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Zhang L, Lin W, Sardans J, Li X, Hui D, Yang Z, Wang H, Lin H, Wang Y, Guo J, Peñuelas J, Yang Y. Soil warming-induced reduction in water content enhanced methane uptake at different soil depths in a subtropical forest. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:171994. [PMID: 38561130 DOI: 10.1016/j.scitotenv.2024.171994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/05/2024] [Accepted: 03/24/2024] [Indexed: 04/04/2024]
Abstract
Global warming can significantly impact soil CH4 uptake in subtropical forests due to changes in soil moisture, temperature sensitivity of methane-oxidizing bacteria (MOB), and shifts in microbial communities. However, the specific effects of climate warming and the underlying mechanisms on soil CH4 uptake at different soil depths remain poorly understood. To address this knowledge gap, we conducted a soil warming experiment (+4 °C) in a natural forest. From August 2020 to October 2021, we measured soil temperature, soil moisture, and CH4 uptake rates at four different soil depths: 0-10 cm, 10-20 cm, 20-40 cm, and 40-60 cm. Additionally, we assessed the soil MOB community structure and pmoA gene (with qPCR) at the 0-10 and 10-20 cm depths. Our findings revealed that warming significantly enhanced soil net CH4 uptake rate by 12.28 %, 29.51 %, and 61.05 % in the 0-10, 20-40, and 40-60 cm soil layers, respectively. The warming also led to reduced soil moisture levels, with more pronounced reductions observed at the 20-40 cm depth compared to the 0-20 cm depth. At the 0-10 cm depth, warming increased the relative abundance of upland soil cluster α (a type of MOB) and decreased the relative abundance of Methylocystis, but it did not significantly increase the pmoA gene copies. Our structural equation model analysis indicated that warming directly regulated soil CH4 uptake rate through the decrease in soil moisture, rather than through changes in the pmoA gene and MOB community structure at the 0-20 cm depth. In summary, our results demonstrate that warming enhances soil CH4 uptake at different depths, with soil moisture playing a crucial role in this process. Under warming conditions, the drier soil pores allow for better CH4 penetration, thereby promoting more efficient activity of MOB.
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Affiliation(s)
- Lei Zhang
- Fujian Provincial Key Laboratory for Plant Eco-physiology, Fujian Normal University, Fuzhou 350117, China
| | - Weisheng Lin
- Fujian Provincial Key Laboratory for Plant Eco-physiology, Fujian Normal University, Fuzhou 350117, China; Institute of Geography, Fujian Normal University, Fuzhou 350117, China; Fujian Sanming Forest Ecosystem National Observation and Research Station, Fujian normal University, Sanming 365002, China.
| | - Jordi Sardans
- CSIC, Global Ecology Unit, CREAF-CSIC-UAB, Bellaterra, Barcelona 08193, Catalonia, Spain; CREAF, Cerdanyola del Vallès, Barcelona 08193, Catalonia, Spain
| | - Xiaoling Li
- Fujian Provincial Key Laboratory for Plant Eco-physiology, Fujian Normal University, Fuzhou 350117, China
| | - Dafeng Hui
- Department of Biological Sciences, Tennessee State University, Nashville, TN 37209, USA
| | - Zhijie Yang
- Fujian Provincial Key Laboratory for Plant Eco-physiology, Fujian Normal University, Fuzhou 350117, China; Institute of Geography, Fujian Normal University, Fuzhou 350117, China; Fujian Sanming Forest Ecosystem National Observation and Research Station, Fujian normal University, Sanming 365002, China
| | - Haizhen Wang
- Fujian Provincial Key Laboratory for Plant Eco-physiology, Fujian Normal University, Fuzhou 350117, China
| | - Hao Lin
- Fujian Provincial Key Laboratory for Plant Eco-physiology, Fujian Normal University, Fuzhou 350117, China
| | - Yufang Wang
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, Gansu Province, China
| | - Jianfen Guo
- Fujian Provincial Key Laboratory for Plant Eco-physiology, Fujian Normal University, Fuzhou 350117, China; Institute of Geography, Fujian Normal University, Fuzhou 350117, China; Fujian Sanming Forest Ecosystem National Observation and Research Station, Fujian normal University, Sanming 365002, China.
| | - Josep Peñuelas
- CSIC, Global Ecology Unit, CREAF-CSIC-UAB, Bellaterra, Barcelona 08193, Catalonia, Spain; CREAF, Cerdanyola del Vallès, Barcelona 08193, Catalonia, Spain
| | - Yusheng Yang
- Institute of Geography, Fujian Normal University, Fuzhou 350117, China; Fujian Sanming Forest Ecosystem National Observation and Research Station, Fujian normal University, Sanming 365002, China
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2
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Cao W, Zhao J, Cai Y, Mo Y, Ma J, Zhang G, Jiang X, Jia Z. Ridge with no-tillage facilitates microbial N 2 fixation associated with methane oxidation in rice soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 923:171172. [PMID: 38402982 DOI: 10.1016/j.scitotenv.2024.171172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 02/14/2024] [Accepted: 02/20/2024] [Indexed: 02/27/2024]
Abstract
Aerobic methane-oxidizing bacteria (MOB) play a crucial role in mitigating the greenhouse gas methane emission, particularly prevalent in flooded wetlands. The implementation of ridge with no-tillage practices within a rice-rape rotation system proves effective in overcoming the restrictive redox conditions associated with waterlogging. This approach enhances capillary water availability from furrows, especially during periods of low rainfall, thereby supporting plant growth on the ridges. However, the microbe-mediated accumulation of soil organic carbon and nitrogen remains insufficiently understood under this agricultural practice, particularly concerning methane oxidation, which holds ecological and agricultural significance in the rice fields. In this study, the ridge and ditch soils from a 28-year-old ridge with no-tillage rice field experiment were utilized for incubation with 13C-CH4 and 15NN2 to estimate the methane-oxidizing and N2-fixing potentials. Our findings reveal a significantly higher net production of fresh soil organic carbon in the ridge compared to the ditch soil during methane oxidation, with values of 626 and 543 μg 13C g-1 dry weight soil, respectively. Additionally, the fixed 15N exhibited a twofold increase in the ridge soil (14.1 μg 15N g-1 dry weight soil) compared to the ditch soil. Interestingly, the result of DNA-based stable isotope probing indicated no significant differences in active MOB and N2 fixers between ridge and ditch soils. Both Methylocystis-like type II and Methylosarcina/Methylomonas-like type I MOB catalyzed methane into organic biomass carbon pools. Soil N2-fixing activity was associated with the 15N-labeling of methane oxidizers and non-MOB, such as methanol oxidizers (Hyphomicrobium) and conventional N2 fixers (Burkholderia). Methane oxidation also fostered microbial interactions, as evidenced by co-occurrence patterns. These results underscore the dual role of microbial methane oxidation - not only as a recognized sink for the potent greenhouse gas methane but also as a source of soil organic carbon and bioavailable nitrogen. This emphasizes the pivotal role of microbial methane metabolism in contributing to soil carbon and nitrogen accumulation in ridge with no-tillage systems.
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Affiliation(s)
- Weiwei Cao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Jun Zhao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; Institute for Food and Agricultural Sciences (IFAS), Department of Microbiology & Cell Science, Fort Lauderdale Research and Education Center, University of Florida, Davie, FL 33314, USA
| | - Yuanfeng Cai
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Yongliang Mo
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; College of Environmental Science and Engineering, China West Normal University, Nanchong 637002, PR China
| | - Jingjing Ma
- Northeast Institute of Geography and Agroecology, Chinese Academy of Science, Changchun 130102, PR China
| | - Guangbin Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Xianjun Jiang
- College of Resources and Environment, Southwest University, Chongqing 400715, PR China
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China; Northeast Institute of Geography and Agroecology, Chinese Academy of Science, Changchun 130102, PR China.
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3
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Wen F, Biederman JA, Hao Y, Qian R, Zheng Z, Cui X, Zhao T, Xue K, Wang Y. Extreme drought alters methane uptake but not methane sink in semi-arid steppes of Inner Mongolia. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 915:169834. [PMID: 38190902 DOI: 10.1016/j.scitotenv.2023.169834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/25/2023] [Accepted: 12/30/2023] [Indexed: 01/10/2024]
Abstract
Global climate change, particularly drought, is expected to alter grassland methane (CH4) oxidation, a key natural process against atmospheric greenhouse gas accumulation, yet the extent of this effect and its interaction with future atmospheric CH4 concentrations increases remains uncertain. To address this research gap, we measured CH4 flux during an imposed three-month rain-free period corresponding to a 100-year recurrence drought in soil mesocosms collected from 16 different Eurasian steppe sites. We also investigated the abundance and composition of methanotrophs. Additionally, we conducted a laboratory experiment to explore the impact of elevated CH4 concentration on the CH4 uptake capacity of grassland soil under drought conditions. We found that regardless of the type of grassland, CH4 flux was still being absorbed at its peak, meaning that all grasslands functioned as persistent CH4 sinks even when the soil water content (SWC) was <5 %. A bell-shaped relationship between SWC and CH4 uptake was observed in the soils. The average maximum CH4 oxidation rate in the meadow steppe was higher than that in the typical and desert steppe soils during extreme drought. The experimental elevation of atmospheric CH4 concentration counteracted the anticipated reduction in CH4 uptake related to physiological water stress on methanotrophic soil microbes under the drought stress. On the contrary, we found that across the regional scale, nitrogen, phosphorous, and total soil organic content played a crucial role in moderating the duration and magnitude of CH4 uptake with respect to SWC. USC-γ (Upland Soil Cluster γ) and JR-3 (Jasper Ridge Cluster) were the dominant group of soil methanotrophic bacteria in three types of grassland. However, the methanotrophic abundance, rather than the methanotrophic community composition, was the dominant microbiological factor governing CH4 uptake during the drought.
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Affiliation(s)
- Fuqi Wen
- College of Life Sciences, University Chinese Academy of Sciences, Beijing, China
| | - Joel A Biederman
- Southwest Watershed Research Center, Agricultural Research Service, Tucson, AZ, USA
| | - Yanbin Hao
- College of Life Sciences, University Chinese Academy of Sciences, Beijing, China; Yanshan Earth Critical Zone and Surface Fluxes Research Station, Chinese Academy of Sciences, Beijing 101408, China..
| | - Ruyan Qian
- College of Life Sciences, University Chinese Academy of Sciences, Beijing, China
| | - Zhenzhen Zheng
- College of Life Sciences, University Chinese Academy of Sciences, Beijing, China
| | - Xiaoyong Cui
- College of Life Sciences, University Chinese Academy of Sciences, Beijing, China; Yanshan Earth Critical Zone and Surface Fluxes Research Station, Chinese Academy of Sciences, Beijing 101408, China
| | - Tong Zhao
- School of Mathematics Sciences, University Chinese Academy of Sciences, Beijing 101408, China
| | - Kai Xue
- Yanshan Earth Critical Zone and Surface Fluxes Research Station, Chinese Academy of Sciences, Beijing 101408, China.; Key Laboratory of Adaptation and Evolution of Plateau Biota, Chinese Academy of Sciences, Xining 810001, China; College of Resources and Environment, University Chinese Academy of Sciences, Beijing 101408, China
| | - Yanfen Wang
- Yanshan Earth Critical Zone and Surface Fluxes Research Station, Chinese Academy of Sciences, Beijing 101408, China.; College of Resources and Environment, University Chinese Academy of Sciences, Beijing 101408, China
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Venetz J, Żygadłowska OM, Dotsios N, Wallenius AJ, van Helmond NAGM, Lenstra WK, Klomp R, Slomp CP, Jetten MSM, Veraart AJ. Seasonal dynamics of the microbial methane filter in the water column of a eutrophic coastal basin. FEMS Microbiol Ecol 2024; 100:fiae007. [PMID: 38281061 PMCID: PMC10939384 DOI: 10.1093/femsec/fiae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/08/2023] [Accepted: 01/25/2024] [Indexed: 01/29/2024] Open
Abstract
In coastal waters, methane-oxidizing bacteria (MOB) can form a methane biofilter and mitigate methane emissions. The metabolism of these MOBs is versatile, and the resilience to changing oxygen concentrations is potentially high. It is still unclear how seasonal changes in oxygen availability and water column chemistry affect the functioning of the methane biofilter and MOB community composition. Here, we determined water column methane and oxygen depth profiles, the methanotrophic community structure, methane oxidation potential, and water-air methane fluxes of a eutrophic marine basin during summer stratification and in the mixed water in spring and autumn. In spring, the MOB diversity and relative abundance were low. Yet, MOB formed a methane biofilter with up to 9% relative abundance and vertical niche partitioning during summer stratification. The vertical distribution and potential methane oxidation of MOB did not follow the upward shift of the oxycline during summer, and water-air fluxes remained below 0.6 mmol m-2 d-1. Together, this suggests active methane removal by MOB in the anoxic water. Surprisingly, with a weaker stratification, and therefore potentially increased oxygen supply, methane oxidation rates decreased, and water-air methane fluxes increased. Thus, despite the potential resilience of the MOB community, seasonal water column dynamics significantly influence methane removal.
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Affiliation(s)
- Jessica Venetz
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Olga M Żygadłowska
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, 3508 TA Utrecht, The Netherlands
| | - Nicky Dotsios
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Anna J Wallenius
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Niels A G M van Helmond
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, 6525 AJ Nijmegen, The Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, 3508 TA Utrecht, The Netherlands
| | - Wytze K Lenstra
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, 6525 AJ Nijmegen, The Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, 3508 TA Utrecht, The Netherlands
| | - Robin Klomp
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, 6525 AJ Nijmegen, The Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, 3508 TA Utrecht, The Netherlands
| | - Caroline P Slomp
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, 6525 AJ Nijmegen, The Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, 3508 TA Utrecht, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Annelies J Veraart
- Department of Aquatic Ecology and Environmental Biology, Radboud Institute for Biological and Environmental Sciences, Radboud University, 6525 AJ Nijmegen, The Netherlands
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5
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Lim J, Wehmeyer H, Heffner T, Aeppli M, Gu W, Kim PJ, Horn MA, Ho A. Resilience of aerobic methanotrophs in soils; spotlight on the methane sink under agriculture. FEMS Microbiol Ecol 2024; 100:fiae008. [PMID: 38327184 PMCID: PMC10872700 DOI: 10.1093/femsec/fiae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 01/19/2024] [Accepted: 02/06/2024] [Indexed: 02/09/2024] Open
Abstract
Aerobic methanotrophs are a specialized microbial group, catalyzing the oxidation of methane. Disturbance-induced loss of methanotroph diversity/abundance, thus results in the loss of this biological methane sink. Here, we synthesized and conceptualized the resilience of the methanotrophs to sporadic, recurring, and compounded disturbances in soils. The methanotrophs showed remarkable resilience to sporadic disturbances, recovering in activity and population size. However, activity was severely compromised when disturbance persisted or reoccurred at increasing frequency, and was significantly impaired following change in land use. Next, we consolidated the impact of agricultural practices after land conversion on the soil methane sink. The effects of key interventions (tillage, organic matter input, and cover cropping) where much knowledge has been gathered were considered. Pairwise comparisons of these interventions to nontreated agricultural soils indicate that the agriculture-induced impact on the methane sink depends on the cropping system, which can be associated to the physiology of the methanotrophs. The impact of agriculture is more evident in upland soils, where the methanotrophs play a more prominent role than the methanogens in modulating overall methane flux. Although resilient to sporadic disturbances, the methanotrophs are vulnerable to compounded disturbances induced by anthropogenic activities, significantly affecting the methane sink function.
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Affiliation(s)
- Jiyeon Lim
- Institute for Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Helena Wehmeyer
- Nestlè Research, Route du Jorat 57, CH 1000 Lausanne 26, Switzerland
| | - Tanja Heffner
- Institute for Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Meret Aeppli
- Environmental Engineering Institute IIE-ENAC, Laboratory SOIL, Ecole Polytechnique Fédérale de Lausanne (EPFL), Valais Wallis, CH 1950 Sion, Switzerland
| | - Wenyu Gu
- Environmental Engineering Institute IIE-ENAC, Laboratory MICROBE, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH 1015 Lausanne, Switzerland
| | - Pil Joo Kim
- Division of Applied Life Science, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Marcus A Horn
- Institute for Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Adrian Ho
- Nestlè Research, Route du Jorat 57, CH 1000 Lausanne 26, Switzerland
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Cantera S, Rodríguez E, Santaella Vecchini N, López JC, García-Encina PA, Sousa DZ, Muñoz R. Resilience and robustness of alphaproteobacterial methanotrophs upon methane feast-famine scenarios. ENVIRONMENTAL RESEARCH 2023; 239:117376. [PMID: 37832766 DOI: 10.1016/j.envres.2023.117376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/27/2023] [Accepted: 10/10/2023] [Indexed: 10/15/2023]
Abstract
Most of methane (CH4) emissions contain low CH4 concentrations and typically occur at irregular intervals, which hinders the implementation and performance of methane abatement processes. This study aimed at understanding the metabolic mechanisms that allow methane oxidizing bacteria (MOB) to survive for long periods of time under methane starvation. To this aim, we used an omics-approach and studied the diversity and metabolism of MOB and non-MOB in bioreactors exposed to low CH4 concentrations under feast-famine cycles of 5 days and supplied with nutrient-rich broth. The 16S rRNA and the pmoA transcripts revealed that the most abundant and active MOB during feast and famine conditions belonged to the alphaproteobacterial genus Methylocystis (91-65%). The closest Methylocystis species were M. parvus and M. echinoides. Nitrifiers and denitrifiers were the most representative non-MOB communities, which likely acted as detoxifiers of the system. During starvation periods, the induced activity of CH4 oxidation was not lost, with the particulate methane monooxygenase of alphaproteobacterial MOB playing a key role in energy production. The polyhydroxyalkanoate and nitrification metabolisms of MOB had also an important role during feast-famine cycles, maintaining cell viability when CH4 concentrations were negligible. This research shows that there is an emergence and resilience of conventional alphaproteobacterial MOB, being the genus Methylocystis a centrepiece in environments exposed to dilute and intermittent methane emissions. This knowledge can be applied to the operation of bioreactors subjected to the treatment of dilute and discontinuous emissions via controlled bioaugmentation.
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Affiliation(s)
- Sara Cantera
- Institute of Sustainable Processes, University of Valladolid, Dr. Mergelina s/n., Valladolid, 47011, Spain; Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708WE, Wageningen, the Netherlands.
| | - Elisa Rodríguez
- Institute of Sustainable Processes, University of Valladolid, Dr. Mergelina s/n., Valladolid, 47011, Spain; Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina s/n., Valladolid, 47011, Spain
| | - Nicolás Santaella Vecchini
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708WE, Wageningen, the Netherlands
| | - Juan Carlos López
- Institute of Sustainable Processes, University of Valladolid, Dr. Mergelina s/n., Valladolid, 47011, Spain; Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina s/n., Valladolid, 47011, Spain
| | - Pedro A García-Encina
- Institute of Sustainable Processes, University of Valladolid, Dr. Mergelina s/n., Valladolid, 47011, Spain; Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina s/n., Valladolid, 47011, Spain
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708WE, Wageningen, the Netherlands
| | - Raul Muñoz
- Institute of Sustainable Processes, University of Valladolid, Dr. Mergelina s/n., Valladolid, 47011, Spain; Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina s/n., Valladolid, 47011, Spain.
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7
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Jiang O, Li Y, Zheng Y, Gustave W, Tang X, Xu J. Cadmium reduced methane emissions by stimulating methane oxidation in paddy soils. ENVIRONMENTAL RESEARCH 2023; 238:117096. [PMID: 37683790 DOI: 10.1016/j.envres.2023.117096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/17/2023] [Accepted: 09/05/2023] [Indexed: 09/10/2023]
Abstract
Flooded rice paddy fields are a significant source of anthropogenic methane (CH4) emissions. Cadmium (Cd) is one of the most common and toxic contaminants in paddy soils. However, little is known about how the soil microbial communities associated with CH4 emissions respond to the increasing Cd-stress in paddies. In this study, we employed isotopically 13C-labelled CH4, high-throughput sequencing analysis, and gene quantification analysis to reveal the effect and mechanism of Cd on CH4 emissions in paddy soils. Results showed that 4.0 mg kg-1 Cd addition reduced CH4 emissions by 16-99% in the four tested paddy soils, and significantly promoted the transformation of 13CH4 to 13CO2. Quantitative polymerase chain reaction (qPCR) demonstrated that Cd addition increased the abundances of pmoA gene, the ratios of methanogens to methanotrophs (mcrA/pmoA) showed a positive correlation with CH4 emissions (R2 = 0.798, p < 0.01). Furthermore, the composition of the microbial community containing the pmoA gene was barely affected by Cd addition (p > 0.05). This observation was consistent with the findings of a pure incubation experiment where methanotrophs exhibited high tolerance to Cd. We argue that microbial feedback to Cd stress amplifies the contribution of methanotrophs to CH4 oxidation in rice fields through the complex interactions occurring among soil microbes. Our study highlights the overlooked association between Cd and CH4 dynamics, offering a better understanding of the role of rice paddies in global CH4 cycling.
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Affiliation(s)
- Ouyuan Jiang
- MOE Key Lab of Environmental Remediation and Ecosystem Health, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yong Li
- MOE Key Lab of Environmental Remediation and Ecosystem Health, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yue Zheng
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Williamson Gustave
- Chemistry, Environmental & Life Sciences, University of The Bahamas, New Providence, Nassau, China
| | - Xianjin Tang
- MOE Key Lab of Environmental Remediation and Ecosystem Health, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Jianming Xu
- MOE Key Lab of Environmental Remediation and Ecosystem Health, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
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8
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Aliperti L, Aptekmann AA, Farfañuk G, Couso LL, Soler-Bistué A, Sánchez IE. r/K selection of GC content in prokaryotes. Environ Microbiol 2023; 25:3255-3268. [PMID: 37813828 DOI: 10.1111/1462-2920.16511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 09/16/2023] [Indexed: 10/11/2023]
Abstract
The guanine/cytosine (GC) content of prokaryotic genomes is species-specific, taking values from 16% to 77%. This diversity of selection for GC content remains contentious. We analyse the correlations between GC content and a range of phenotypic and genotypic data in thousands of prokaryotes. GC content integrates well with these traits into r/K selection theory when phenotypic plasticity is considered. High GC-content prokaryotes are r-strategists with cheaper descendants thanks to a lower average amino acid metabolic cost, colonize unstable environments thanks to flagella and a bacillus form and are generalists in terms of resource opportunism and their defence mechanisms. Low GC content prokaryotes are K-strategists specialized for stable environments that maintain homeostasis via a high-cost outer cell membrane and endospore formation as a response to nutrient deprivation, and attain a higher nutrient-to-biomass yield. The lower proteome cost of high GC content prokaryotes is driven by the association between GC-rich codons and cheaper amino acids in the genetic code, while the correlation between GC content and genome size may be partly due to functional diversity driven by r/K selection. In all, molecular diversity in the GC content of prokaryotes may be a consequence of ecological r/K selection.
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Affiliation(s)
- Lucio Aliperti
- Facultad de Ciencias Exactas y Naturales. Laboratorio de Fisiología de Proteínas, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Ariel A Aptekmann
- Marine and Coastal Sciences Department, Rutgers University, New Brunswick, New Jersey, USA
| | - Gonzalo Farfañuk
- Facultad de Ciencias Exactas y Naturales. Laboratorio de Fisiología de Proteínas, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Luciana L Couso
- Facultad de Agronomía, Cátedra de Genética, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Alfonso Soler-Bistué
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo A. Ugalde, CONICET, Universidad Nacional de San Martín, San Martin, Argentina
| | - Ignacio E Sánchez
- Facultad de Ciencias Exactas y Naturales. Laboratorio de Fisiología de Proteínas, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Buenos Aires, Argentina
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Couso LL, Soler-Bistué A, Aptekmann AA, Sánchez IE. Ecology theory disentangles microbial dichotomies. Environ Microbiol 2023; 25:3052-3063. [PMID: 37658654 DOI: 10.1111/1462-2920.16495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 08/09/2023] [Indexed: 09/03/2023]
Abstract
Microbes are often discussed in terms of dichotomies such as copiotrophic/oligotrophic and fast/slow-growing microbes, defined using the characterisation of microbial growth in isolated cultures. The dichotomies are usually qualitative and/or study-specific, sometimes precluding clear-cut results interpretation. We can unravel microbial dichotomies as life history strategies by combining ecology theory with Monod curves, a laboratory mathematical tool of bacterial physiology that relates the specific growth rate of a microbe with the concentration of a limiting nutrient. Fitting of Monod curves provides quantities that directly correspond to key parameters in ecological theories addressing species coexistence and diversity, such as r/K selection theory, resource competition and community structure theory and the CSR triangle of life strategies. The resulting model allows us to reconcile the copiotrophic/oligotrophic and fast/slow-growing dichotomies as different subsamples of a life history strategy triangle that also includes r/K strategists. We also used the number of known carbon sources together with community structure theory to partially explain the diversity of heterotrophic microbes observed in metagenomics experiments. In sum, we propose a theoretical framework for the study of natural microbial communities that unifies several existing proposals. Its application would require the integration of metagenomics, metametabolomics, Monod curves and carbon source data.
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Affiliation(s)
- Luciana L Couso
- Facultad de Agronomía. Cátedra de Genética, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Alfonso Soler-Bistué
- Instituto de Investigaciones Biotecnológicas "Rodolfo A. Ugalde", IIB-IIBIO, Universidad Nacional de San Martín-CONICET, San Martín, Buenos Aires, Argentina
| | - Ariel A Aptekmann
- Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, Laboratorio de Fisiología de Proteínas, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Ignacio E Sánchez
- Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, Laboratorio de Fisiología de Proteínas, Universidad de Buenos Aires, Buenos Aires, Argentina
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10
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Pérez G, Krause SMB, Bodelier PLE, Meima-Franke M, Pitombo L, Irisarri P. Interactions between Cyanobacteria and Methane Processing Microbes Mitigate Methane Emissions from Rice Soils. Microorganisms 2023; 11:2830. [PMID: 38137974 PMCID: PMC10745823 DOI: 10.3390/microorganisms11122830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/16/2023] [Accepted: 11/18/2023] [Indexed: 12/24/2023] Open
Abstract
Cyanobacteria play a relevant role in rice soils due to their contribution to soil fertility through nitrogen (N2) fixation and as a promising strategy to mitigate methane (CH4) emissions from these systems. However, information is still limited regarding the mechanisms of cyanobacterial modulation of CH4 cycling in rice soils. Here, we focused on the response of methane cycling microbial communities to inoculation with cyanobacteria in rice soils. We performed a microcosm study comprising rice soil inoculated with either of two cyanobacterial isolates (Calothrix sp. and Nostoc sp.) obtained from a rice paddy. Our results demonstrate that cyanobacterial inoculation reduced CH4 emissions by 20 times. Yet, the effect on CH4 cycling microbes differed for the cyanobacterial strains. Type Ia methanotrophs were stimulated by Calothrix sp. in the surface layer, while Nostoc sp. had the opposite effect. The overall pmoA transcripts of Type Ib methanotrophs were stimulated by Nostoc. Methanogens were not affected in the surface layer, while their abundance was reduced in the sub surface layer by the presence of Nostoc sp. Our results indicate that mitigation of methane emission from rice soils based on cyanobacterial inoculants depends on the proper pairing of cyanobacteria-methanotrophs and their respective traits.
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Affiliation(s)
- Germán Pérez
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands or (G.P.); (S.M.B.K.); (M.M.-F.)
- Laboratory of Microbiology, Department of Plant Biology, Agronomy Faculty, University of the Republic, Montevideo 12900, Uruguay;
| | - Sascha M. B. Krause
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands or (G.P.); (S.M.B.K.); (M.M.-F.)
- School of Ecology and Environmental Sciences, East China Normal University, Shanghai 200062, China
| | - Paul L. E. Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands or (G.P.); (S.M.B.K.); (M.M.-F.)
| | - Marion Meima-Franke
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands or (G.P.); (S.M.B.K.); (M.M.-F.)
| | - Leonardo Pitombo
- Department of Environmental Sciences, Federal University of São Carlos (UFSCar), São Paulo 18052-780, Brazil;
| | - Pilar Irisarri
- Laboratory of Microbiology, Department of Plant Biology, Agronomy Faculty, University of the Republic, Montevideo 12900, Uruguay;
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11
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Baril X, Constant P. Carbon amendments in soil microcosms induce uneven response on H2 oxidation activity and microbial community composition. FEMS Microbiol Ecol 2023; 99:fiad159. [PMID: 38040657 PMCID: PMC10716739 DOI: 10.1093/femsec/fiad159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/27/2023] [Accepted: 11/30/2023] [Indexed: 12/03/2023] Open
Abstract
High-affinity H2-oxidizing bacteria (HA-HOB) thriving in soil are responsible for the most important sink of atmospheric H2. Their activity increases with soil organic carbon content, but the incidence of different carbohydrate fractions on the process has received little attention. Here we tested the hypothesis that carbon amendments impact HA-HOB activity and diversity differentially depending on their recalcitrance and their concentration. Carbon sources (sucrose, starch, cellulose) and application doses (0, 0.1, 1, 3, 5% Ceq soildw-1) were manipulated in soil microcosms. Only 0.1% Ceq soildw-1 cellulose treatment stimulated the HA-HOB activity. Sucrose amendments induced the most significant changes, with an abatement of 50% activity at 1% Ceq soildw-1. This was accompanied with a loss of bacterial and fungal alpha diversity and a reduction of high-affinity group 1 h/5 [NiFe]-hydrogenase gene (hhyL) abundance. A quantitative classification framework was elaborated to assign carbon preference traits to 16S rRNA gene, ITS and hhyL genotypes. The response was uneven at the taxonomic level, making carbon preference a difficult trait to predict. Overall, the results suggest that HA-HOB activity is more susceptible to be stimulated by low doses of recalcitrant carbon, while labile carbon-rich environment is an unfavorable niche for HA-HOB, inducing catabolic repression of hydrogenase.
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Affiliation(s)
- Xavier Baril
- Institut national de la recherche scientifique, Centre Armand-Frappier Santé Biotechnologie, 531 boulevard des Prairies, Laval, Québec H7V 1B7, Canada
| | - Philippe Constant
- Institut national de la recherche scientifique, Centre Armand-Frappier Santé Biotechnologie, 531 boulevard des Prairies, Laval, Québec H7V 1B7, Canada
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12
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Venetz J, Żygadłowska OM, Lenstra WK, van Helmond NAGM, Nuijten GHL, Wallenius AJ, Dalcin Martins P, Slomp CP, Jetten MSM, Veraart AJ. Versatile methanotrophs form an active methane biofilter in the oxycline of a seasonally stratified coastal basin. Environ Microbiol 2023; 25:2277-2288. [PMID: 37381163 DOI: 10.1111/1462-2920.16448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 05/31/2023] [Indexed: 06/30/2023]
Abstract
The potential and drivers of microbial methane removal in the water column of seasonally stratified coastal ecosystems and the importance of the methanotrophic community composition for ecosystem functioning are not well explored. Here, we combined depth profiles of oxygen and methane with 16S rRNA gene amplicon sequencing, metagenomics and methane oxidation rates at discrete depths in a stratified coastal marine system (Lake Grevelingen, The Netherlands). Three amplicon sequence variants (ASVs) belonging to different genera of aerobic Methylomonadaceae and the corresponding three methanotrophic metagenome-assembled genomes (MOB-MAGs) were retrieved by 16S rRNA sequencing and metagenomic analysis, respectively. The abundances of the different methanotrophic ASVs and MOB-MAGs peaked at different depths along the methane oxygen counter-gradient and the MOB-MAGs show a quite diverse genomic potential regarding oxygen metabolism, partial denitrification and sulphur metabolism. Moreover, potential aerobic methane oxidation rates indicated high methanotrophic activity throughout the methane oxygen counter-gradient, even at depths with low in situ methane or oxygen concentration. This suggests that niche-partitioning with high genomic versatility of the present Methylomonadaceae might contribute to the functional resilience of the methanotrophic community and ultimately the efficiency of methane removal in the stratified water column of a marine basin.
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Affiliation(s)
- Jessica Venetz
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Olga M Żygadłowska
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Wytze K Lenstra
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Niels A G M van Helmond
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Guylaine H L Nuijten
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Anna J Wallenius
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Paula Dalcin Martins
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Caroline P Slomp
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Annelies J Veraart
- Department of Aquatic Ecology and Environmental Biology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
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13
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Wood JL, Malik AA, Greening C, Green PT, McGeoch M, Franks AE. Rethinking CSR theory to incorporate microbial metabolic diversity and foraging traits. THE ISME JOURNAL 2023; 17:1793-1797. [PMID: 37596410 PMCID: PMC10579239 DOI: 10.1038/s41396-023-01486-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 07/20/2023] [Accepted: 07/24/2023] [Indexed: 08/20/2023]
Affiliation(s)
- J L Wood
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Melbourne, VIC, Australia.
- Research Centre for Future Landscapes, La Trobe University, Melbourne, VIC, Australia.
| | - A A Malik
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK
| | - C Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
- Securing Antarctica's Environmental Future, Monash University, Clayton, VIC, 3800, Australia
| | - P T Green
- Research Centre for Future Landscapes, La Trobe University, Melbourne, VIC, Australia
- Department of Environment and Genetics, La Trobe University, Melbourne, VIC, Australia
| | - M McGeoch
- Securing Antarctica's Environmental Future, Monash University, Clayton, VIC, 3800, Australia
- Department of Environment and Genetics, La Trobe University, Melbourne, VIC, Australia
| | - A E Franks
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Melbourne, VIC, Australia
- Research Centre for Future Landscapes, La Trobe University, Melbourne, VIC, Australia
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14
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van den Bergh SG, Chardon I, Meima-Franke M, Costa OYA, Korthals GW, de Boer W, Bodelier PLE. The intrinsic methane mitigation potential and associated microbes add product value to compost. WASTE MANAGEMENT (NEW YORK, N.Y.) 2023; 170:17-32. [PMID: 37542791 DOI: 10.1016/j.wasman.2023.07.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/20/2023] [Accepted: 07/23/2023] [Indexed: 08/07/2023]
Abstract
Conventional agricultural activity reduces the uptake of the potent greenhouse gas methane by agricultural soils. However, the recently observed improved methane uptake capacity of agricultural soils after compost application is promising but needs mechanistic understanding. In this study, the methane uptake potential and microbiomes involved in methane cycling were assessed in green compost and household-compost with and without pre-digestion. In bottle incubations of different composts with both high and near-atmospheric methane concentrations (∼10.000 & ∼10 ppmv, respectively), green compost showed the highest potential methane uptake rates (up to 305.19 ± 94.43 nmol h-1 g dw compost-1 and 25.19 ± 6.75 pmol h-1 g dw compost-1, respectively). 16S, pmoA and mcrA amplicon sequencing revealed that its methanotrophic and methanogenic communities were dominated by type Ib methanotrophs, and more specifically by Methylocaldum szegediense and other Methylocaldum species, and Methanosarcina species, respectively. Ordination analyses showed that the abundance of type Ib methanotrophic bacteria was the main steering factor of the intrinsic methane uptake rates of composts, whilst the ammonium content was the main limiting factor, being most apparent in household composts. These results emphasize the potential of compost to contribute to methane mitigation, providing added value to compost as a product for industrial, commercial, governmental and public interests relevant to waste management. Compost could serve as a vector for the introduction of active methanotrophic bacteria in agricultural soils, potentially improving the methane uptake potential of agricultural soils and contributing to global methane mitigation, which should be the focus of future research.
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Affiliation(s)
- Stijn G van den Bergh
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO Box 50, 6700AB Wageningen, the Netherlands; Soil Biology Group, Wageningen University and Research, PO Box 47, 6700AA Wageningen, the Netherlands.
| | - Iris Chardon
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO Box 50, 6700AB Wageningen, the Netherlands.
| | - Marion Meima-Franke
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO Box 50, 6700AB Wageningen, the Netherlands.
| | - Ohana Y A Costa
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO Box 50, 6700AB Wageningen, the Netherlands.
| | - Gerard W Korthals
- Biointeractions and Plant Health, Wageningen Plant Research, PO Box 16, 6700AA Wageningen, the Netherlands.
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO Box 50, 6700AB Wageningen, the Netherlands; Soil Biology Group, Wageningen University and Research, PO Box 47, 6700AA Wageningen, the Netherlands.
| | - Paul L E Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO Box 50, 6700AB Wageningen, the Netherlands.
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15
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Bruggeman FJ, Teusink B, Steuer R. Trade-offs between the instantaneous growth rate and long-term fitness: Consequences for microbial physiology and predictive computational models. Bioessays 2023; 45:e2300015. [PMID: 37559168 DOI: 10.1002/bies.202300015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 07/14/2023] [Accepted: 07/19/2023] [Indexed: 08/11/2023]
Abstract
Microbial systems biology has made enormous advances in relating microbial physiology to the underlying biochemistry and molecular biology. By meticulously studying model microorganisms, in particular Escherichia coli and Saccharomyces cerevisiae, increasingly comprehensive computational models predict metabolic fluxes, protein expression, and growth. The modeling rationale is that cells are constrained by a limited pool of resources that they allocate optimally to maximize fitness. As a consequence, the expression of particular proteins is at the expense of others, causing trade-offs between cellular objectives such as instantaneous growth, stress tolerance, and capacity to adapt to new environments. While current computational models are remarkably predictive for E. coli and S. cerevisiae when grown in laboratory environments, this may not hold for other growth conditions and other microorganisms. In this contribution, we therefore discuss the relationship between the instantaneous growth rate, limited resources, and long-term fitness. We discuss uses and limitations of current computational models, in particular for rapidly changing and adverse environments, and propose to classify microbial growth strategies based on Grimes's CSR framework.
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Affiliation(s)
- Frank J Bruggeman
- Systems Biology Lab/AIMMS, VU University, Amsterdam, The Netherlands
| | - Bas Teusink
- Systems Biology Lab/AIMMS, VU University, Amsterdam, The Netherlands
| | - Ralf Steuer
- Institute for Theoretical Biology (ITB), Institute for Biology, Humboldt-University of Berlin, Berlin, Germany
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16
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Tian W, Wang H, Xiang X, Loni PC, Qiu X, Wang R, Huang X, Tuovinen OH. Water table level controls methanogenic and methanotrophic communities and methane emissions in a Sphagnum-dominated peatland. Microbiol Spectr 2023; 11:e0199223. [PMID: 37747896 PMCID: PMC10580971 DOI: 10.1128/spectrum.01992-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/27/2023] [Indexed: 09/27/2023] Open
Abstract
Peatlands are important sources of the greenhouse gas methane emissions equipoised by methanogens and methanotrophs. However, knowledge about how microbial functional groups associated with methane production and oxidation respond to water table fluctuations has been limited to date. Here, methane-related microbial communities and the potentials of methane production and oxidation were determined along sectioned peat layers in a subalpine peatland across four Sphagnum-dominated sites with different water table levels. Methane fluxes were also monitored at these sites. The results showed that mcrA gene copies for methanogens were the highest in the 10- to 15-cm peat layer, which was also characterized by the maximum potential methane production (24.53 ± 1.83 nmol/g/h). Copy numbers of the pmoA gene for type Ia and Ib methanotrophs were enriched in the 0-5 cm peat layer with the highest potential methane oxidation (43.09 ± 3.44 nmol/g/h). For the type II methanotrophs, the pmoA gene copies were higher in the 10- to 15-cm peat layer. Hydrogenotrophic methanogens and type II methanotrophs dominated the methane functional groups. Deterministic process contributed more to methanogenic and methanotrophic community assemblages in comparison with stochastic process. The level of water table significantly shaped methanogenic and methanotrophic community structures and regulated methane fluxes. Compared with vascular plants, Sphagnum mosses significantly reduced the methane emissions in peatlands. Collectively, these findings enhance a comprehensive understanding of the effect of the water table level on methane functional groups, with consequential implications for reducing methane emissions within peatland ecosystems.IMPORTANCEThe water table level is recognized as a critical factor in regulating methane emissions, which are largely dependent on the balance of methanogens and methanotrophs. Previous studies on peat methane emissions have been mostly focused on spatial-temporal variations and the relationship with meteorological conditions. However, the role of the water table level in methane emissions remains unknown. In this work, four representative microhabitats along a water table gradient in a Sphagnum-dominated peatland were sampled to gain an insight into methane functional communities and methane emissions as affected by the water table level. The changes in methane-related microbial community structure and assembly were used to characterize the response to the water table level. This study improves the understanding of the changes in methane-related microbial communities and methane emissions with water table levels in peatlands.
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Affiliation(s)
- Wen Tian
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
- College of Resource and Environment, Anhui Science and Technology of University, Chuzhou, China
- Hubei Key Laboratory of Critical Zone Evolution, China University of Geosciences, Wuhan, China
| | - Hongmei Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Xing Xiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
- College of Life Science, Shangrao Normal University, Shangrao, China
| | - Prakash C. Loni
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Xuan Qiu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Ruicheng Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Xianyu Huang
- Hubei Key Laboratory of Critical Zone Evolution, China University of Geosciences, Wuhan, China
| | - Olli H. Tuovinen
- Department of Microbiology, Ohio State University, Columbus, Ohio, USA
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17
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Heffner T, Brami SA, Mendes LW, Kaupper T, Hannula ES, Poehlein A, Horn MA, Ho A. Interkingdom interaction: the soil isopod Porcellio scaber stimulates the methane-driven bacterial and fungal interaction. ISME COMMUNICATIONS 2023; 3:62. [PMID: 37355679 PMCID: PMC10290665 DOI: 10.1038/s43705-023-00271-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/06/2023] [Accepted: 06/14/2023] [Indexed: 06/26/2023]
Abstract
Porcellio scaber (woodlice) are (sub-)surface-dwelling isopods, widely recognized as "soil bioengineers", modifying the edaphic properties of their habitat, and affecting carbon and nitrogen mineralization that leads to greenhouse gas emissions. Yet, the impact of soil isopods on methane-cycling processes remains unknown. Using P. scaber as a model macroinvertebrate in a microcosm study, we determined how the isopod influences methane uptake and the associated interaction network in an agricultural soil. Stable isotope probing (SIP) with 13C-methane was combined to a co-occurrence network analysis to directly link activity to the methane-oxidizing community (bacteria and fungus) involved in the trophic interaction. Compared to microcosms without the isopod, P. scaber significantly induced methane uptake, associated to a more complex bacteria-bacteria and bacteria-fungi interaction, and modified the soil nutritional status. Interestingly, 13C was transferred via the methanotrophs into the fungi, concomitant to significantly higher fungal abundance in the P. scaber-impacted soil, indicating that the fungal community utilized methane-derived substrates in the food web along with bacteria. Taken together, results showed the relevance of P. scaber in modulating methanotrophic activity with implications for bacteria-fungus interaction.
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Affiliation(s)
- Tanja Heffner
- Leibniz Universität Hannover, Institute for Microbiology, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Semi A Brami
- Leibniz Universität Hannover, Institute for Microbiology, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Lucas W Mendes
- University of São Paulo CENA-USP, Center for Nuclear Energy in Agriculture, Avenida Centenario, 303, 13416-000, Piracicaba (SP), Brazil
| | - Thomas Kaupper
- Leibniz Universität Hannover, Institute for Microbiology, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Emilia S Hannula
- Leiden University, Department of Environmental Biology, Institute of Environmental Sciences, Einsteinweg 2, 2333CC, Leiden, the Netherlands
| | - Anja Poehlein
- Georg-August University Göttingen, Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Grisebachstr. 8, D-37077, Göttingen, Germany
| | - Marcus A Horn
- Leibniz Universität Hannover, Institute for Microbiology, Herrenhäuser Str. 2, 30419, Hannover, Germany.
| | - Adrian Ho
- Leibniz Universität Hannover, Institute for Microbiology, Herrenhäuser Str. 2, 30419, Hannover, Germany.
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18
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Hagh-Doust N, Mikryukov V, Anslan S, Bahram M, Puusepp R, Dulya O, Tedersoo L. Effects of nitrogen deposition on carbon and nutrient cycling along a natural soil acidity gradient as revealed by metagenomics. THE NEW PHYTOLOGIST 2023; 238:2607-2620. [PMID: 36949609 DOI: 10.1111/nph.18897] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 03/15/2023] [Indexed: 05/19/2023]
Abstract
Nitrogen (N) deposition and soil acidification are environmental challenges affecting ecosystem functioning, health, and biodiversity, but their effects on functional genes are poorly understood. Here, we utilized metabarcoding and metagenomics to investigate the responses of soil functional genes to N deposition along a natural soil pH gradient. Soil N content was uncorrelated with pH, enabling us to investigate their effects separately. Soil acidity strongly and negatively affected the relative abundances of most cluster of orthologous gene categories of the metabolism supercategory. Similarly, soil acidity negatively affected the diversity of functional genes related to carbon and N but not phosphorus cycling. Multivariate analyses showed that soil pH was the most important factor affecting microbial and functional gene composition, while the effects of N deposition were less important. Relative abundance of KEGG functional modules related to different parts of the studied cycles showed variable responses to soil acidity and N deposition. Furthermore, our results suggested that the diversity-function relationship reported for other organisms also applies to soil microbiomes. Since N deposition and soil pH affected microbial taxonomic and functional composition to a different extent, we conclude that N deposition effects might be primarily mediated through soil acidification in forest ecosystems.
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Affiliation(s)
- Niloufar Hagh-Doust
- Institute of Ecology and Earth Sciences, University of Tartu, Juhan Liivi 2, 50409, Tartu, Estonia
- Mycology and Microbiology Center, University of Tartu, Juhan Liivi 2, 50409, Tartu, Estonia
| | - Vladimir Mikryukov
- Institute of Ecology and Earth Sciences, University of Tartu, Juhan Liivi 2, 50409, Tartu, Estonia
- Mycology and Microbiology Center, University of Tartu, Juhan Liivi 2, 50409, Tartu, Estonia
| | - Sten Anslan
- Institute of Ecology and Earth Sciences, University of Tartu, Juhan Liivi 2, 50409, Tartu, Estonia
- Mycology and Microbiology Center, University of Tartu, Juhan Liivi 2, 50409, Tartu, Estonia
| | - Mohammad Bahram
- Institute of Ecology and Earth Sciences, University of Tartu, Juhan Liivi 2, 50409, Tartu, Estonia
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls Väg 16, 75651, Uppsala, Sweden
| | - Rasmus Puusepp
- Institute of Ecology and Earth Sciences, University of Tartu, Juhan Liivi 2, 50409, Tartu, Estonia
| | - Olesya Dulya
- Institute of Ecology and Earth Sciences, University of Tartu, Juhan Liivi 2, 50409, Tartu, Estonia
- Mycology and Microbiology Center, University of Tartu, Juhan Liivi 2, 50409, Tartu, Estonia
| | - Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Juhan Liivi 2, 50409, Tartu, Estonia
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Jensen S, Siljanen HM, Dörsch P. Activity and abundance of methanotrophic bacteria in a northern mountainous gradient of wetlands. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:206-215. [PMID: 36786058 PMCID: PMC10464705 DOI: 10.1111/1758-2229.13137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 11/23/2022] [Indexed: 05/06/2023]
Abstract
Methane uptake and diversity of methanotrophic bacteria was investigated across six hydrologically connected wetlands in a mountainous forest landscape upstream of lake Langtjern, southern Norway. From floodplain through shrubs, forest and sedges to a Sphagnum covered site, growing season CH4 production was insufficiently consumed to balance release into the atmosphere. Emission increased by soil moisture ranging 0.6-6.8 mg CH4 m-2 h-1 . Top soils of all sites consumed CH4 including at the lowest 78 ppmv CH4 supplied, thus potentially oxidizing 17-51 nmol CH4 g-1 dw h-1 , with highest Vmax 440 nmol g-1 dw h-1 under Sphagnum and lowest Km 559 nM under hummocked Carex. Nine genera and several less understood type I and type II methanotrophs were detected by the key functional gene pmoA involved in methane oxidation. Microarray signal intensities from all sites revealed Methylococcus, the affiliated Lake Washington cluster, Methylocaldum, a Japanese rice cluster, Methylosinus, Methylocystis and the affiliated Peat264 cluster. Notably enriched by site was a floodplain Methylomonas and a Methylocapsa-affiliated watershed cluster in the Sphagnum site. The climate sensitive water table was shown to be a strong controlling factor highlighting its link with the CH4 cycle in elevated wetlands.
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Affiliation(s)
- Sigmund Jensen
- Department of Biological SciencesUniversity of BergenBergenNorway
| | - Henri M.P. Siljanen
- Department of Environmental and Biological SciencesUniversity of Eastern FinlandKuopioFinland
| | - Peter Dörsch
- Norwegian University of Life SciencesFaculty for Environmental Sciences and Natural Resource ManagementNorway
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20
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He X, Zhang S, Lv X, Liu M, Ma Y, Guo S. Eichhornia crassipes-rhizospheric biofilms contribute to nutrients removal and methane oxidization in wastewater stabilization ponds receiving simulative sewage treatment plants effluents. CHEMOSPHERE 2023; 322:138100. [PMID: 36764618 DOI: 10.1016/j.chemosphere.2023.138100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/18/2023] [Accepted: 02/07/2023] [Indexed: 06/18/2023]
Abstract
Wastewater stabilization ponds (WSPs) have been used in treating sewage treatment plants (STPs) effluents. However, little is known about the role of rhizospheric biofilms on methane release in WSPs with floating plants. In the present study, the nutrient removal, CH4 fluxes, CH4 oxidization potential and rhizospheric bacterial community were investigated in WSPs with Eichhornia crassipes under simulate STPs effluents for 31 days. At the end of the experiment, E. crassipes biomass was 5.60-8.81 times of initial weight and increased with increasing nutrients concentration. E. crassipes effectively reduced methane release and nutrients. Compared to control, E. crassipes reduced 52.30%-83.21% of CH4 fluxes at water-atmosphere interface and had better inhibition effect on CH4 fluxes in treatments with high nutrients. However, methane oxidization rates of E. crassipes roots were higher in low nutrients (0.83 ± 0.046 mg CH4 (kg fresh plant)-1 day-1) than high nutrients (0.12 ± 0.04 mg CH4 (kg fresh plant)-1 day-1). Structural equation modeling revealed that biomass of E. crassipes has negative effect on CH4 fluxes (-0.453, p = 0.000). Proteobacteria, Bacteroidetes, Planctomycetes, Chloroflexi and Actinobacteria were the predominant phyla in the rhizospheric biofilm of E. crassipes and contributed to nutrients removal. Aerobic methanotrophs and pomA abundances were higher in rhizospheric biofilm exposed to high nutrients than low nutrients and aerobic methanotrophs had close interactions with other microorganisms and participated in the carbon and nitrogen cycle, demonstrating that many bacteria harboring pmoA gene did not fully involve in methane oxidization. These data highlight plants E. crassipes have an important role in both reducing methane release and nutrients removal.
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Affiliation(s)
- Xin He
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, PR China; College of Environment, Hohai University, Nanjing 210098, PR China
| | - Songhe Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, PR China; College of Environment, Hohai University, Nanjing 210098, PR China.
| | - Xin Lv
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, PR China; College of Environment, Hohai University, Nanjing 210098, PR China
| | - Min Liu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, PR China; College of Environment, Hohai University, Nanjing 210098, PR China
| | - Yu Ma
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, PR China; College of Environment, Hohai University, Nanjing 210098, PR China
| | - Shaozhuang Guo
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, PR China; College of Environment, Hohai University, Nanjing 210098, PR China
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21
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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. THE SCIENCE OF THE TOTAL ENVIRONMENT 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] [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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22
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Kim C, Staver LW, Chen X, Bulseco A, Cornwell JC, Malkin SY. Microbial Community Succession Along a Chronosequence in Constructed Salt Marsh Soils. MICROBIAL ECOLOGY 2023; 85:931-950. [PMID: 36764950 DOI: 10.1007/s00248-023-02189-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 02/02/2023] [Indexed: 05/04/2023]
Abstract
In this study, we examined the succession of soil microbial communities across a chronosequence of newly constructed salt marshes constructed primarily of fine-grained dredge material, using 16S rRNA amplicon sequences. Alpha diversity in the subsurface horizons was initially low and increased to reference levels within 3 years of marsh construction, while alpha diversity in the newly accumulating organic matter-rich surface soils was initially high and remained unchanged. Microbial community succession was fastest in the surface horizon (~ 24 years to reference equivalency) and became progressively slower with depth in the subsurface horizons (~ 30-67 years). Random forest linear regression analysis was used to identify important taxa driving the trajectories toward reference conditions. In the parent material, putative sulfate-reducers (Desulfobacterota), methanogens (Crenarchaeota, especially Methanosaeta), and fermenters (Chloroflexi and Clostridia) increased over time, suggesting an enrichment of these metabolisms over time, similar to natural marshes. Concurrently in the surface soils, the relative abundances of putative methane-, methyl-, and sulfide oxidizers, especially among Gammaproteobacteria, increased over time, suggesting the co-development of sulfide and methane removal metabolisms in marsh soils. Finally, we observed that the surface soil communities at one of the marshes did not follow the trajectory of the others, exhibiting a greater relative abundance of anaerobic taxa. Uniquely in this dataset, this marsh was developing signs of excessive inundation stress in terms of vegetation coverage and soil geochemistry. Therefore, we suggest that soil microbial community structure may be effective bioindicators of salt marsh inundation and are worthy of further targeted investigation.
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Affiliation(s)
- Carol Kim
- Horn Point Laboratory, University of Maryland Center for Environmental Science (UMCES), Cambridge, MD, USA
| | - Lorie W Staver
- Horn Point Laboratory, University of Maryland Center for Environmental Science (UMCES), Cambridge, MD, USA
| | - Xuan Chen
- Department of Biology, Salisbury University, Salisbury, MD, USA
| | | | - Jeffrey C Cornwell
- Horn Point Laboratory, University of Maryland Center for Environmental Science (UMCES), Cambridge, MD, USA
| | - Sairah Y Malkin
- Horn Point Laboratory, University of Maryland Center for Environmental Science (UMCES), Cambridge, MD, USA.
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23
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Kropochev AI, Lashin SA, Matushkin YG, Klimenko AI. Trait-Based Method of Quantitative Assessment of Ecological Functional Groups in the Human Intestinal Microbiome. BIOLOGY 2023; 12:biology12010115. [PMID: 36671807 PMCID: PMC9855786 DOI: 10.3390/biology12010115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/15/2022] [Accepted: 12/30/2022] [Indexed: 01/15/2023]
Abstract
We propose the trait-based method for quantifying the activity of functional groups in the human gut microbiome based on metatranscriptomic data. It allows one to assess structural changes in the microbial community comprised of the following functional groups: butyrate-producers, acetogens, sulfate-reducers, and mucin-decomposing bacteria. It is another way to perform a functional analysis of metatranscriptomic data by focusing on the ecological level of the community under study. To develop the method, we used published data obtained in a carefully controlled environment and from a synthetic microbial community, where the problem of ambiguity between functionality and taxonomy is absent. The developed method was validated using RNA-seq data and sequencing data of the 16S rRNA amplicon on a simplified community. Consequently, the successful verification provides prospects for the application of this method for analyzing natural communities of the human intestinal microbiota.
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Affiliation(s)
- Andrew I. Kropochev
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia
- Kurchatov Genomic Center of ICG SB RAS, Novosibirsk 630090, Russia
- Correspondence:
| | - Sergey A. Lashin
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia
- Kurchatov Genomic Center of ICG SB RAS, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Yury G. Matushkin
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Alexandra I. Klimenko
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia
- Kurchatov Genomic Center of ICG SB RAS, Novosibirsk 630090, Russia
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24
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Sharma U, Rawat D, Mukherjee P, Farooqi F, Mishra V, Sharma RS. Ecological life strategies of microbes in response to antibiotics as a driving factor in soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 854:158791. [PMID: 36108841 DOI: 10.1016/j.scitotenv.2022.158791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/31/2022] [Accepted: 09/11/2022] [Indexed: 06/15/2023]
Abstract
Antibiotics as a selection pressure driving the evolution of soil microbial communities is not well understood. Since microbial functions govern ecosystem services, an ecological framework is required to understand and predict antibiotic-induced functional and structural changes in microbial communities. Therefore, metagenomic studies explaining the impacts of antibiotics on soil microbial communities were mined, and alterations in microbial taxa were analyzed through an ecological lens using Grimes's Competitor-Stress tolerator-Ruderal (CSR) model. We propose considering antibiotics as the primary abiotic factor mentioned in the CSR model and classifying non-susceptible microbial taxa as degraders, resistant, and resilient groups analogous to competitors, stress tolerators, and ruderal strategists, respectively. Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria were among the phyla harboring most members with antibiotic-resistant groups. However, some antibiotic-resistant microbes in these phyla could not only tolerate but also subsist solely on antibiotics, while others degraded antibiotics as a part of secondary metabolism. Irrespective of their taxonomic affiliation, microbes with each life strategy displayed similar phenotypic characteristics. Therefore, it is recommended to consider microbial functional traits associated with each life strategy while analyzing the ecological impacts of antibiotics. Also, potential ecological crises posed by antibiotics through changes in microbial community and ecosystem functions were visualized. Applying ecological theory to understand and predict antibiotics-induced changes in microbial communities will also provide better insight into microbial behavior in the background of emerging contaminants and help develop a robust ecological classification system of microbes.
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Affiliation(s)
- Udita Sharma
- Bioresources & Environmental Biotechnology Laboratory, Department of Environmental Studies, University of Delhi, Delhi 110007, India
| | - Deepak Rawat
- Bioresources & Environmental Biotechnology Laboratory, Department of Environmental Studies, University of Delhi, Delhi 110007, India; Department of Environmental Studies, Janki Devi Memorial College, University of Delhi, Delhi 110060, India
| | - Paromita Mukherjee
- Bioresources & Environmental Biotechnology Laboratory, Department of Environmental Studies, University of Delhi, Delhi 110007, India
| | - Furqan Farooqi
- Bioresources & Environmental Biotechnology Laboratory, Department of Environmental Studies, University of Delhi, Delhi 110007, India
| | - Vandana Mishra
- Bioresources & Environmental Biotechnology Laboratory, Department of Environmental Studies, University of Delhi, Delhi 110007, India; Centre for Interdisciplinary Studies on Mountain & Hill Environment (CISMHE), University of Delhi, Delhi 110007, India.
| | - Radhey Shyam Sharma
- Bioresources & Environmental Biotechnology Laboratory, Department of Environmental Studies, University of Delhi, Delhi 110007, India; Delhi School of Climate Change & Sustainability, Institute of Eminence, University of Delhi, Delhi 110007, India.
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25
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Wang S, Sun P, Liu J, Xu Y, Dolfing J, Wu Y. Distribution of methanogenic and methanotrophic consortia at soil-water interfaces in rice paddies across climate zones. iScience 2022; 26:105851. [PMID: 36636345 PMCID: PMC9829807 DOI: 10.1016/j.isci.2022.105851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/15/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Periphytic biofilms (PB) at the soil-water interface contributes 7-38% of the methane emission from rice paddies, yet the biogeographical mechanism underlying and affecting the process remain elusive. In this study, rice fields along an edapho-vclimatic gradient were sampled, and the environmental drivers affecting distribution of methanogenic and methanotrophic communities were evaluated. The methanogenic and methanotrophic communities at soil-water interface showed less complex inter/intra-generic interactions than those in soil, and their relative abundances were weakly driven by spatial distance, soil organic carbon, soil total nitrogen and pH. The nutrient supply and buffering capacity of extracellular polymeric substance released by PB reduced their interaction and enhanced the resilience on edaphic environment changes. Climate affected soil metal content, extracellular polymeric substance content, and thus the methane-related communities, and caused geographical variation in the impacts of PB on methane emissions from rice paddies. This study facilitates our understanding of geographical differences in the contribution of PB to methane emission.
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Affiliation(s)
- Sichu Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China,Institute of Agricultural Resources and Environment, Jiangsu Academy of Agriculture Sciences (JAAS), 50 Zhongling Road, Nanjing 210014, China,Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resources of the People’s Republic of China, Shuitianba Zigui, Yichang 443605, China
| | - Pengfei Sun
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China,Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resources of the People’s Republic of China, Shuitianba Zigui, Yichang 443605, China
| | - Junzhuo Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China,Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resources of the People’s Republic of China, Shuitianba Zigui, Yichang 443605, China
| | - Ying Xu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China,Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resources of the People’s Republic of China, Shuitianba Zigui, Yichang 443605, China
| | - Jan Dolfing
- Faculty of Energy and Environment, Northumbria University, Newcastle upon Tyne NE1 8QH, UK
| | - Yonghong Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China,Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resources of the People’s Republic of China, Shuitianba Zigui, Yichang 443605, China,Corresponding author
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26
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Dillon KP, Krumins V, Deshpande A, Kerkhof LJ, Mainelis G, Fennell DE. Characterization and DNA Stable-Isotope Probing of Methanotrophic Bioaerosols. Microbiol Spectr 2022; 10:e0342122. [PMID: 36409096 PMCID: PMC9769660 DOI: 10.1128/spectrum.03421-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 10/15/2022] [Indexed: 11/23/2022] Open
Abstract
The growth and activity of bacteria have been extensively studied in nearly every environment on Earth, but there have been limited studies focusing on the air. Suspended bacteria (outside of water droplets) may stay in the atmosphere for time frames that could allow for growth on volatile compounds, including the potent greenhouse gas methane. We investigated the ability of aerosolized methanotrophic bacteria to grow on methane in the airborne state in rotating gas-phase bioreactors. The physical half-life of the aerial bacterium-sized particles was 3 days. To assess the potential for airborne growth, gas-phase bioreactors containing the aerosolized cultures were amended with 1,500 ppmv 13CH4 or 12CH4. Three of seven experiments demonstrated 13C incorporation into DNA, indicating growth in air. Bacteria associated with the genera Methylocystis and Methylocaldum were detected in 13C-DNA fractions, thus indicating that they were synthesizing new DNA, suggesting growth in air. We conclude that methanotrophs outside of water droplets in the air can potentially grow under certain conditions. Based on our data, humidity seems to be a major limitation to bacterial growth in air. Furthermore, low biomass levels can pose problems for detecting 13C-DNA synthesis in our experimental system. IMPORTANCE Currently, the cellular activities of bacteria in the airborne state outside of water droplets have not been heavily studied. Evidence suggests that these airborne bacteria produce ribosomes and metabolize gaseous compounds. Despite having a potentially important impact on atmospheric chemistry, the ability of bacteria in the air to metabolize substrates such as methane is not well understood. Demonstrating that bacteria in the air can metabolize and grow on substrates will expand knowledge about the potential activities and functions of the atmospheric microbiome. This study provides evidence for DNA synthesis and, ultimately, growth of airborne methanotrophs.
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Affiliation(s)
- Kevin P. Dillon
- Department of Environmental Sciences, Rutgers University, New Brunswick, New Jersey, USA
| | - Valdis Krumins
- Department of Environmental Sciences, Rutgers University, New Brunswick, New Jersey, USA
| | - Aishwarya Deshpande
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, USA
| | - Lee J. Kerkhof
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey, USA
| | - Gediminas Mainelis
- Department of Environmental Sciences, Rutgers University, New Brunswick, New Jersey, USA
| | - Donna E. Fennell
- Department of Environmental Sciences, Rutgers University, New Brunswick, New Jersey, USA
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27
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Cheng X, Wang H, Zeng Z, Li L, Zhao R, Bodelier PLE, Wang Y, Liu X, Su C, Liu S. Niche differentiation of atmospheric methane-oxidizing bacteria and their community assembly in subsurface karst caves. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:886-896. [PMID: 35925016 DOI: 10.1111/1758-2229.13112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/05/2022] [Accepted: 07/17/2022] [Indexed: 06/17/2023]
Abstract
Karst caves are recently proposed as atmospheric methane sinks in terrestrial ecosystems. Despite of the detection of atmospheric methane-oxidizing bacteria (atmMOB) in caves, we still know little about their ecology and potential ability of methane oxidation in this ecosystem. To understand atmMOB ecology and their potential in methane consumption, we collected weathered rocks and sediments from three different caves in southwestern China. We determined the potential methane oxidization rates in the range of 1.25 ± 0.08 to 1.87 ± 0.41 ng CH4 g-1 DW h-1 , which are comparable to those reported in forest and grassland soils. Results showed that alkaline oligotrophic caves harbour high numbers of atmMOB, particularly upland soil cluster (USC), which significantly correlated with temperature, CH4 and CO2 concentrations. The absolute abundance of USCγ was higher than that of USCα. USCγ-OPS (open patch soil) and USCγ-SS (subsurface soil) dominated in most samples, whereas USCα-BFS (boreal forest soil) only predominated in the sediments near cave entrances, indicating niche differentiation of atmMOB in caves. Overwhelming dominance of homogenous selection in community assembly resulted in convergence of atmMOB communities. Collectively, our results demonstrated the niche differentiation of USC in subsurface alkaline caves and their non-negligible methane-oxidizing potential, providing brand-new knowledge about atmMOB ecology in subsurface biosphere.
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Affiliation(s)
- Xiaoyu Cheng
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, P. R. China
- School of Environmental Studies, China University of Geosciences, Wuhan, P. R. China
| | - Hongmei Wang
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, P. R. China
- School of Environmental Studies, China University of Geosciences, Wuhan, P. R. China
| | - Zhilin Zeng
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, P. R. China
- School of Environmental Studies, China University of Geosciences, Wuhan, P. R. China
| | - Lu Li
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, P. R. China
- School of Environmental Studies, China University of Geosciences, Wuhan, P. R. China
| | - Rui Zhao
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Paul L E Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Yiheng Wang
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, P. R. China
- School of Environmental Studies, China University of Geosciences, Wuhan, P. R. China
| | - Xiaoyan Liu
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, P. R. China
- School of Environmental Studies, China University of Geosciences, Wuhan, P. R. China
| | - Chuntian Su
- CAGS/Key Laboratory of Karst Dynamics, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin, P. R. China
| | - Shuangjiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
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28
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Ho A, Zuan ATK, Mendes LW, Lee HJ, Zulkeflee Z, van Dijk H, Kim PJ, Horn MA. Aerobic Methanotrophy and Co-occurrence Networks of a Tropical Rainforest and Oil Palm Plantations in Malaysia. MICROBIAL ECOLOGY 2022; 84:1154-1165. [PMID: 34716776 PMCID: PMC9747831 DOI: 10.1007/s00248-021-01908-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 10/21/2021] [Indexed: 05/11/2023]
Abstract
Oil palm (OP) plantations are gradually replacing tropical rainforest in Malaysia, one of the largest palm oil producers globally. Conversion of lands to OP plantations has been associated with compositional shifts of the microbial community, with consequences on the greenhouse gas (GHG) emissions. While the impact of the change in land use has recently been investigated for microorganisms involved in N2O emission, the response of the aerobic methanotrophs to OP agriculture remains to be determined. Here, we monitored the bacterial community composition, focusing on the aerobic methanotrophs, in OP agricultural soils since 2012, 2006, and 1993, as well as in a tropical rainforest, in 2019 and 2020. High-affinity methane uptake was confirmed, showing significantly lower rates in the OP plantations than in the tropical rainforest, but values increased with continuous OP agriculture. The bacterial, including the methanotrophic community composition, was modified with ongoing OP agriculture. The methanotrophic community composition was predominantly composed of unclassified methanotrophs, with the canonical (Methylocystis) and putative methanotrophs thought to catalyze high-affinity methane oxidation present at higher relative abundance in the oldest OP plantation. Results suggest that the methanotrophic community was relatively more stable within each site, exhibiting less temporal variations than the total bacterial community. Uncharacteristically, a 16S rRNA gene-based co-occurrence network analysis revealed a more complex and connected community in the OP agricultural soil, which may influence the resilience of the bacterial community to disturbances. Overall, we provide a first insight into the ecology and role of the aerobic methanotrophs as a methane sink in OP agricultural soils.
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Affiliation(s)
- Adrian Ho
- Institute for Microbiology, Leibniz Universität Hannover, Hannover, Germany.
| | - Ali Tan Kee Zuan
- Department of Land Management, Faculty of Agriculture, Universiti Putra Malaysia, Seri Kembangan, Selangor, Malaysia
| | - Lucas W Mendes
- Center for Nuclear Energy in Agriculture, University of São Paulo (CENA-USP), Sao Paulo, Brazil
| | - Hyo Jung Lee
- Department of Biology, Kunsan National University, Gunsan, South Korea
| | - Zufarzaana Zulkeflee
- Department of Environment, Faculty of Forestry and Environment, Universiti Putra Malaysia, Seri Kembangan, Selangor, Malaysia
| | - Hester van Dijk
- Institute for Microbiology, Leibniz Universität Hannover, Hannover, Germany
| | - Pil Joo Kim
- Division of Applied Life Science, Gyeongsang National University, Jinju, South Korea
| | - Marcus A Horn
- Institute for Microbiology, Leibniz Universität Hannover, Hannover, Germany
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Jiang M, Xu P, Wu L, Zhao J, Wu H, Lin S, Yang T, Tu J, Hu R. Methane emission, methanogenic and methanotrophic communities during rice-growing seasons differ in diversified rice rotation systems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 842:156781. [PMID: 35724786 DOI: 10.1016/j.scitotenv.2022.156781] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/23/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
Appropriate crop rotation in rice field is an important measure to maintain soil fertility and rice productivity. However, the effects of different rice rotation systems on methane (CH4) emission and the underlying mechanisms, as well as rice grain yields have not been well assessed. Here, a 2-year field study involving three rice rotation systems (Wh-PR: wheat-flooded rice rotation, Ra-PR: rapeseed-flooded rice rotation, Ra-UR: rapeseed-aerobic rice rotation) was conducted. CH4 emissions, methanogenic and methanotrophic communities and rice grain yields were measured during rice growing seasons to determine which rice rotation pattern can reduce CH4 emissions and improve rice grain yields. The average cumulative CH4 emission was 136.19 kg C ha-1 in Ra-PR system, which was significantly higher than that in Wh-PR and Ra-UR systems by 60.6 % and 14.6-fold, respectively. These results were mainly attributed to the low soil dissolved organic carbon in Wh-PR system and the well aerated soil condition in Ra-UR system, as compared with Ra-PR system. Rice grain yields exhibited no significant differences among the three rotation systems in 2019 and 2020. The abundances of methanogens in Ra-PR system were obviously higher than those in Wh-PR and Ra-UR systems. While the abundances of methanotrophs were comparable between Ra-PR and Wh-PR systems, which exhibited significantly lower abundances than that in Ra-UR system. CH4 fluxes showed markedly positive relations to the abundances of methanogens, while exhibited no relationship with the abundances of methanotrophs. Both methanogenic and methanotrophic community compositions differed considerably in Wh-PR and Ra-UR systems in comparison with Ra-PR system. Specifically, the relative low abundances of Methanothrix and Type I methanotrophs occurred in Wh-PR and Ra-UR systems, whereas Methanosarcina, Methanocella, Methanomassiliicoccus and type II methanotrophs (Methylocystis and Methylosinus) were found in higher relative abundances in Wh-PR and Ra-UR systems. Overall, changing the preceding upland crop types or introducing aerobic rice to substitute flooded rice in rice-based rotation systems could diminish CH4 emissions, mainly by regulating soil properties and eventually changing soil methanogenic and methanotrophic communities.
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Affiliation(s)
- Mengdie Jiang
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 43070, China
| | - Peng Xu
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 43070, China; Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu 610041, China
| | - Lei Wu
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Jinsong Zhao
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 43070, China
| | - Hongtao Wu
- College of Urban and Environmental Sciences, Hubei Normal University, Huangshi 435002, China
| | - Shan Lin
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 43070, China
| | - Tewu Yang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Junming Tu
- Huanggang Academy of Agriculture Science, Huanggang 43800, China
| | - Ronggui Hu
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 43070, China.
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30
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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. ENVIRONMENTAL RESEARCH 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] [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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Insights into the Genomic Potential of a Methylocystis sp. from Amazonian Floodplain Sediments. Microorganisms 2022; 10:microorganisms10091747. [PMID: 36144349 PMCID: PMC9506196 DOI: 10.3390/microorganisms10091747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/23/2022] [Accepted: 08/02/2022] [Indexed: 11/26/2022] Open
Abstract
Although floodplains are recognized as important sources of methane (CH4) in the Amazon basin, little is known about the role of methanotrophs in mitigating CH4 emissions in these ecosystems. Our previous data reported the genus Methylocystis as one of the most abundant methanotrophs in these floodplain sediments. However, information on the functional potential and life strategies of these organisms living under seasonal flooding is still missing. Here, we described the first metagenome-assembled genome (MAG) of a Methylocystis sp. recovered from Amazonian floodplains sediments, and we explored its functional potential and ecological traits through phylogenomic, functional annotation, and pan-genomic approaches. Both phylogenomics and pan-genomics identified the closest placement of the bin.170_fp as Methylocystis parvus. As expected for Type II methanotrophs, the Core cluster from the pan-genome comprised genes for CH4 oxidation and formaldehyde assimilation through the serine pathway. Furthermore, the complete set of genes related to nitrogen fixation is also present in the Core. Interestingly, the MAG singleton cluster revealed the presence of unique genes related to nitrogen metabolism and cell motility. The study sheds light on the genomic characteristics of a dominant, but as yet unexplored methanotroph from the Amazonian floodplains. By exploring the genomic potential related to resource utilization and motility capability, we expanded our knowledge on the niche breadth of these dominant methanotrophs in the Amazonian floodplains.
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32
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Indigenous microbial populations of abandoned mining sites and their role in natural attenuation. Arch Microbiol 2022; 204:251. [PMID: 35411412 DOI: 10.1007/s00203-022-02861-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 03/17/2022] [Accepted: 03/20/2022] [Indexed: 11/02/2022]
Abstract
Environmental contamination by toxic effluents discharged by anthropogenic activities including the mining industries has increased extensively in the recent past. Microbial communities and their biofilms inhabiting these extreme habitats have developed different adaptive strategies in metabolizing and transforming the persistent pollutants. They also play a crucial role in natural attenuation of these abandoned mining sites and act as a major driver of many biogeochemical processes, which helps in ecological rehabilitation and is a viable approach for restoration of wide stretches of land. In this review, the types of mine wastes including the overburden and mine drainage and the types of microbial communities thriving in such environments were probed in detail. The types of biofilms formed along with their possible role in metal bioremediation were also reviewed. This review also provides an overview of the shift in microbial communities in natural reclamation process and also provides an insight into the restoration of the enzyme activities of the soils which may help in further revegetation of abundant mining areas in a sustainable manner. Moreover, the role of indigenous microbiota in bioremediation of heavy metals and their plant growth-promoting activity weres discussed to assess their role in phytoremedial processes.
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Kaupper T, Mendes LW, Poehlein A, Frohloff D, Rohrbach S, Horn MA, Ho A. The methane-driven interaction network in terrestrial methane hotspots. ENVIRONMENTAL MICROBIOME 2022; 17:15. [PMID: 35382875 PMCID: PMC8981696 DOI: 10.1186/s40793-022-00409-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Biological interaction affects diverse facets of microbial life by modulating the activity, diversity, abundance, and composition of microbial communities. Aerobic methane oxidation is a community function, with emergent community traits arising from the interaction of the methane-oxidizers (methanotrophs) and non-methanotrophs. Yet little is known of the spatial and temporal organization of these interaction networks in naturally-occurring complex communities. We hypothesized that the assembled bacterial community of the interaction network in methane hotspots would converge, driven by high substrate availability that favors specific methanotrophs, and in turn influences the recruitment of non-methanotrophs. These environments would also share more co-occurring than site-specific taxa. RESULTS We applied stable isotope probing (SIP) using 13C-CH4 coupled to a co-occurrence network analysis to probe trophic interactions in widespread methane-emitting environments, and over time. Network analysis revealed predominantly unique co-occurring taxa from different environments, indicating distinctly co-evolved communities more strongly influenced by other parameters than high methane availability. Also, results showed a narrower network topology range over time than between environments. Co-occurrence pattern points to Chthoniobacter as a relevant yet-unrecognized interacting partner particularly of the gammaproteobacterial methanotrophs, deserving future attention. In almost all instances, the networks derived from the 13C-CH4 incubation exhibited a less connected and complex topology than the networks derived from the unlabelledC-CH4 incubations, likely attributable to the exclusion of the inactive microbial population and spurious connections; DNA-based networks (without SIP) may thus overestimate the methane-dependent network complexity. CONCLUSION We demonstrated that site-specific environmental parameters more strongly shaped the co-occurrence of bacterial taxa than substrate availability. Given that members of the interactome without the capacity to oxidize methane can exert interaction-induced effects on community function, understanding the co-occurrence pattern of the methane-driven interaction network is key to elucidating community function, which goes beyond relating activity to community composition, abundances, and diversity. More generally, we provide a methodological strategy that substantiates the ecological linkages between potentially interacting microorganisms with broad applications to elucidate the role of microbial interaction in community function.
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Affiliation(s)
- Thomas Kaupper
- Institute for Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Lucas W Mendes
- Center for Nuclear Energy in Agriculture, University of São Paulo CENA-USP, Piracicaba, SP, Brazil
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, George-August University Göttingen, Grisebachstr. 8, 37077, Göttingen, Germany
| | - Daria Frohloff
- Institute for Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Stephan Rohrbach
- Institute for Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Marcus A Horn
- Institute for Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany.
| | - Adrian Ho
- Institute for Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany.
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Microbial storage and its implications for soil ecology. THE ISME JOURNAL 2022; 16:617-629. [PMID: 34593996 PMCID: PMC8857262 DOI: 10.1038/s41396-021-01110-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 08/31/2021] [Accepted: 09/07/2021] [Indexed: 02/08/2023]
Abstract
Organisms throughout the tree of life accumulate chemical resources, in particular forms or compartments, to secure their availability for future use. Here we review microbial storage and its ecological significance by assembling several rich but disconnected lines of research in microbiology, biogeochemistry, and the ecology of macroscopic organisms. Evidence is drawn from various systems, but we pay particular attention to soils, where microorganisms play crucial roles in global element cycles. An assembly of genus-level data demonstrates the likely prevalence of storage traits in soil. We provide a theoretical basis for microbial storage ecology by distinguishing a spectrum of storage strategies ranging from surplus storage (storage of abundant resources that are not immediately required) to reserve storage (storage of limited resources at the cost of other metabolic functions). This distinction highlights that microorganisms can invest in storage at times of surplus and under conditions of scarcity. We then align storage with trait-based microbial life-history strategies, leading to the hypothesis that ruderal species, which are adapted to disturbance, rely less on storage than microorganisms adapted to stress or high competition. We explore the implications of storage for soil biogeochemistry, microbial biomass, and element transformations and present a process-based model of intracellular carbon storage. Our model indicates that storage can mitigate against stoichiometric imbalances, thereby enhancing biomass growth and resource-use efficiency in the face of unbalanced resources. Given the central roles of microbes in biogeochemical cycles, we propose that microbial storage may be influential on macroscopic scales, from carbon cycling to ecosystem stability.
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35
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Liu X, Shi Y, Yang T, Gao GF, Zhang L, Xu R, Li C, Liu R, Liu J, Chu H. Distinct Co-occurrence Relationships and Assembly Processes of Active Methane-Oxidizing Bacterial Communities Between Paddy and Natural Wetlands of Northeast China. Front Microbiol 2022; 13:809074. [PMID: 35154054 PMCID: PMC8826055 DOI: 10.3389/fmicb.2022.809074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 01/04/2022] [Indexed: 11/27/2022] Open
Abstract
Studies of methane-oxidizing bacteria are updating our views of their composition and function in paddy and natural wetlands. However, few studies have characterized differences in the methane-oxidizing bacterial communities between paddy and natural wetlands. Here, we conducted a 13C stable isotope-probing experiment and high-throughput sequencing to determine the structure profiling, co-occurrence relationships, and assembly processes of methanotrophic communities in four wetlands of Northeast China. There was a clear difference in community structure between paddy and natural wetlands. LEfSe analyses revealed that Methylobacter, FWs, and Methylosinus were enriched in natural wetlands, while Methylosarcina were prevailing in paddy, all identified as indicative methanotrophs. We observed distinct co-occurrence relationships between paddy and natural wetlands: more robust and complex connections in natural wetlands than paddy wetlands. Furthermore, the relative importance of stochastic processes was greater than that of deterministic processes, as stochastic processes explained >50% of the variation in communities. These results demonstrated that the co-occurrence relationships and assembly processes of active methanotrophic communities in paddy and natural wetlands were distinct. Overall, the results of this study enhance our understanding of the communities of methane-oxidizing bacteria in paddy and natural wetlands of Northeast China.
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Affiliation(s)
- Xu Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yu Shi
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Teng Yang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Gui-Feng Gao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Liyan Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Ruoyu Xu
- High School Affiliated to Nanjing Normal University, Nanjing, China
| | - Chenxin Li
- High School Affiliated to Nanjing Normal University, Nanjing, China
| | - Ruiyang Liu
- High School Affiliated to Nanjing Normal University, Nanjing, China
| | - Junjie Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,University of Chinese Academy of Sciences, Beijing, China
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Pan H, Feng H, Liu Y, Lai CY, Zhuge Y, Zhang Q, Tang C, Di H, Jia Z, Gubry-Rangin C, Li Y, Xu J. Grazing weakens competitive interactions between active methanotrophs and nitrifiers modulating greenhouse-gas emissions in grassland soils. ISME COMMUNICATIONS 2021; 1:74. [PMID: 36765259 PMCID: PMC9723554 DOI: 10.1038/s43705-021-00068-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 10/14/2021] [Accepted: 10/18/2021] [Indexed: 11/09/2022]
Abstract
Grassland soils serve as a biological sink and source of the potent greenhouse gases (GHG) methane (CH4) and nitrous oxide (N2O). The underlying mechanisms responsible for those GHG emissions, specifically, the relationships between methane- and ammonia-oxidizing microorganisms in grazed grassland soils are still poorly understood. Here, we characterized the effects of grazing on in situ GHG emissions and elucidated the putative relations between the active microbes involving in methane oxidation and nitrification activity in grassland soils. Grazing significantly decreases CH4 uptake while it increases N2O emissions basing on 14-month in situ measurement. DNA-based stable isotope probing (SIP) incubation experiment shows that grazing decreases both methane oxidation and nitrification processes and decreases the diversity of active methanotrophs and nitrifiers, and subsequently weakens the putative competition between active methanotrophs and nitrifiers in grassland soils. These results constitute a major advance in our understanding of putative relationships between methane- and ammonia-oxidizing microorganisms and subsequent effects on nitrification and methane oxidation, which contribute to a better prediction and modeling of future balance of GHG emissions and active microbial communities in grazed grassland ecosystems.
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Affiliation(s)
- Hong Pan
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Daizong Road, Tai'an City, Shandong, 271018, China
| | - Haojie Feng
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Daizong Road, Tai'an City, Shandong, 271018, China
| | - Yaowei Liu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Chun-Yu Lai
- Advanced Water Management Centre, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Yuping Zhuge
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Daizong Road, Tai'an City, Shandong, 271018, China
| | - Qichun Zhang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Caixian Tang
- Department of Animal, Plant and Soil Sciences, Centre for AgriBioscience, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Hongjie Di
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Cécile Gubry-Rangin
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK.
| | - Yong Li
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China.
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
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Barnett SE, Youngblut ND, Koechli CN, Buckley DH. Multisubstrate DNA stable isotope probing reveals guild structure of bacteria that mediate soil carbon cycling. Proc Natl Acad Sci U S A 2021; 118:e2115292118. [PMID: 34799453 PMCID: PMC8617410 DOI: 10.1073/pnas.2115292118] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/10/2021] [Indexed: 11/18/2022] Open
Abstract
Soil microorganisms determine the fate of soil organic matter (SOM), and their activities compose a major component of the global carbon (C) cycle. We employed a multisubstrate, DNA-stable isotope probing experiment to track bacterial assimilation of C derived from distinct sources that varied in bioavailability. This approach allowed us to measure microbial contributions to SOM processing by measuring the C assimilation dynamics of diverse microorganisms as they interacted within soil. We identified and tracked 1,286 bacterial taxa that assimilated 13C in an agricultural soil over a period of 48 d. Overall 13C-assimilation dynamics of bacterial taxa, defined by the source and timing of the 13C they assimilated, exhibited low phylogenetic conservation. We identified bacterial guilds composed of taxa that had similar 13C assimilation dynamics. We show that C-source bioavailability explained significant variation in both C mineralization dynamics and guild structure, and that the growth dynamics of bacterial guilds differed significantly in response to C addition. We also demonstrate that the guild structure explains significant variation in the biogeographical distribution of bacteria at continental and global scales. These results suggest that an understanding of in situ growth dynamics is essential for understanding microbial contributions to soil C cycling. We interpret these findings in the context of bacterial life history strategies and their relationship to terrestrial C cycling.
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Affiliation(s)
- Samuel E Barnett
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
| | - Nicholas D Youngblut
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Chantal N Koechli
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
- Department of Biological Sciences, University of the Sciences, Philadelphia, PA 19104
| | - Daniel H Buckley
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853;
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38
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Westoby M, Nielsen DA, Gillings MR, Gumerov VM, Madin JS, Paulsen IT, Tetu SG. Strategic traits of bacteria and archaea vary widely within substrate-use groups. FEMS Microbiol Ecol 2021; 97:6402898. [PMID: 34665251 DOI: 10.1093/femsec/fiab142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 10/14/2021] [Indexed: 11/12/2022] Open
Abstract
Quantitative traits such as maximum growth rate and cell radial diameter are one facet of ecological strategy variation across bacteria and archaea. Another facet is substrate-use pathways, such as iron reduction or methylotrophy. Here, we ask how these two facets intersect, using a large compilation of data for culturable species and examining seven quantitative traits (genome size, signal transduction protein count, histidine kinase count, growth temperature, temperature-adjusted maximum growth rate, cell radial diameter and 16S rRNA operon copy number). Overall, quantitative trait variation within groups of organisms possessing a particular substrate-use pathway was very broad, outweighing differences between substrate-use groups. Although some substrate-use groups had significantly different means for some quantitative traits, standard deviation of quantitative trait values within each substrate-use pathway mostly averaged between 1.6 and 1.8 times larger than standard deviation across group means. Most likely, this wide variation reflects ecological strategy: for example, fast maximum growth rate is likely to express an early successional or copiotrophic strategy, and maximum growth varies widely within most substrate-use pathways. In general, it appears that these quantitative traits express different and complementary information about ecological strategy, compared with substrate use.
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Affiliation(s)
- Mark Westoby
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2019, Australia
| | - Daniel A Nielsen
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2019, Australia
| | - Michae R Gillings
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2019, Australia
| | - Vadim M Gumerov
- Department of Microbiology, Ohio State University, 318 W. 12th Avenue, Columbus, OH 43210, USA
| | - Joshua S Madin
- Hawaii Institute of Marine Biology, University of Hawaii, Kaneohe, HI 96744, USA
| | - Ian T Paulsen
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2019, Australia
| | - Sasha G Tetu
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2019, Australia
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39
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Martin G, Rissanen AJ, Garcia SL, Mehrshad M, Buck M, Peura S. Candidatus Methylumidiphilus Drives Peaks in Methanotrophic Relative Abundance in Stratified Lakes and Ponds Across Northern Landscapes. Front Microbiol 2021; 12:669937. [PMID: 34456882 PMCID: PMC8397446 DOI: 10.3389/fmicb.2021.669937] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 06/30/2021] [Indexed: 11/21/2022] Open
Abstract
Boreal lakes and ponds produce two-thirds of the total natural methane emissions above the latitude of 50° North. These lake emissions are regulated by methanotrophs which can oxidize up to 99% of the methane produced in the sediments and the water column. Despite their importance, the diversity and distribution of the methanotrophs in lakes are still poorly understood. Here, we used shotgun metagenomic data to explore the diversity and distribution of methanotrophs in 40 oxygen-stratified water bodies in boreal and subarctic areas in Europe and North America. In our data, gammaproteobacterial methanotrophs (order Methylococcales) generally dominated the methanotrophic communities throughout the water columns. A recently discovered lineage of Methylococcales, Candidatus Methylumidiphilus, was present in all the studied water bodies and dominated the methanotrophic community in lakes with a high relative abundance of methanotrophs. Alphaproteobacterial methanotrophs were the second most abundant group of methanotrophs. In the top layer of the lakes, characterized by low CH4 concentration, their abundance could surpass that of the gammaproteobacterial methanotrophs. These results support the theory that the alphaproteobacterial methanotrophs have a high affinity for CH4 and can be considered stress-tolerant strategists. In contrast, the gammaproteobacterial methanotrophs are competitive strategists. In addition, relative abundances of anaerobic methanotrophs, Candidatus Methanoperedenaceae and Candidatus Methylomirabilis, were strongly correlated, suggesting possible co-metabolism. Our data also suggest that these anaerobic methanotrophs could be active even in the oxic layers. In non-metric multidimensional scaling, alpha- and gammaproteobacterial methanotrophs formed separate clusters based on their abundances in the samples, except for the gammaproteobacterial Candidatus Methylumidiphilus, which was separated from these two clusters. This may reflect similarities in the niche and environmental requirements of the different genera within alpha- and gammaproteobacterial methanotrophs. Our study confirms the importance of O2 and CH4 in shaping the methanotrophic communities and suggests that one variable cannot explain the diversity and distribution of the methanotrophs across lakes. Instead, we suggest that the diversity and distribution of freshwater methanotrophs are regulated by lake-specific factors.
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Affiliation(s)
- Gaëtan Martin
- Department of Forest Mycology and Plant Pathology, Science for Life Laboratory, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Antti J. Rissanen
- Faculty of Engineering and Natural Sciences, Tampere University, Tampere, Finland
| | - Sarahi L. Garcia
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Maliheh Mehrshad
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Moritz Buck
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Sari Peura
- Department of Forest Mycology and Plant Pathology, Science for Life Laboratory, Swedish University of Agricultural Sciences, Uppsala, Sweden
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40
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Nijman TPA, Davidson TA, Weideveld STJ, Audet J, Esposito C, Levi EE, Ho A, Lamers LPM, Jeppesen E, Veraart AJ. Warming and eutrophication interactively drive changes in the methane-oxidizing community of shallow lakes. ISME COMMUNICATIONS 2021; 1:32. [PMID: 37938256 PMCID: PMC9723669 DOI: 10.1038/s43705-021-00026-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 05/25/2021] [Accepted: 05/28/2021] [Indexed: 06/14/2023]
Abstract
Freshwater ecosystems are the largest natural source of the greenhouse gas methane (CH4), with shallow lakes a particular hot spot. Eutrophication and warming generally increase lake CH4 emissions but their impacts on the sole biological methane sink-methane oxidation-and methane-oxidizer community dynamics are poorly understood. We used the world's longest-running freshwater climate-change mesocosm experiment to determine how methane-oxidizing bacterial (MOB) abundance and composition, and methane oxidation potential in the sediment respond to eutrophication, short-term nitrogen addition and warming. After nitrogen addition, MOB abundance and methane oxidation potential increased, while warming increased MOB abundance without altering methane oxidation potential. MOB community composition was driven by both temperature and nutrient availability. Eutrophication increased relative abundance of type I MOB Methyloparacoccus. Warming favoured type II MOB Methylocystis over type I MOB Methylomonadaceae, shifting the MOB community from type I dominance to type I and II co-dominance, thereby altering MOB community traits involved in growth and stress-responses. This shift to slower-growing MOB may explain why higher MOB abundance in warmed mesocosms did not coincide with higher methane oxidation potential. Overall, we show that eutrophication and warming differentially change the MOB community, resulting in an altered ability to mitigate CH4 emissions from shallow lakes.
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Affiliation(s)
- Thomas P A Nijman
- Department of Aquatic Ecology and Environmental Biology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands.
| | - Thomas A Davidson
- Lake Group, Department of Bioscience and Arctic Research Centre, Aarhus University, Silkeborg, Denmark
- WATEC Aarhus University Centre for Water Technology, Aarhus University, Silkeborg, Denmark
| | - Stefan T J Weideveld
- Department of Aquatic Ecology and Environmental Biology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Joachim Audet
- Lake Group, Department of Bioscience and Arctic Research Centre, Aarhus University, Silkeborg, Denmark
- WATEC Aarhus University Centre for Water Technology, Aarhus University, Silkeborg, Denmark
| | - Chiara Esposito
- Lake Group, Department of Bioscience and Arctic Research Centre, Aarhus University, Silkeborg, Denmark
- WATEC Aarhus University Centre for Water Technology, Aarhus University, Silkeborg, Denmark
| | - Eti E Levi
- Lake Group, Department of Bioscience and Arctic Research Centre, Aarhus University, Silkeborg, Denmark
- WATEC Aarhus University Centre for Water Technology, Aarhus University, Silkeborg, Denmark
| | - Adrian Ho
- Institute for Microbiology, Liebniz Universität Hannover, Hannover, Germany
| | - Leon P M Lamers
- Department of Aquatic Ecology and Environmental Biology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Erik Jeppesen
- Lake Group, Department of Bioscience and Arctic Research Centre, Aarhus University, Silkeborg, Denmark
- WATEC Aarhus University Centre for Water Technology, Aarhus University, Silkeborg, Denmark
- Sino-Danish Centre for Education and Research (SDC), University of Chinese Academy of Sciences, Beijing, China
- Limnology Laboratory, Department of Biological Sciences and Centre for Ecosystem Research and implementation, Middle East Technical University, Ankara, Turkey
- Institute of Marine Sciences, Middle East Technical University, Erdemli-Mersin, Turkey
| | - Annelies J Veraart
- Department of Aquatic Ecology and Environmental Biology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
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41
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Matthews A, Majeed A, Barraclough TG, Raymond B. Function is a better predictor of plant rhizosphere community membership than 16S phylogeny. Environ Microbiol 2021; 23:6089-6103. [PMID: 34190398 DOI: 10.1111/1462-2920.15652] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/23/2021] [Accepted: 06/28/2021] [Indexed: 11/26/2022]
Abstract
Rhizobacterial communities are important for plant health but we still have limited understanding of how they are constructed or how they can be manipulated. High-throughput 16S rRNA sequencing provides good information on taxonomic composition but remains an unreliable proxy for phenotypes. In this study, we tested the hypothesis that experimentally observed functional traits would be better predictors of community membership than phylogenetic origin. To test this hypothesis, we sampled communities on four plant species grown in two soil types and characterized 593 bacterial isolates in terms of antibiotic susceptibility, carbon metabolism, resource use and plant growth-promoting traits. In support of our hypothesis we found that three of the four plant species had phylogenetically diverse, but functionally constrained communities. Notably, communities did not grow best on complex media mimicking their host of origin but were distinguished by variation in overall growth characteristics (copiotrophy/oligotrophy) and antibiotic susceptibility. These data, combined with variation in phylogenetic structure, suggest that different classes of traits (antagonistic competition or resource-based) are more important in different communities. This culture-based approach supports and complements the findings of a previous high-throughput 16S rRNA analysis of this experiment and provides functional insights into the patterns observed with culture-independent methods.
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Affiliation(s)
- Andrew Matthews
- College of Life and Environmental Sciences, University of Exeter, Penryn, UK.,Department of Life Sciences, Imperial College London, Ascot, UK
| | - Afshan Majeed
- Department of Soil and Environmental Sciences, University of the Poonch, Rawalakot, Azad Jammu and Kashmir, Pakistan
| | | | - Ben Raymond
- College of Life and Environmental Sciences, University of Exeter, Penryn, UK.,Department of Life Sciences, Imperial College London, Ascot, UK
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42
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Lu L, Li X, Li Z, Chen Y, Sabio Y García CA, Yang J, Luo F, Zou X. Aerobic methanotrophs in an urban water cycle system: Community structure and network interaction pattern. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 772:145045. [PMID: 33770879 DOI: 10.1016/j.scitotenv.2021.145045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/20/2020] [Accepted: 12/30/2020] [Indexed: 06/12/2023]
Abstract
Aerobic methane-oxidizing bacteria (MOB) play an important role in reducing methane emissions in nature. Most current researches focus on the natural habitats (e.g., lakes, reservoirs, wetlands, paddy fields, etc.). However, methanotrophs and the methane-oxidizing process remain essentially unclear in artificial habitat, such as the urban water cycle systems. Here, high-throughput sequencing and qPCR were used to analyze the community structure and abundance of MOB. Six different systems were selected from Yunyang City, Chongqing, China, including the raw water system (RW), the water supply pipe network system (SP), the wastewater pipe network system (WP), the hospital wastewater treatment system (HP), the municipal wastewater treatment plant system (WT) and the downstream river system (ST) of a wastewater treatment plant. Results clearly showed that the MOB community structure and network interaction patterns of the urban water cycle system were different from those of natural water bodies. Type I MOB was the dominant clade in HP. Methylocysis in Type II was the most abundant genus among the whole urban water cycle system, indicating that this genus had a high adaptability to the environment. Temperature, dissolved oxygen, pH and concentration significantly affected the MOB communities in the urban water cycle system. The network of MOB in WT was the most complicated, and there were competitive relationships among species in WP. The structure of the network in HP was unstable, and therefore, it was vulnerable to environmental disturbances. Methylocystis (Type II) and Methylomonas (Type I) were the most important keystone species in the entire urban water cycle system. Overall, these findings broaden the understanding of the distribution and interaction patterns of MOB communities in an urban water cycle system and provide valuable clues for ecosystem restoration and environmental management.
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Affiliation(s)
- Lunhui Lu
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
| | - Xinrui Li
- Key Laboratory of Hydraulic and Waterway Engineering of the Ministry of Education, Chongqing Jiaotong University, Chongqing 400074, China
| | - Zhe Li
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China.
| | - Yao Chen
- Key Laboratory of Hydraulic and Waterway Engineering of the Ministry of Education, Chongqing Jiaotong University, Chongqing 400074, China
| | - Carmen A Sabio Y García
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Depto. Ecología, Genética y Evolución, Int. Güiraldes 2620, Pabellón II, Ciudad Universitaria, CP 1428 Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), Argentina
| | - Jixiang Yang
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
| | - Fang Luo
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; Key Laboratory of Hydraulic and Waterway Engineering of the Ministry of Education, Chongqing Jiaotong University, Chongqing 400074, China
| | - Xi Zou
- Key Laboratory of Ecological Impacts of Hydraulic-Projects and Restoration of Aquatic Ecosystem of Ministry of Water Resources, Institute of Hydroecology, Ministry of Water Resources and Chinese Academy of Sciences, Wuhan 430079, PR China
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43
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Finn DR, Bergk-Pinto B, Hazard C, Nicol GW, Tebbe CC, Vogel TM. Functional trait relationships demonstrate life strategies in terrestrial prokaryotes. FEMS Microbiol Ecol 2021; 97:6271318. [PMID: 33960387 DOI: 10.1093/femsec/fiab068] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 05/05/2021] [Indexed: 01/13/2023] Open
Abstract
Functional, physiological traits are the underlying drivers of niche differentiation. A common framework related to niches occupied by terrestrial prokaryotes is based on copiotrophy or oligotrophy, where resource investment is primarily in either rapid growth or stress tolerance, respectively. A quantitative trait-based approach sought relationships between taxa, traits and niche in terrestrial prokaryotes. With 175 taxa from 11 Phyla and 35 Families (n = 5 per Family), traits were considered as discrete counts of shared genome-encoded proteins. Trait composition strongly supported non-random functional distributions as preferential clustering of related taxa via unweighted pair-group method with arithmetic mean. Trait similarity between taxa increased as taxonomic rank decreased. A suite of Random Forest models identified traits significantly enriched or depleted in taxonomic groups. These traits conveyed functions related to rapid growth, nutrient acquisition and stress tolerance consistent with their presence in copiotroph-oligotroph niches. Hierarchical clustering of traits identified a clade of competitive, copiotrophic Families resilient to oxidative stress versus glycosyltransferase-enriched oligotrophic Families resistant to antimicrobials and environmental stress. However, the formation of five clades suggested a more nuanced view to describe niche differentiation in terrestrial systems is necessary. We suggest considering traits involved in both resource investment and acquisition when predicting niche.
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Affiliation(s)
- Damien R Finn
- School of Agriculture and Food Sciences, University of Queensland, St Lucia, Brisbane 4072, Australia.,Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Avenue Guy de Collongue 36 Écully 69134, France.,Thünen Institut für Biodiversität, Johann Heinrich von Thünen Institut, Bundesallee 65 Braunschweig 38116, Germany
| | - Benoît Bergk-Pinto
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Avenue Guy de Collongue 36 Écully 69134, France
| | - Christina Hazard
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Avenue Guy de Collongue 36 Écully 69134, France
| | - Graeme W Nicol
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Avenue Guy de Collongue 36 Écully 69134, France
| | - Christoph C Tebbe
- Thünen Institut für Biodiversität, Johann Heinrich von Thünen Institut, Bundesallee 65 Braunschweig 38116, Germany
| | - Timothy M Vogel
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Avenue Guy de Collongue 36 Écully 69134, France
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44
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Guerrero-Cruz S, Vaksmaa A, Horn MA, Niemann H, Pijuan M, Ho A. Methanotrophs: Discoveries, Environmental Relevance, and a Perspective on Current and Future Applications. Front Microbiol 2021; 12:678057. [PMID: 34054786 PMCID: PMC8163242 DOI: 10.3389/fmicb.2021.678057] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 04/12/2021] [Indexed: 11/13/2022] Open
Abstract
Methane is the final product of the anaerobic decomposition of organic matter. The conversion of organic matter to methane (methanogenesis) as a mechanism for energy conservation is exclusively attributed to the archaeal domain. Methane is oxidized by methanotrophic microorganisms using oxygen or alternative terminal electron acceptors. Aerobic methanotrophic bacteria belong to the phyla Proteobacteria and Verrucomicrobia, while anaerobic methane oxidation is also mediated by more recently discovered anaerobic methanotrophs with representatives in both the bacteria and the archaea domains. The anaerobic oxidation of methane is coupled to the reduction of nitrate, nitrite, iron, manganese, sulfate, and organic electron acceptors (e.g., humic substances) as terminal electron acceptors. This review highlights the relevance of methanotrophy in natural and anthropogenically influenced ecosystems, emphasizing the environmental conditions, distribution, function, co-existence, interactions, and the availability of electron acceptors that likely play a key role in regulating their function. A systematic overview of key aspects of ecology, physiology, metabolism, and genomics is crucial to understand the contribution of methanotrophs in the mitigation of methane efflux to the atmosphere. We give significance to the processes under microaerophilic and anaerobic conditions for both aerobic and anaerobic methane oxidizers. In the context of anthropogenically influenced ecosystems, we emphasize the current and potential future applications of methanotrophs from two different angles, namely methane mitigation in wastewater treatment through the application of anaerobic methanotrophs, and the biotechnological applications of aerobic methanotrophs in resource recovery from methane waste streams. Finally, we identify knowledge gaps that may lead to opportunities to harness further the biotechnological benefits of methanotrophs in methane mitigation and for the production of valuable bioproducts enabling a bio-based and circular economy.
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Affiliation(s)
- Simon Guerrero-Cruz
- Catalan Institute for Water Research (ICRA), Girona, Spain
- Universitat de Girona, Girona, Spain
| | - Annika Vaksmaa
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, ’t Horntje, Netherlands
| | - Marcus A. Horn
- Institute of Microbiology, Leibniz Universität Hannover, Hannover, Germany
| | - Helge Niemann
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, ’t Horntje, Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
- Centre for Arctic Gas Hydrate, Environment and Climate, Department of Geosciences, UiT the Arctic University of Norway, Tromsø, Norway
| | - Maite Pijuan
- Catalan Institute for Water Research (ICRA), Girona, Spain
- Universitat de Girona, Girona, Spain
| | - Adrian Ho
- Institute of Microbiology, Leibniz Universität Hannover, Hannover, Germany
- Division of Applied Life Sciences, Gyeongsang National University, Jinju, South Korea
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45
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Zhang B, Liu J, Sheng Y, Shi J, Dong H. Disentangling Microbial Syntrophic Mechanisms for Hexavalent Chromium Reduction in Autotrophic Biosystems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:6340-6351. [PMID: 33866784 DOI: 10.1021/acs.est.1c00383] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Hexavalent chromium [Cr(VI)] is one of the common heavy-metal contaminants in groundwater, and the availability of electron donors is considered to be a key parameter for Cr(VI) biotransformation. During the autotrophic remediation process, however, much remains to be illuminated about how complex syntrophic microbial communities couple Cr(VI) reduction with other elemental cycles. Two series of Cr(VI)-reducing groundwater bioreactors were independently amended by elemental sulfur and iron and inoculated with the same inoculum. After 160 days of incubation, both bioreactors showed similar archaea-dominating microbiota compositions, whereas a higher Cr(VI)-reducing rate and more methane production were detected in the Fe0-driven one. Metabolic reconstruction of 23 retrieved genomes revealed complex symbiotic relationships driving distinct elemental cycles coupled with Cr(VI) reduction in bioreactors. In both bioreactors, these Cr(VI) reducers were assumed to live in syntrophy with oxidizers of sulfur, iron, hydrogen, and volatile fatty acids and methane produced by carbon fixers and multitrophic methanogens, respectively. The significant difference in methane production was mainly due to the fact that the yielded sulfate greatly retarded acetoclastic methanogenesis in the S-bioreactor. These findings provide insights into mutualistic symbioses of carbon, sulfur, iron, and chromium metabolisms in groundwater systems and have implications for bioremediation of Cr(VI)-contaminated groundwater.
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Affiliation(s)
- Baogang Zhang
- School of Water Resources and Environment, Key Laboratory of Groundwater Circulation and Environmental Evolution (China University of Geosciences Beijing), Ministry of Education, Beijing 100083, China
| | - Jun Liu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China
- Department of Geology and Environmental Earth Science, Miami University, Oxford, Ohio 45056, United States
| | - Yizhi Sheng
- Department of Geology and Environmental Earth Science, Miami University, Oxford, Ohio 45056, United States
| | - Jiaxin Shi
- School of Water Resources and Environment, Key Laboratory of Groundwater Circulation and Environmental Evolution (China University of Geosciences Beijing), Ministry of Education, Beijing 100083, China
| | - Hailiang Dong
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China
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46
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Westoby M, Gillings MR, Madin JS, Nielsen DA, Paulsen IT, Tetu SG. Trait dimensions in bacteria and archaea compared to vascular plants. Ecol Lett 2021; 24:1487-1504. [PMID: 33896087 DOI: 10.1111/ele.13742] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 02/25/2021] [Accepted: 03/04/2021] [Indexed: 01/04/2023]
Abstract
Bacteria and archaea have very different ecology compared to plants. One similarity, though, is that much discussion of their ecological strategies has invoked concepts such as oligotrophy or stress tolerance. For plants, so-called 'trait ecology'-strategy description reframed along measurable trait dimensions-has made global syntheses possible. Among widely measured trait dimensions for bacteria and archaea three main axes are evident. Maximum growth rate in association with rRNA operon copy number expresses a rate-yield trade-off that is analogous to the acquisitive-conservative spectrum in plants, though underpinned by different trade-offs. Genome size in association with signal transduction expresses versatility. Cell size has influence on diffusive uptake and on relative wall costs. These trait dimensions, and potentially others, offer promise for interpreting ecology. At the same time, there are very substantial differences from plant trait ecology. Traits and their underpinning trade-offs are different. Also, bacteria and archaea use a variety of different substrates. Bacterial strategies can be viewed both through the facet of substrate-use pathways, and also through the facet of quantitative traits such as maximum growth rate. Preliminary evidence shows the quantitative traits vary widely within substrate-use pathways. This indicates they convey information complementary to substrate use.
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Affiliation(s)
- Mark Westoby
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - Michael R Gillings
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - Joshua S Madin
- Hawaii Institute of Marine Biology, University of Hawaii, Kaneohe, HI, USA
| | - Daniel A Nielsen
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - Ian T Paulsen
- Dept of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Sasha G Tetu
- Dept of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
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47
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Bell TH, Bell T. Many roads to bacterial generalism. FEMS Microbiol Ecol 2021; 97:6006266. [PMID: 33238305 DOI: 10.1093/femsec/fiaa240] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 11/23/2020] [Indexed: 12/13/2022] Open
Abstract
The fundamental niches of bacteria can be defined along many environmental axes, including temperature tolerance and resources consumed, while interactions with other organisms can constrain (e.g. competition) or enlarge (e.g. cross-feeding) realized niches. Organisms are often categorized as generalists or specialists, corresponding to broad or narrow niche requirements, which can then be linked to their functional role in an ecosystem. We show how these terms are applied to bacteria, make predictions about how the type and extent of generalism displayed by an organism relates to its functional potential and discuss the value of collecting different types of generalist bacteria. We believe that new approaches that take advantage of both high-throughput sequencing and environmental manipulation can allow us to understand the many types of generalism found within both cultivated and yet-to-be-cultivated bacteria.
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Affiliation(s)
- Terrence H Bell
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, USA.,Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Thomas Bell
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire, SL5 7PY, UK
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Alster CJ, Allison SD, Glassman SI, Martiny AC, Treseder KK. Exploring Trait Trade-Offs for Fungal Decomposers in a Southern California Grassland. Front Microbiol 2021; 12:655987. [PMID: 33995318 PMCID: PMC8118720 DOI: 10.3389/fmicb.2021.655987] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/05/2021] [Indexed: 11/14/2022] Open
Abstract
Fungi are important decomposers in terrestrial ecosystems, so their responses to climate change might influence carbon (C) and nitrogen (N) dynamics. We investigated whether growth and activity of fungi under drought conditions were structured by trade-offs among traits in 15 fungal isolates from a Mediterranean Southern California grassland. We inoculated fungi onto sterilized litter that was incubated at three moisture levels (4, 27, and 50% water holding capacity, WHC). For each isolate, we characterized traits that described three potential lifestyles within the newly proposed “YAS” framework: growth yield, resource acquisition, and stress tolerance. Specifically, we measured fungal hyphal length per unit litter decomposition for growth yield; the potential activities of the extracellular enzymes cellobiohydrolase (CBH), β-glucosidase (BG), β-xylosidase (BX), and N-acetyl-β-D-glucosaminidase (NAG) for resource acquisition; and ability to grow in drought vs. higher moisture levels for drought stress tolerance. Although, we had hypothesized that evolutionary and physiological trade-offs would elicit negative relationships among traits, we found no supporting evidence for this hypothesis. Across isolates, growth yield, drought stress tolerance, and extracellular enzyme activities were not significantly related to each other. Thus, it is possible that drought-induced shifts in fungal community composition may not necessarily lead to changes in fungal biomass or decomposer ability in this arid grassland.
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Affiliation(s)
- Charlotte J Alster
- Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, United States
| | - Steven D Allison
- Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, United States.,Department of Earth System Science, University of California Irvine, Irvine, CA, United States
| | - Sydney I Glassman
- Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, United States.,Department of Microbiology and Plant Pathology, University of California, Riverside, CA, United States
| | - Adam C Martiny
- Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, United States.,Department of Earth System Science, University of California Irvine, Irvine, CA, United States
| | - Kathleen K Treseder
- Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, United States
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Gontijo JB, Paula FS, Venturini AM, Yoshiura CA, Borges CD, Moura JMS, Bohannan BJM, Nüsslein K, Rodrigues JLM, Tsai SM. Not just a methane source: Amazonian floodplain sediments harbour a high diversity of methanotrophs with different metabolic capabilities. Mol Ecol 2021; 30:2560-2572. [PMID: 33817881 DOI: 10.1111/mec.15912] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 03/22/2021] [Accepted: 03/26/2021] [Indexed: 01/03/2023]
Abstract
The Amazonian floodplain forests are dynamic ecosystems of great importance for the regional hydrological and biogeochemical cycles and function as a significant CH4 source contributing to the global carbon balance. Unique geochemical factors may drive the microbial community composition and, consequently, affect CH4 emissions across floodplain areas. Here, we report the in situ composition of CH4 cycling microbial communities in Amazonian floodplain sediments. We considered how abiotic factors may affect the microbial community composition and, more specifically, CH4 cycling groups. We collected sediment samples during wet and dry seasons from three different types of floodplain forests, along with upland forest soil samples, from the Eastern Amazon, Brazil. We used high-resolution sequencing of archaeal and bacterial 16S rRNA genes combined with real-time PCR to quantify Archaea and Bacteria, as well as key functional genes indicative of the presence of methanogenic (mcrA) and methanotrophic (pmoA) microorganisms. Methanogens were found to be present in high abundance in floodplain sediments, and they seem to resist the dramatic environmental changes between flooded and nonflooded conditions. Methanotrophs known to use different pathways to oxidise CH4 were detected, including anaerobic archaeal and bacterial taxa, indicating that a wide metabolic diversity may be harboured in this highly variable environment. The floodplain environmental variability, which is affected by the river origin, drives not only the sediment chemistry but also the composition of the microbial communities. These environmental changes seem also to affect the pools of methanotrophs occupying distinct niches. Understanding these shifts in the methanotrophic communities could improve our comprehension of the CH4 emissions in the region.
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Affiliation(s)
- Júlia B Gontijo
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Fabiana S Paula
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil.,Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, São Paulo, Brazil
| | - Andressa M Venturini
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Caio A Yoshiura
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Clovis D Borges
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - José Mauro S Moura
- Center for Interdisciplinary Formation, Federal University of Western Pará, Santarém, Brazil
| | - Brendan J M Bohannan
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Klaus Nüsslein
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA
| | - Jorge L Mazza Rodrigues
- Department of Land, Air and Water Resources, University of California, Davis, CA, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Siu M Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
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50
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Rainer EM, Seppey CVW, Tveit AT, Svenning MM. Methanotroph populations and CH4 oxidation potentials in high-Arctic peat are altered by herbivory induced vegetation change. FEMS Microbiol Ecol 2021; 96:5868763. [PMID: 32639555 PMCID: PMC8202349 DOI: 10.1093/femsec/fiaa140] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 07/07/2020] [Indexed: 01/11/2023] Open
Abstract
Methane oxidizing bacteria (methanotrophs) within the genus
Methylobacter constitute the biological filter for methane
(CH4) in many Arctic soils. Multiple Methylobacter strains
have been identified in these environments but we seldom know the ecological significance
of the different strains. High-Arctic peatlands in Svalbard are heavily influenced by
herbivory, leading to reduced vascular plant and root biomass. Here, we have measured
potential CH4 oxidation rates and identified the active methantrophs in grazed
peat and peat protected from grazing by fencing (exclosures) for 18 years. Grazed peat
sustained a higher water table, higher CH4 concentrations and lower oxygen
(O2) concentrations than exclosed peat. Correspondingly, the highest
CH4 oxidation potentials were closer to the O2 rich surface in the
grazed than in the protected peat. A comparison of 16S rRNA genes showed that the majority
of methanotrophs in both sites belong to the genus Methylobacter. Further
analyses of pmoA transcripts revealed that several
Methylobacter OTUs were active in the peat but that different OTUs
dominated the grazed peat than the exclosed peat. We conclude that grazing influences soil
conditions, the active CH4 filter and that different
Methylobacter populations are responsible for CH4 oxidation
depending on the environmental conditions.
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Affiliation(s)
- Edda M Rainer
- Department of Arctic and Marine Biology, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Christophe V W Seppey
- Department of Arctic and Marine Biology, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Alexander T Tveit
- Department of Arctic and Marine Biology, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Mette M Svenning
- Department of Arctic and Marine Biology, UiT - The Arctic University of Norway, Tromsø, Norway
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