies should address the effects of N enrichment on the active microbes of those functional groups at multiple scales along with parameterization of microbial communities for the application to climate models at the global scale.
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Affiliation(s)
- Hojeong Kang
- School of Civil and Environmental Engineering, Yonsei University, Seoul, Korea.
| | - Jaehyun Lee
- School of Civil and Environmental Engineering, Yonsei University, Seoul, Korea
| | - Xue Zhou
- School of Civil and Environmental Engineering, Yonsei University, Seoul, Korea
- College of Agricultural Science and Engineering, Hohai University, Nanjing, China
| | - Jinhyun Kim
- School of Civil and Environmental Engineering, Yonsei University, Seoul, Korea
| | - Yerang Yang
- School of Civil and Environmental Engineering, Yonsei University, Seoul, Korea
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Li Z, Chen H. Elucidating the role of solids content in low-temperature thermal hydrolysis and anaerobic digestion of sewage sludge. Bioresour Technol 2022; 362:127859. [PMID: 36037837 DOI: 10.1016/j.biortech.2022.127859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
The role of total solids content in low-temperature thermal hydrolysis and anaerobic digestion of sewage sludge was investigated. Increasing total solids from 2% to 6% improved thermal hydrolysis and anaerobic digestion performance, while increasing it further to 12% decreased methane production. Maximum sludge solubility (22.9% ± 0.6%) and methane production (320 ± 7 mL/g volatile solids) were achieved at 6% solids. The increase in solids content from 2% to 6% improved heating efficiency and volatile fraction content, which facilitated sludge solubilization and enrichment of methanogens. However, further increases in solids content resulted in a stable floc structure with excess ammonia nitrogen and volatile fatty acids, which limited the release of substrates and reduced the abundance of acidifying bacteria and methanogens, ultimately leading to reduced methane production. An in-depth understanding of the role of solids content opens up new avenues for improved low-temperature thermal hydrolysis of sludge.
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Affiliation(s)
- Zeyu Li
- College of Environment and Resources, Xiangtan University, Xiangtan 411105, China
| | - Hongbo Chen
- College of Environment and Resources, Xiangtan University, Xiangtan 411105, China.
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Zhou C, Zhang Y, Li S, Jiang Q, Chen H, Zhu T, Xu X, Liu H, Qiu S, Wu J, Nie M, Li B. Exogenous nitrogen from riverine exports promotes soil methane production in saltmarshes in China. Sci Total Environ 2022; 838:156203. [PMID: 35618128 DOI: 10.1016/j.scitotenv.2022.156203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 06/15/2023]
Abstract
Methane emissions from saltmarshes can potentially promote climate warming. Soil methane production is positively correlated with methane emissions from saltmarshes. Understanding the factors influencing soil methane production will improve the prediction of methane emissions, but an investigation of these factors has not been conducted in saltmarshes in China. We collected soils from native Phragmites australis and invasive Spartina alterniflora saltmarshes along the coast of China; the soil potential methane production (PMP) was determined by incubation experiments. The large-scale investigation results showed that the ratios of methanogens relative to sulfate-reducing bacteria (RMRS) and total organic carbon (TOC) were positively correlated with soil PMP for both species. Dissolved inorganic nitrogen (DIN) was positively correlated with the soil PMP of P. australis saltmarshes, and plant biomass was positively correlated with the soil PMP of S. alterniflora saltmarshes. Our results showed that exogenous nitrogen from riverine exports was positively correlated with DIN and plant biomass in both P. australis and S. alterniflora saltmarshes. In addition, exogenous nitrogen was also positively correlated with TOC in S. alterniflora saltmarshes. Consequently, exogenous nitrogen indirectly promoted soil methane production in P. australis saltmarshes by increasing the DIN and promoted soil methane production in S. alterniflora saltmarshes by enhancing the TOC and plant biomass. Moreover, we found that the promoting effect of DIN on the soil PMP of P. australis saltmarshes increased when the incubation temperature increased from 15 °C to 25 °C. Thus, the promoting effect of exogenous nitrogen on the soil methane production in P. australis saltmarshes might be strengthened in the peak of growing season. Our findings are the first to confirm that exogenous nitrogen inputs from rivers indirectly promote soil methane production in P. australis and S. alterniflora saltmarshes and provide new insights into the factors responsible for soil methane production in saltmarshes.
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Affiliation(s)
- Chenhao Zhou
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yan Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Songshuo Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Qiuyue Jiang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Hongyang Chen
- Center for Ecological Research, Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Ting Zhu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xiao Xu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Hao Liu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Shiyun Qiu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jihua Wu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ming Nie
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Bo Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai 200438, China; Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650504, Yunnan, China.
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Venturini AM, Dias NMS, Gontijo JB, Yoshiura CA, Paula FS, Meyer KM, Nakamura FM, da França AG, Borges CD, Barlow J, Berenguer E, Nüsslein K, Rodrigues JLM, Bohannan BJM, Tsai SM. Increased soil moisture intensifies the impacts of forest-to-pasture conversion on methane emissions and methane-cycling communities in the Eastern Amazon. Environ Res 2022; 212:113139. [PMID: 35337832 DOI: 10.1016/j.envres.2022.113139] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 02/24/2022] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
Climatic changes are altering precipitation patterns in the Amazon and may influence soil methane (CH4) fluxes due to the differential responses of methanogenic and methanotrophic microorganisms. However, it remains unclear if these climate feedbacks can amplify land-use-related impacts on the CH4 cycle. To better predict the responses of soil CH4-cycling microorganisms and emissions under altered moisture levels in the Eastern Brazilian Amazon, we performed a 30-day microcosm experiment manipulating the moisture content (original moisture; 60%, 80%, and 100% of field capacity - FC) of forest and pasture soils. Gas samples were collected periodically for gas chromatography analysis, and methanogenic archaeal and methanotrophic bacterial communities were assessed using quantitative PCR and metagenomics. Positive and negative daily CH4 fluxes were observed for forest and pasture, indicating that these soils can act as both CH4 sources and sinks. Cumulative emissions and the abundance of methanogenesis-related genes and taxonomic groups were affected by land use, moisture, and their interaction. Pasture soils at 100% FC had the highest abundance of methanogens and CH4 emissions, 22 times higher than forest soils under the same treatment. Higher ratios of methanogens to methanotrophs were found in pasture than in forest soils, even at field capacity conditions. Land use and moisture were significant factors influencing the composition of methanogenic and methanotrophic communities. The diversity and evenness of methanogens did not change throughout the experiment. In contrast, methanotrophs exhibited the highest diversity and evenness in pasture soils at 100% FC. Taken together, our results suggest that increased moisture exacerbates soil CH4 emissions and microbial responses driven by land-use change in the Amazon. This is the first report on the microbial CH4 cycle in Amazonian upland soils that combined one-month gas measurements with advanced molecular methods.
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Affiliation(s)
- Andressa M Venturini
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13416-000, Brazil; Princeton Institute for International and Regional Studies, Princeton University, Princeton, NJ, 08544, USA.
| | - Naissa M S Dias
- Environmental Biogeochemistry Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13416-000, Brazil
| | - Júlia B Gontijo
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13416-000, Brazil
| | - Caio A Yoshiura
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13416-000, Brazil
| | - Fabiana S Paula
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13416-000, Brazil; Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, São Paulo, SP, 05508-120, Brazil
| | - Kyle M Meyer
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA; Department of Integrative Biology, University of California - Berkeley, Berkeley, CA, 94720, USA
| | - Fernanda M Nakamura
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13416-000, Brazil
| | - Aline G da França
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13416-000, Brazil
| | - Clovis D Borges
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13416-000, Brazil
| | - Jos Barlow
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Erika Berenguer
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK; Environmental Change Institute, University of Oxford, Oxford, OX1 3QY, UK
| | - Klaus Nüsslein
- Department of Microbiology, University of Massachusetts, Amherst, MA, 01003, USA
| | - Jorge L M Rodrigues
- Department of Land, Air, and Water Resources, University of California - Davis, Davis, CA, 95616, USA
| | - Brendan J M Bohannan
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA
| | - Siu M Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13416-000, Brazil
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Berninghaus AE, Radniecki TS. Anaerobic digester microbiome dynamics in response to moderate and failure-inducing shock loads of fats, oils and greases. Bioresour Technol 2022; 359:127400. [PMID: 35654324 DOI: 10.1016/j.biortech.2022.127400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/26/2022] [Accepted: 05/28/2022] [Indexed: 06/15/2023]
Abstract
Accidental organic overloading (shock loading) is common during the anaerobic co-digestion of fats, oils and greases (FOG) and may lead to decreased performance or reactor failure due to the effects on the microbiome. Here, adapted and non-adapted lab-scale anaerobic digesters were exposed to FOG shocks of varying organic strengths. The microbiome was sequenced during the recovery periods employed between each shock event. Non-failure-inducing shocks resulted in enrichment of fermentative bacteria, and acetoclastic and methylotrophic methanogens. However, sub-dominant bacterial populations were largely responsible for increased biogas production observed after adaptation. Following failure events, early recovery communities were dominated by Pseudomonas and Methanosaeta while late recovery communities shifted toward sub-dominant bacterial taxa and Methanosarcina. Generally, the recovered microbiome structure diverged from that of both the initial and optimized microbiomes. Thus, while non-failure-inducing FOG shocks can be beneficial, the adaptations gained are lost after a failure event and adaptation must begin again.
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Affiliation(s)
- Ashley E Berninghaus
- School of Chemical, Biological, and Environmental Engineering, Oregon State University, Corvallis, OR 97331 USA
| | - Tyler S Radniecki
- School of Chemical, Biological, and Environmental Engineering, Oregon State University, Corvallis, OR 97331 USA.
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Du J, Yin Q, Zhou X, Guo Q, Wu G. Distribution of extracellular amino acids and their potential functions in microbial cross-feeding in anaerobic digestion systems. Bioresour Technol 2022; 360:127535. [PMID: 35779747 DOI: 10.1016/j.biortech.2022.127535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 06/15/2023]
Abstract
Anaerobic digestion is a prevalent bioenergy production process relying on a complex network of symbiotic interactions, where the nutrient based cross-feeding is an essential microbial mechanism. Here, the cross-feeding function was assessed by analyzing extracellular polymeric substances-associated amino acids in microbial aggregates collected from 14 lab-scale anaerobic digesters, as well as deciphering their genetically biosynthetic potential by syntrophic bacteria and methanogens. The total concentration of essential amino acids ranged from 1.2 mg/g VSS to 174.0 mg/g VSS. The percentages of glutamic acid (8.5 ∼ 37.6%), lysine (2.7 ∼ 22.6%), alanine (5.6 ∼ 13.2%), and valine (3.0 ∼ 10.4%) to the total amount of detected amino acids were the highest in most samples. Through metagenomics analysis, several investigated syntrophs (i.e., Smithella, Syntrophobacter, Syntrophomonas, and Mesotoga) and methanogens (i.e., Methanothrix and Methanosarcina) were auxotrophies, but the genetic ability of syntrophs and methanogens to synthesize some essential amino acids could be complementary, implying potential cross-feeding partnership.
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Affiliation(s)
- Jin Du
- Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong, China
| | - Qidong Yin
- Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong, China
| | - Xingzhao Zhou
- Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong, China
| | - Qiannan Guo
- Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong, China
| | - Guangxue Wu
- Civil Engineering, School of Engineering, College of Science and Engineering, National University of Ireland, Galway, Galway H91 TK33, Ireland.
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Nimonkar YS, Kajale S, Dake M, Ranade DR, Yadav KK, Kumar R, Prakash O. A culture-based and culture-independent approach to the study of landfill leachate bacterial and archaeal communities. Anaerobe 2022;:102626. [PMID: 35977655 DOI: 10.1016/j.anaerobe.2022.102626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 07/14/2022] [Accepted: 08/09/2022] [Indexed: 11/20/2022]
Abstract
The landfill is a convenient and affordable method of municipal solid waste (MSW) management. Landfill leachate contains a heavy load of pollutants and pathogens. Discharge of untreated leachate is the leading cause of surface and groundwater contamination and a threat to public and environmental health. To develop an efficient leachate treatment technology, an in-depth understanding of landfill chemistry and microbiology is essential. In the present manuscript, we conducted a comparative study of three different landfill leachate samples using cultivation-based and culture-independent molecular studies. We cultivated 85 species of aerobic, anaerobic bacteria and archaea from leachate represented by a total of 200 strains using extensive culturomics approaches. Twelve out of 200 cultivated strains of bacteria showed very low 16S rRNA gene sequence similarity (84-98.6%) with their closest relatives and could be the potential novel taxa, the first time cultivated from leachate. Members of the six genera only have 2-5 representatives from past studies from other habitats but first time cultivated from leachate. In addition to bacteria, we also cultivated and characterized different groups of methanogenic archaea. Our chemistry data indicate that leachate is a highly stressed ecosystem with an assemblage of many toxic wastes like sulfur, zinc, mercury, chromium, etc. 16S rRNA gene-based amplicon analysis showed the dominance of (30-55%) methanogens and haloarachaea. Our data suggest that archaea are the significant regulators of leachate ecology, and more in-depth studies with multiple leachate samples are required to understand their role in leachate nutrient cycling and the development of effective leachate treatment technology.
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Li W, Sangeetha T, Han X, Yan WM, Yang L, Zhao J, Cai W, Yao H. Tracking the diversity and interaction of methanogens in the energy recovery process of a full-scale wastewater treatment plant. Environ Res 2022; 211:113010. [PMID: 35219628 DOI: 10.1016/j.envres.2022.113010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/07/2022] [Accepted: 02/20/2022] [Indexed: 06/14/2023]
Abstract
Methanogens have been significant for the achievement of carbon neutrality in wastewater treatment plants due to their crucial roles in the anaerobic digestion of sludge. Nevertheless, the phylogenetic diversity of methanogens and their versatile metabolism have been continuously investigated, the current scientific knowledge regarding these microbes appears inadequate and requires more evaluations. This study is considered an endeavor in which functional genes sequencing was used to reveal the diversity of methanogens in the sludge process of the wastewater treatment plant. The information obtained was substantially more than that employing 16s sequencing. The methanogenic microbial resources were appropriate to sustain a self-inoculated energy recovery with a potential ability to boost methane production. A constancy was observed in 16 S rRNA gene and mcrA gene sequencing results, where the bacterial or Methanosaeta concilii dominated community of DS (digest sludge) was distinct from the inoculum sources TS (total sludge), CTS (concentrated total sludge), and HTS (hydrolysis total sludge), indicating the independent development of DS. A quantitative cross-network was constructed by coupling the absolute quantify of 16 S rRNA and mcrA sequences. The Methanobacterium petrolearium actively interacted with bacteria in the DS community rather than the dominant species (Methanosaeta concilii). Moreover, the unclassified methanogens were identified to be significantly prevalent in all communities, suggesting that unknown methanogenic taxa might be imperative in accomplishing community functions. Collectively, the findings of this research study will shed light on the comprehensive knowledge of microbial communities, especially the methanogenic microbiota. This will further enhance the exploration of the phylogenetic diversity of methanogens and their corresponding impacts in energy recovery from wastewater treatment plants.
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Affiliation(s)
- Wei Li
- Department of Municipal and Environmental Engineering, School of Civil Engineering, Beijing Jiaotong University, Beijing, 100044, China; Beijing DaBeiNong Science and Technology Group Co., Ltd., Beijing, 100080, China
| | - Thangavel Sangeetha
- Research Center of Energy Conservation for New Generation of Residential, Commercial, and Industrial Sectors; National Taipei University of Technology, Taipei, 10608, Taiwan; Department of Energy and Refrigeration Air-Conditioning Engineering, National Taipei University of Technology, Taipei, 10608, Taiwan
| | - Xiangyu Han
- Department of Municipal and Environmental Engineering, School of Civil Engineering, Beijing Jiaotong University, Beijing, 100044, China
| | - Wei-Mon Yan
- Research Center of Energy Conservation for New Generation of Residential, Commercial, and Industrial Sectors; National Taipei University of Technology, Taipei, 10608, Taiwan; Department of Energy and Refrigeration Air-Conditioning Engineering, National Taipei University of Technology, Taipei, 10608, Taiwan
| | - Lijun Yang
- Department of Municipal and Environmental Engineering, School of Civil Engineering, Beijing Jiaotong University, Beijing, 100044, China
| | - Jing Zhao
- Department of Municipal and Environmental Engineering, School of Civil Engineering, Beijing Jiaotong University, Beijing, 100044, China
| | - Weiwei Cai
- Department of Municipal and Environmental Engineering, School of Civil Engineering, Beijing Jiaotong University, Beijing, 100044, China.
| | - Hong Yao
- Department of Municipal and Environmental Engineering, School of Civil Engineering, Beijing Jiaotong University, Beijing, 100044, China
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Malik P, Trivedi S, Kolte A, Sejian V, Bhatta R, Rahman H. Diversity of rumen microbiota using metagenome sequencing and methane yield in Indian sheep fed on straw and concentrate diet. Saudi J Biol Sci 2022; 29:103345. [PMID: 35770269 PMCID: PMC9234715 DOI: 10.1016/j.sjbs.2022.103345] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 05/06/2022] [Accepted: 06/10/2022] [Indexed: 11/18/2022] Open
Abstract
Bacteroidetes and Firmicutes were most prevalent bacteria in the sheep rumen. Bacteroidetes were negatively correlated with the Euryarchaeota. Archaea constituted ∼2.5% of the ruminal microbiota. Methanobrevibacter gottschalkii constituted > 50% of the ruminal archaea. Hydrogenotrophic methanogens distribution leads to the variability in methane yield.
An in vivo study aiming to investigate the rumen methanogens community structure was conducted in Mandya sheep fed on straw and concentrate diet. The ruminal fluid samples were collected and processed for unravelling the rumen microbiota and methanogens diversity. Further, the daily enteric methane emission and methane yield was also quantified using the SF6 tracer technique. Results indicated that the Bacteroidetes (∼57%) and Firmicutes (25%) were two prominent affiliates of the bacterial community. Archaea represented about 2.5% of the ruminal microbiota. Methanobacteriales affiliated methanogens were the most prevalent in sheep rumen. The study inveterate that the ruminal archaea community in sheep is composed of 9 genera and 18 species. Methanobrevibacter represented the largest genus of the archaeome, while methylotrophs genera constituted only 13% of the community. Methanobrevibacter gottschalkii was the prominent methanogen, and Methaobrevibacter ruminantium distributed at a lower frequency (∼2.5%). Among Methanomassiliicoccales, Group 12 sp. ISO4-H5 constituted the most considerable fraction (∼11%). KEGG reference pathway for methane metabolism indicated the formation of methane through hydrogenotrophic and methylotrophic pathways, whereas the acetoclastic pathway was not functional in sheep. The enteric methane emission and methane yield was 19.7 g/d and 20.8 g/kg DMI, respectively. Various species of Methanobrevibacter were differently correlated, and the distribution of hydrogenotrophic methanogens mainly explained the variability in methane yield between the individual sheep. It can be inferred from the study that the hydrogenotrophic methanogens dominate the rumen archaeal community in sheep and methylotrophic/aceticlastic methanogens represent a minor fraction of the community. Further studies are warranted for establishing the metabolic association between the prevalent hydrogenotrophs and methylotrophs to identify the key reaction for reducing methane emission.
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Affiliation(s)
- P.K. Malik
- Bioenergetics and Environmental Science Division, ICAR-National Institute of Animal Nutrition and Physiology, Bangalore 560030, India
- Corresponding author.
| | - S. Trivedi
- Bioenergetics and Environmental Science Division, ICAR-National Institute of Animal Nutrition and Physiology, Bangalore 560030, India
| | - A.P. Kolte
- Animal Nutrition Division, ICAR-National Institute of Animal Nutrition and Physiology, Bangalore 560030, India
| | - V. Sejian
- Animal Physiology Division, ICAR-National Institute of Animal Nutrition and Physiology, Bangalore 560030, India
| | - R. Bhatta
- Director, ICAR-National Institute of Animal Nutrition and Physiology, Bangalore 560030, India
| | - H. Rahman
- International Livestock Research Institute, South Asia Regional Office, New Delhi 110 012, India
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Harris RL, Vetter MCYL, van Heerden E, Cason E, Vermeulen JG, Taneja A, Kieft TL, DeCoste CJ, Laevsky GS, Onstott TC. FISH-TAMB, a Fixation-Free mRNA Fluorescent Labeling Technique to Target Transcriptionally Active Members in Microbial Communities. Microb Ecol 2022; 84:182-197. [PMID: 34406445 PMCID: PMC9250922 DOI: 10.1007/s00248-021-01809-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 06/23/2021] [Indexed: 06/13/2023]
Abstract
Keystone species or ecological engineers are vital to the health of an ecosystem; however, often, their low abundance or biomass present challenges for their discovery, identification, visualization and selection. We report the development of fluorescent in situ hybridization of transcript-annealing molecular beacons (FISH-TAMB), a fixation-free protocol that is applicable to archaea and bacteria. The FISH-TAMB method differs from existing FISH methods by the absence of fixatives or surfactants in buffers, the fast hybridization time of as short as 15 min at target cells' growth temperature, and the omission of washing steps. Polyarginine cell-penetrating peptides are employed to deliver molecular beacons (MBs) across prokaryotic cell walls and membranes, fluorescently labeling cells when MBs hybridize to target mRNA sequences. Here, the detailed protocol of the preparation and application of FISH-TAMB is presented. To demonstrate FISH-TAMB's ability to label intracellular mRNA targets, differentiate transcriptional states, detect active and rare taxa, and keep cell viability, labeling experiments were performed that targeted the messenger RNA (mRNA) of methyl-coenzyme M reductase A (mcrA) expressed in (1) Escherichia coli containing a plasmid with a partial mcrA gene of the methanogen Methanosarcina barkeri (E. coli mcrA+); (2) M. barkeri; and (3) an anaerobic methanotrophic (ANME) enrichment from a deep continental borehole. Although FISH-TAMB was initially envisioned for mRNA of any functional gene of interest without a requirement of prior knowledge of 16S ribosomal RNA (rRNA)-based taxonomy, FISH-TAMB has the potential for multiplexing and going beyond mRNA and thus is a versatile addition to the molecular ecologist's toolkit, with potentially widespread application in the field of environmental microbiology.
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Affiliation(s)
- Rachel L Harris
- Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA.
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.
| | - Maggie C Y Lau Vetter
- Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA.
- Laboratory of Extraterrestrial Ocean Systems, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, Hainan, China.
| | - Esta van Heerden
- Centre for Water Sciences and Management, North West University, Potchefstroom, South Africa
- iWater Pty Ltd, 5 Walter Sisulu Rd, Park West, Bloemfontein, 9301, South Africa
| | - Errol Cason
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, 9301, South Africa
- Department of Animal-, Wildlife- and Grassland Sciences, University of the Free State, Bloemfontein, 9301, South Africa
| | - Jan-G Vermeulen
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, 9301, South Africa
- Department of Virology, University of the Free State, Bloemfontein, 9301, South Africa
| | - Anjali Taneja
- Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA
- McCourt School of Public Policy, Georgetown University, Washington, DC, 20057, USA
| | - Thomas L Kieft
- Department of Biology, New Mexico Institute of Mining and Technology, Socorro, NM, 87801, USA
| | - Christina J DeCoste
- Flow Cytometry Resource Facility, Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Gary S Laevsky
- Confocal Imaging Facility, Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Tullis C Onstott
- Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA
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Djemai K, Drancourt M, Tidjani Alou M. Bacteria and Methanogens in the Human Microbiome: a Review of Syntrophic Interactions. Microb Ecol 2022; 83:536-554. [PMID: 34169332 DOI: 10.1007/s00248-021-01796-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
Methanogens are microorganisms belonging to the Archaea domain and represent the primary source of biotic methane. Methanogens encode a series of enzymes which can convert secondary substrates into methane following three major methanogenesis pathways. Initially recognized as environmental microorganisms, methanogens have more recently been acknowledged as host-associated microorganisms after their detection and initial isolation in ruminants in the 1950s. Methanogens have also been co-detected with bacteria in various pathological situations, bringing their role as pathogens into question. Here, we review reported associations between methanogens and bacteria in physiological and pathological situations in order to understand the metabolic interactions explaining these associations. To do so, we describe the origin of the metabolites used for methanogenesis and highlight the central role of methanogens in the syntrophic process during carbon cycling. We then focus on the metabolic abilities of co-detected bacterial species described in the literature and infer from their genomes the probable mechanisms of their association with methanogens. The syntrophic interactions between bacteria and methanogens are paramount to gut homeostasis. Therefore, any dysbiosis affecting methanogens might impact human health. Thus, the monitoring of methanogens may be used as a bio-indicator of dysbiosis. Moreover, new therapeutic approaches can be developed based on their administration as probiotics. We thus insist on the importance of investigating methanogens in clinical microbiology.
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Affiliation(s)
- Kenza Djemai
- IRD, MEPHI, IHU Méditerranée Infection, Aix-Marseille-University, 19-12 Bd Jean Moulin, 13005, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Michel Drancourt
- IRD, MEPHI, IHU Méditerranée Infection, Aix-Marseille-University, 19-12 Bd Jean Moulin, 13005, Marseille, France
| | - Maryam Tidjani Alou
- IRD, MEPHI, IHU Méditerranée Infection, Aix-Marseille-University, 19-12 Bd Jean Moulin, 13005, Marseille, France.
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de Amarante MCA, Guerreiro PEG, Radmann EM, de Souza MDRAZ. Effect of fruits and vegetables in the anaerobic digestion of food waste from university restaurant. Appl Biochem Biotechnol 2022; 194:3365-3383. [PMID: 35357662 DOI: 10.1007/s12010-022-03895-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 03/14/2022] [Indexed: 11/30/2022]
Abstract
The aim of this study was to evaluate the theoretical potential of methane production of the food waste generated by a university restaurant, as well as to verify the influence of the fruit and vegetable waste in the feeding composition of an anaerobic bioreactor treating this type of waste. Four feeding compositions combining three fractions of the food waste (fruit and vegetable fraction, soy protein and beans fraction, and rice fraction) at different concentrations were tested in anaerobic processes lasting 10 and 30 days. Additionally, a study of the theoretical potential of methane production from each fraction that composes the food waste was carried out, as well as the evaluation of the specific methanogenic activity of the anaerobic sludge. Despite its low theoretical potential of methane production (0.037 LCH4/g), the presence of the fruit and vegetable mixture in three of the feeding compositions led to greater organic matter degradation (above 69%) and CH4 yields (above 0.20 LCH4/gVS) in both periods tested, in comparison with the achieved by the feeding composition lacking this fraction. The results suggest that the presence of the fruit and vegetable mixture contributed with the supplementation of micro- and macroelements to the anaerobic sludge during the digestion of food waste.
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Affiliation(s)
- Marina Campos Assumpção de Amarante
- School of Chemistry and Food, Universidade Federal do Rio Grande (FURG), Campus Carreiros, Avenue Italia, km 08, Mail box 474, Rio Grande, RS, 96.203-900, Brazil. .,School of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham, B15 2TT, West Midlands, UK.
| | - Pablo Eduardo Godinho Guerreiro
- School of Chemistry and Food, Universidade Federal do Rio Grande (FURG), Campus Carreiros, Avenue Italia, km 08, Mail box 474, Rio Grande, RS, 96.203-900, Brazil
| | - Elisangela Martha Radmann
- School of Chemistry and Food, Universidade Federal do Rio Grande (FURG), Campus Carreiros, Avenue Italia, km 08, Mail box 474, Rio Grande, RS, 96.203-900, Brazil
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Kong Z, Li L, Wu J, Rong C, Wang T, Chen R, Sano D, Li YY. Unveiling the characterization and development of prokaryotic community during the start-up and long-term operation of a pilot-scale anaerobic membrane bioreactor for the treatment of real municipal wastewater. Sci Total Environ 2022; 813:152643. [PMID: 34963601 DOI: 10.1016/j.scitotenv.2021.152643] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/16/2021] [Accepted: 12/19/2021] [Indexed: 06/14/2023]
Abstract
The anaerobic membrane bioreactor (AnMBR) is a promising sustainable process and technology for the treatment of municipal wastewater from the perspective of carbon neutrality. In this study, a large pilot-scale AnMBR was constructed and the microbial community development of the anaerobic digested sludge in the AnMBR was determined during the treatment of municipal wastewater. The AnMBR system was conducted for 217 days during a long-term operation with the feed of real municipal wastewater. The characterization and dynamics of the microorganisms revealed that a stable prokaryotic community was gradually achieved. In the community of methane-producing archaea (or methanogens), the acetotrophic methanogen Methanosaeta was significantly enriched at an ambient temperature of 25 °C with an overwhelming relative abundance in the entire community. The abundance of Methanosaeta was even higher than the most abundant bacterial phyla Chloroflexi, Firmicutes, Proteobacteria and Bacteroidetes. This phenomenon is quite different from that found in other typical anaerobic systems. The massive enrichment of methanogens is the key to maintaining stable methane production in the treatment of municipal wastewater by the AnMBR. The interspecies cooperation of major functional bacterial groups including protein/carbohydrate/cellulose-degrading (genera Anaerovorax, Aminomonas, Levilinea, Flexilinea and Ruminococcus etc.), sulfate-reducing (Desulfovibrio and Desulfomicrobium etc.) and syntrophic (Syntrophorhabdus and Syntrophus etc.) bacteria with acetotrophic and hydrogenotrophic archaea enhances the stability of reactor operation and help to acclimate the entire prokaryotic community to the characteristics of real municipal wastewater.
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Affiliation(s)
- Zhe Kong
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China; National and Local Joint Engineering Laboratory of Municipal Sewage Resource Utilization Technology, Suzhou University of Science and Technology, Suzhou 215009, China; Jiangsu Collaborative Innovation Center of Water Treatment Technology and Material, Suzhou University of Science and Technology, Suzhou 215009, China; Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Aoba Ward, Sendai, Miyagi 980-8579, Japan.
| | - Lu Li
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China; Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Aoba Ward, Sendai, Miyagi 980-8579, Japan
| | - Jiang Wu
- Center for Material Cycles and Waste Management Research, National Institute for Environmental Studies, Tsukuba 305-8506, Japan
| | - Chao Rong
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Aoba Ward, Sendai, Miyagi 980-8579, Japan
| | - Tianjie Wang
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Aoba Ward, Sendai, Miyagi 980-8579, Japan
| | - Rong Chen
- International S&T Cooperation Center for Urban Alternative Water Resources Development, Key Lab of Environmental Engineering, Shaanxi Province, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an 710055, PR China
| | - Daisuke Sano
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Aoba Ward, Sendai, Miyagi 980-8579, Japan
| | - Yu-You Li
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Aoba Ward, Sendai, Miyagi 980-8579, Japan.
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50
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Cho SR, Verma PP, Das S, Kim GW, Lim JY, Kim PJ. A new approach to suppress methane emissions from rice cropping systems using ethephon. Sci Total Environ 2022; 804:150159. [PMID: 34509846 DOI: 10.1016/j.scitotenv.2021.150159] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/30/2021] [Accepted: 09/01/2021] [Indexed: 06/13/2023]
Abstract
Rice is the main staple food for more than half of the world's population. Yet, rice cultivation is subjected to criticism because of its important role in methane (CH4) emissions. Although several agronomic practices such as controlled irrigation and conservation tillage have been widely adopted to mitigate CH4 emissions from rice cultivation, the benefits gained by these practices are highly dependent on site-specific soil and climate conditions, and often offset by yield reduction. The use of plant growth regulating compounds having the potential to increase the crop yield and mitigate CH4 emissions may be an innovative approach to sustainable agriculture. Ethylene (C2H4), a plant growth regulator is known to have a strong inhibitory effect on methanogenesis. However, due to gaseous form and low water solubility, C2H4 has not been used to suppress methanogenesis in paddy fields. To develop C2H4 as a prospective soil amendment for reducing methane (CH4) emissions, ethephon (2-Chloroethylphosphonic acid), a precursor of C2H4 was tested. We found that ethephon reduced CH4 formation by 43%, similar to other well known methanogenic inhibitors (2-Bromoethanesulfonate, 2-Chlomoethanesulfonate, 2-Mercaptoethanesulfonate). However, ethephon rapidly hydrolyzed to C2H4 and methanogenic activity recuperated completely after C2H4 removal. To slow down the release of C2H4, ethephon was mixed with bio-degradable polymers such as cellulose acetate and applied to paddy soils. We found that compared with the control, the C2H4 release of ethephon slowed down to 90 days, and the CH4 emissions were reduced by 90%. The application of ethephon at lower concentrations did not significantly alter bacterial communities, their relative abundance, and the abundance of methanotrophs, but it significantly reduced archaeal communities and the relative abundance and expression level of methanogens in paddy soils. Results suggest that cellulose acetate-mixed ethephon has great promise to suppress CH4 emissions in rice paddies while ensuring sustainable yields.
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Affiliation(s)
- Song Rae Cho
- Division of Applied Life Science (BK 21 plus program), Graduate School, Gyeongsang National University (GNU), Jinju-city 52828, South Korea
| | - Pankaj Prakash Verma
- Institute of Agriculture and Life Sciences (IALS), Gyeongsang National University (GNU), Jinju-city 52828, South Korea
| | - Suvendu Das
- Institute of Agriculture and Life Sciences (IALS), Gyeongsang National University (GNU), Jinju-city 52828, South Korea
| | - Gil Won Kim
- Institute of Agriculture and Life Sciences (IALS), Gyeongsang National University (GNU), Jinju-city 52828, South Korea
| | - Ji Yeon Lim
- Institute of Agriculture and Life Sciences (IALS), Gyeongsang National University (GNU), Jinju-city 52828, South Korea
| | - Pil Joo Kim
- Division of Applied Life Science (BK 21 plus program), Graduate School, Gyeongsang National University (GNU), Jinju-city 52828, South Korea; Institute of Agriculture and Life Sciences (IALS), Gyeongsang National University (GNU), Jinju-city 52828, South Korea.
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