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Jurburg SD, Blowes SA, Shade A, Eisenhauer N, Chase JM. Synthesis of recovery patterns in microbial communities across environments. MICROBIOME 2024; 12:79. [PMID: 38711157 DOI: 10.1186/s40168-024-01802-3] [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: 12/08/2023] [Accepted: 03/25/2024] [Indexed: 05/08/2024]
Abstract
BACKGROUND Disturbances alter the diversity and composition of microbial communities. Yet a generalized empirical assessment of microbiome responses to disturbance across different environments is needed to understand the factors driving microbiome recovery, and the role of the environment in driving these patterns. RESULTS To this end, we combined null models with Bayesian generalized linear models to examine 86 time series of disturbed mammalian, aquatic, and soil microbiomes up to 50 days following disturbance. Overall, disturbances had the strongest effect on mammalian microbiomes, which lost taxa and later recovered their richness, but not their composition. In contrast, following disturbance, aquatic microbiomes tended away from their pre-disturbance composition over time. Surprisingly, across all environments, we found no evidence of increased compositional dispersion (i.e., variance) following disturbance, in contrast to the expectations of the Anna Karenina Principle. CONCLUSIONS This is the first study to systematically compare secondary successional dynamics across disturbed microbiomes, using a consistent temporal scale and modeling approach. Our findings show that the recovery of microbiomes is environment-specific, and helps to reconcile existing, environment-specific research into a unified perspective. Video Abstract.
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Affiliation(s)
- Stephanie D Jurburg
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany.
- Department of Applied Microbial Ecology, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318, Leipzig, Germany.
- Institute of Biology, Leipzig University, 04103, Leipzig, Germany.
| | - Shane A Blowes
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany
- Institute of Computer Science, Martin-Luther University Halle-Wittenberg, 06108, Halle (Saale), Halle, Germany
| | - Ashley Shade
- Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, Universite Claude Bernard Lyon 1, 69622, Villeurbanne, France
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany
- Institute of Biology, Leipzig University, 04103, Leipzig, Germany
| | - Jonathan M Chase
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany
- Institute of Computer Science, Martin-Luther University Halle-Wittenberg, 06108, Halle (Saale), Halle, Germany
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2
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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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3
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Paranaíba JR, Struik Q, Erdociain M, van Dijk G, Smolders AJP, van der Knaap J, Veraart AJ, Kosten S. CO 2, CH 4, and N 2O emissions from dredged material exposed to drying and zeolite addition under field and laboratory conditions. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 337:122627. [PMID: 37769708 DOI: 10.1016/j.envpol.2023.122627] [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: 07/20/2023] [Revised: 09/24/2023] [Accepted: 09/25/2023] [Indexed: 10/01/2023]
Abstract
Dredging, the removal of sediment from water courses, is generally conducted to maintain their navigability and to improve water quality. Recent studies indicate that dredging can significantly reduce aquatic greenhouse gas (GHG) emissions. These studies, however, do not consider the potential emission from the dredged material (sludge) in the depot. In addition, it is unknown if and how GHG emissions from sludge depots can be reduced. Here we present spatiotemporal variations of carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) fluxes, as well as environmental variables from a sludge depot located in the Netherlands. Measurements were conducted monthly from the time the depot was filled until the sludge was dry and the depot was abolished. We also experimentally assessed the GHG mitigation potential of 1) keeping the sludge permanently inundated, and 2) the addition of different amounts of zeolite to increase sludge nitrogen binding capacity to reduce N2O emissions. In the depot and in the laboratory, a decrease in moisture content coincided with increased CO2 and N2O emissions while CH4 emissions decreased. We observed that permanent inundation reduced emissions (∼4 times less CO2-eq than in drying sludge). Adding zeolite lowered N2O fluxes from permanently inundated sludge but did not reduce total GHG emissions. During the depot's operational period, average CO2, CH4, and N2O fluxes were 5078, 27, and 5 mg m-2 d-1, respectively. GHG emissions from drying sludge occurred mainly in the form of CO2 (73% of the total CO2-eq emissions), with average GHG emission rates comparable to those reported for ditches and ponds. We estimate that approximately 14 tons of CO2-eq were emitted from the 0.011 km2 depot, which contained ∼20,000 m3 of sludge, during its entire operational period, and we argue that more studies are needed, considering different sludge origins, to expand our understanding of sludge depots.
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Affiliation(s)
- José R Paranaíba
- Department of Aquatic Ecology and Environmental Biology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, the Netherlands.
| | - Quinten Struik
- Department of Aquatic Ecology and Environmental Biology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, the Netherlands
| | - Maite Erdociain
- Department of Aquatic Ecology and Environmental Biology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, the Netherlands
| | - Gijs van Dijk
- Department of Aquatic Ecology and Environmental Biology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, the Netherlands; B-WARE Research Centre, Radboud University, Nijmegen, the Netherlands
| | - Alfons J P Smolders
- Department of Aquatic Ecology and Environmental Biology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, the Netherlands; B-WARE Research Centre, Radboud University, Nijmegen, the Netherlands
| | - Judith van der Knaap
- Department of Aquatic Ecology and Environmental Biology, 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
| | - Sarian Kosten
- Department of Aquatic Ecology and Environmental Biology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, the Netherlands
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Nijman TPA, Lemmens M, Lurling M, Kosten S, Welte C, Veraart AJ. Phosphorus control and dredging decrease methane emissions from shallow lakes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 847:157584. [PMID: 35882339 DOI: 10.1016/j.scitotenv.2022.157584] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/17/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
Freshwater ecosystems are an important source of the greenhouse gas methane (CH4), and their emissions are expected to increase due to eutrophication. Two commonly applied management techniques to reduce eutrophication are the addition of phosphate-binding lanthanum modified bentonite (LMB, trademark Phoslock©) and dredging, but their effect on CH4 emissions is still poorly understood. Here, this study researched how LMB and dredging affected CH4 emissions using a full-factorial mesocosm design monitored for 18 months. The effect was tested by measuring diffusive and ebullitive CH4 fluxes, plant community composition, methanogen and methanotroph activity and community composition, and a range of physicochemical water and sediment variables. LMB addition decreased total CH4 emissions, while dredging showed a trend towards decreasing CH4 emissions. Total CH4 emissions in all mesocosms were much higher in the summer of the second year, likely because of higher algal decomposition and organic matter availability. First, LMB addition lowered CH4 emissions by decreasing P-availability, which reduced coverage of the floating fern Azolla filiculoides, and thereby prevented anoxia and decreased surface water NH4+ concentrations, lowering CH4 production rates. Second, dredging decreased CH4 emissions in the first summer, possibly it removed the methanogenic community, and in the second year by preventing autumn and winter die-off of the rooted macrophyte Potamogeton cripsus. Finally, methanogen community composition was related to surface water NH4+ and O2, and porewater total phosphorus, while methanotroph community composition was related to organic matter content. To conclude, LMB addition and dredging not only improve water quality, but also decrease CH4 emissions, mitigating climate change.
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Affiliation(s)
- Thomas P A Nijman
- Department of Aquatic Ecology and Environmental Biology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands.
| | - Maxime Lemmens
- Department of Aquatic Ecology and Environmental Biology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Miquel Lurling
- Aquatic Ecology & Water Quality Management Group, Department of Environmental Sciences, Wageningen University, Droevendaalsesteeg 3a, 6708 PB Wageningen, the Netherlands
| | - Sarian Kosten
- Department of Aquatic Ecology and Environmental Biology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Cornelia Welte
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Annelies J Veraart
- Department of Aquatic Ecology and Environmental Biology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
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Rani V, Prasanna R, Kaushik R. Prospecting the significance of methane-utilizing bacteria in agriculture. World J Microbiol Biotechnol 2022; 38:176. [PMID: 35922575 DOI: 10.1007/s11274-022-03331-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/08/2022] [Indexed: 11/29/2022]
Abstract
Microorganisms act as both the source and sink of methane, a potent greenhouse gas, thus making a significant contribution to the environment as an important driver of climate change. The rhizosphere and phyllosphere of plants growing in natural (mangroves) and artificial wetlands (flooded agricultural ecosystems) harbor methane-utilizing bacteria that oxidize methane at the source and reduce its net flux. For several decades, microorganisms have been used as biofertilizers to promote plant growth. However, now their role in reducing net methane flux, especially from flooded agricultural ecosystems is gaining momentum globally. Research in this context has mainly focused on taxonomic aspects related to methanotrophy among diverse bacterial genera, and environmental factors that govern methane utilization in natural and artificial wetland ecosystems. In the last few decades, concerted efforts have been made to develop multifunctional microbial inoculants that can oxidize methane and alleviate greenhouse gas emissions, as well as promote plant growth. In this context, combinations of taxonomic groups commonly found in rice paddies and those used as biofertilizers are being explored. This review deals with methanotrophy among diverse bacterial domains, factors influencing methane-utilizing ability, and explores the potential of novel methane-utilizing microbial consortia with plant growth-promoting traits in flooded ecosystems.
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Affiliation(s)
- Vijaya Rani
- ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
| | - Radha Prasanna
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Rajeev Kaushik
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India.
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6
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Quantification of Ecosystem-Scale Methane Sinks Observed in a Tropical Rainforest in Hainan, China. LAND 2022. [DOI: 10.3390/land11020154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Tropical rainforest ecosystems are important when considering the global methane (CH4) budget and in climate change mitigation. However, there is a lack of direct and year-round observations of ecosystem-scale CH4 fluxes from tropical rainforest ecosystems. In this study, we examined the temporal variations in CH4 flux at the ecosystem scale and its annual budget and environmental controlling factors in a tropical rainforest of Hainan Island, China, using 3 years of continuous eddy covariance measurements from 2016 to 2018. Our results show that CH4 uptake generally occurred in this tropical rainforest, where strong CH4 uptake occurred in the daytime, and a weak CH4 uptake occurred at night with a mean daily CH4 flux of −4.5 nmol m−2 s−1. In this rainforest, the mean annual budget of CH4 for the 3 years was −1260 mg CH4 m−2 year−1. Furthermore, the daily averaged CH4 flux was not distinctly different between the dry season and wet season. Sixty-nine percent of the total variance in the daily CH4 flux could be explained by the artificial neural network (ANN) model, with a combination of air temperature (Tair), latent heat flux (LE), soil volumetric water content (VWC), atmospheric pressure (Pa), and soil temperature at −10 cm (Tsoil), although the linear correlation between the daily CH4 flux and any of these individual variables was relatively low. This indicates that CH4 uptake in tropical rainforests is controlled by multiple environmental factors and that their relationships are nonlinear. Our findings also suggest that tropical rainforests in China acted as a CH4 sink during 2016–2018, helping to counteract global warming.
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7
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Rani V, Bhatia A, Kaushik R. Inoculation of plant growth promoting-methane utilizing bacteria in different N-fertilizer regime influences methane emission and crop growth of flooded paddy. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 775:145826. [PMID: 33631576 DOI: 10.1016/j.scitotenv.2021.145826] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 02/06/2021] [Accepted: 02/08/2021] [Indexed: 06/12/2023]
Abstract
Methane (CH4) emission in rice fields is greatly influenced by the type and quantity of nitrogenous fertilizer used. The net methane emission from paddy fields is also influenced by the activity of methane utilizing bacteria, which inhabit the flooded paddy ecosystem. Efficient methane utilizing and plant growth promoting bacteria Methylobacterium oryzae MNL7 and Paenibacillus polymyxa MaAL70, respectively were co-inoculated along with different nitrogenous fertilizer combinations in flooded paddy to assess their impact on cumulative methane emission and crop growth promotion. Co-inoculation significantly influenced the plant growth parameters of paddy, resulting in an increase in grain yield by 14.04, 11.08, and 12.38% in treatments receiving Urea, Di-ammonium Phosphate (DAP) + Urea, or farm yard manure (FYM), over their respective un-inoculated plots. Significant improvement in the rice grain nutrient quality in term of crude protein, Fe and Zn content was observed as a result of bacterial co-inoculation in FYM fertilized plots as compared to Urea and DAP+ Urea fertilized plots. Significantly higher cumulative methane emission of 63.39 kg ha-1 was observed in uninoculated plots fertilized with FYM treatment as compared to Urea (33.83 kg ha-1) and DAP+Urea (31.66 kg ha-1) treatments. Bacterial co-inoculation significantly reduced the cumulative methane emission by 12.03, 11.47 and 6.92% in Urea, DAP+Urea, and FYM fertilized plots over their respective uninoculated treatments. Among the different fertilizer treatments, bacterial co-inoculation with urea application performed significantly better in reducing cumulative methane emission. These findings suggest that methane utilizing bacteria which also possess plant growth promoting trait can be explored for developing a novel biofertilizer for flooded paddies, as they can aid in managing both the overall methane emission and enhancing crop yield.
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Affiliation(s)
- Vijaya Rani
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Arti Bhatia
- Center for Environemtal Sciences and Climate Resilient Agriculture, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Rajeev Kaushik
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India.
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Meisner A, Snoek BL, Nesme J, Dent E, Jacquiod S, Classen AT, Priemé A. Soil microbial legacies differ following drying-rewetting and freezing-thawing cycles. THE ISME JOURNAL 2021; 15:1207-1221. [PMID: 33408369 PMCID: PMC8115648 DOI: 10.1038/s41396-020-00844-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 11/05/2020] [Accepted: 11/11/2020] [Indexed: 01/29/2023]
Abstract
Climate change alters frequencies and intensities of soil drying-rewetting and freezing-thawing cycles. These fluctuations affect soil water availability, a crucial driver of soil microbial activity. While these fluctuations are leaving imprints on soil microbiome structures, the question remains if the legacy of one type of weather fluctuation (e.g., drying-rewetting) affects the community response to the other (e.g., freezing-thawing). As both phenomenons give similar water availability fluctuations, we hypothesized that freezing-thawing and drying-rewetting cycles have similar effects on the soil microbiome. We tested this hypothesis by establishing targeted microcosm experiments. We created a legacy by exposing soil samples to a freezing-thawing or drying-rewetting cycle (phase 1), followed by an additional drying-rewetting or freezing-thawing cycle (phase 2). We measured soil respiration and analyzed soil microbiome structures. Across experiments, larger CO2 pulses and changes in microbiome structures were observed after rewetting than thawing. Drying-rewetting legacy affected the microbiome and CO2 emissions upon the following freezing-thawing cycle. Conversely, freezing-thawing legacy did not affect the microbial response to the drying-rewetting cycle. Our results suggest that drying-rewetting cycles have stronger effects on soil microbial communities and CO2 production than freezing-thawing cycles and that this pattern is mediated by sustained changes in soil microbiome structures.
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Affiliation(s)
- Annelein Meisner
- grid.4514.40000 0001 0930 2361Microbial Ecology, Department of Biology, Lund University, Ecology Building, SE-223 62 Lund, Sweden ,grid.5254.60000 0001 0674 042XDepartment of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark ,grid.418375.c0000 0001 1013 0288Department of Microbial Ecology, Netherlands Institute of Ecology, Droevendaalsesteeg 10, Wageningen, The Netherlands ,grid.4818.50000 0001 0791 5666Present Address: Wageningen University & Research, Droevendaalsesteeg 4, Wageningen, The Netherlands
| | - Basten L. Snoek
- grid.5477.10000000120346234Theoretical Biology and Bioinformatics, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Joseph Nesme
- grid.5254.60000 0001 0674 042XDepartment of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Elizabeth Dent
- grid.5254.60000 0001 0674 042XDepartment of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Samuel Jacquiod
- grid.5613.10000 0001 2298 9313Agroécologie, AgroSup Dijon, INRAE Centre Dijon, Université de Bourgogne Franche-Comté, Dijon, France
| | - Aimée T. Classen
- grid.214458.e0000000086837370Ecology and Evolutionary Biology Department, University of Michigan, Ann Arbor, MI 48109 USA ,grid.59062.380000 0004 1936 7689The Gund Institute for Environment, University of Vermont, Burlington, VT USA ,grid.5254.60000 0001 0674 042XThe Center for Macroecology, Evolution and Climate, The University of Copenhagen, Copenhagen Ø, Denmark
| | - Anders Priemé
- grid.5254.60000 0001 0674 042XDepartment of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark ,grid.5254.60000 0001 0674 042XDepartment of Geosciences and Natural Resource Management, Center for Permafrost (CENPERM), University of Copenhagen, Øster Voldgade 10, 1350 Copenhagen, Denmark
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Ho A, Mendes LW, Lee HJ, Kaupper T, Mo Y, Poehlein A, Bodelier PLE, Jia Z, Horn MA. Response of a methane-driven interaction network to stressor intensification. FEMS Microbiol Ecol 2021; 96:5898668. [PMID: 32857837 DOI: 10.1093/femsec/fiaa180] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 08/25/2020] [Indexed: 01/04/2023] Open
Abstract
Microorganisms may reciprocally select for specific interacting partners, forming a network with interdependent relationships. The methanotrophic interaction network, comprising methanotrophs and non-methanotrophs, is thought to modulate methane oxidation and give rise to emergent properties beneficial for the methanotrophs. Therefore, microbial interaction may become relevant for community functioning under stress. However, empirical validation of the role and stressor-induced response of the interaction network remains scarce. Here, we determined the response of a complex methane-driven interaction network to a stepwise increase in NH4Cl-induced stress (0.5-4.75 g L-1, in 0.25-0.5 g L-1 increments) using enrichment of a naturally occurring complex community derived from a paddy soil in laboratory-scale incubations. Although ammonium and intermediates of ammonium oxidation are known to inhibit methane oxidation, methanotrophic activity was unexpectedly detected even in incubations with high ammonium levels, albeit rates were significantly reduced. Sequencing analysis of the 16S rRNA and pmoA genes consistently revealed divergent communities in the reference and stressed incubations. The 16S rRNA-based co-occurrence network analysis revealed that NH4Cl-induced stress intensification resulted in a less complex and modular network, likely driven by less stable interaction. Interestingly, the non-methanotrophs formed the key nodes, and appear to be relevant members of the community. Overall, stressor intensification unravels the interaction network, with adverse consequences for community functioning.
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Affiliation(s)
- Adrian Ho
- Institute of Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Lucas W Mendes
- Center of Nuclear Energy in Agriculture, University of São Paulo (CENA-USP), Avenida Centenario 303, 13416-000, Piracicaba-SP, Brazil
| | - Hyo Jung Lee
- Department of Biology, Kunsan National University, 558 Daehak-ro, Gunsan-si 54150, Republic of Korea
| | - Thomas Kaupper
- Institute of Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Yongliang Mo
- Institute of Soil Science, Chinese Academy of Sciences, No. 71 East Beijing Road, Xuan-Wu District, Nanjing 210008, China
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany
| | - Paul L E Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, the Netherlands
| | - Zhongjun Jia
- Institute of Soil Science, Chinese Academy of Sciences, No. 71 East Beijing Road, Xuan-Wu District, Nanjing 210008, China
| | - Marcus A Horn
- Institute of Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
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10
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Xu X, Xia Z, Liu Y, Liu E, Müller K, Wang H, Luo J, Wu X, Beiyuan J, Fang Z, Xu J, Di H, Li Y. Interactions between methanotrophs and ammonia oxidizers modulate the response of in situ methane emissions to simulated climate change and its legacy in an acidic soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 752:142225. [PMID: 33207503 DOI: 10.1016/j.scitotenv.2020.142225] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/31/2020] [Accepted: 09/03/2020] [Indexed: 06/11/2023]
Abstract
Methane (CH4) is one of the most important greenhouse gases which can be formed by methanogens and oxidized by methanotrophs, as well as ammonia oxidizers. Agricultural soils can be both a source and sink for atmospheric CH4. However, it is unclear how climate change, will affect CH4 emissions and the underlying functional guilds. In this field study, we determined the impact of simulated climate change (a warmer and drier condition) and its legacy effect on CH4 emissions and the methanogenic and methanotrophic communities, as well as their relationships with ammonia oxidizers in an acidic soil with urea application. The climate change conditions were simulated in a greenhouse, and the legacy effect was simulated by removing the greenhouse after twelve months. Simulated climate change significantly decreased the in situ CH4 emissions in the urea-treated soils while the legacy effect significantly decreased the in situ CH4 emissions in the control plots, but had very little effect in the urea-treated soils. This indicates that the impact of simulated climate change and its legacy on CH4 emissions was significantly modified by nitrogen fertilization. Methanotrophs were more sensitive than methanogens in response to simulated climate change and its legacy effect, especially in the urea treated soil. Significant negative correlations were observed between the abundances of ammonia oxidizers and methanotrophs. Additionally, results of partial least path modeling (PLS-PM) indicated that the interactions of methanogens and methanotrophs with ammonia oxidizing archaea (AOA) had significant positive relationships with in situ CH4 emissions under the simulated climate change condition. Our work highlights the important role of AOA for CH4 emissions under climate change conditions. Further research is needed to better understand this effect in other ecosystems.
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Affiliation(s)
- Xiaoya Xu
- College of Geography and Environment, Shandong Normal University, Jinan 250014, China; College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China; School of Environment and Chemical Engineering, Foshan University, Foshan, Guangdong 528000, China
| | - Zhidan Xia
- School of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Yaowei Liu
- College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
| | - Enfeng Liu
- College of Geography and Environment, Shandong Normal University, Jinan 250014, China
| | - Karin Müller
- The New Zealand Institute for Plant & Food Research Limited, Ruakura Research Centre, Private Bag 3123, Hamilton, New Zealand
| | - Hailong Wang
- School of Environment and Chemical Engineering, Foshan University, Foshan, Guangdong 528000, China
| | - Jiafa Luo
- AgResearch Ruakura, Hamilton 3214, New Zealand
| | - Xiaolian Wu
- School of Environment and Chemical Engineering, Foshan University, Foshan, Guangdong 528000, China
| | - Jingzi Beiyuan
- School of Environment and Chemical Engineering, Foshan University, Foshan, Guangdong 528000, China
| | - Zheng Fang
- School of Environment and Chemical Engineering, Foshan University, Foshan, Guangdong 528000, China
| | - Jianming Xu
- College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
| | - Hongjie Di
- College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
| | - Yong Li
- College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China.
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11
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Treby S, Carnell PE, Trevathan-Tackett SM, Bonetti G, Macreadie PI. Assessing passive rehabilitation for carbon gains in rain-filled agricultural wetlands. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2020; 256:109971. [PMID: 31989987 DOI: 10.1016/j.jenvman.2019.109971] [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: 06/10/2019] [Revised: 11/26/2019] [Accepted: 12/06/2019] [Indexed: 06/10/2023]
Abstract
Wetland ecosystems have a disproportionally large influence on the global carbon cycle. They can act as carbon sinks or sources depending upon their location, type, and condition. Rehabilitation of wetlands is gaining popularity as a nature-based approach to helping mitigate climate change; however, few studies have empirically tested the carbon benefits of wetland restoration, especially in freshwater environments. Here we investigated the effects of passive rehabilitation (i.e. fencing and agricultural release) of 16 semi-arid rain-filled freshwater wetlands in southeastern Australia. Eight control sites were compared with older (>10 year) or newer (2-5 year) rehabilitated sites, dominated by graminoids or eucalypts. Carbon stocks (soils and plant biomass), and emissions (carbon dioxide - CO2; and methane - CH4) were sampled across three seasons, representing natural filling and drawdown, and soil microbial communities were sampled in spring. We found no significant difference in soil carbon or greenhouse gas emissions between rehabilitated and control sites, however, plant biomass was significantly higher in older rehabilitated sites. Wetland carbon stocks were 19.21 t Corg ha-1 and 2.84 t Corg ha-1 for soils (top 20 cm; n = 137) and plant biomass (n = 288), respectively. Hydrology was a strong driver of wetland greenhouse gas emissions. Diffusive fluxes (n = 356) averaged 117.63 mmol CO2 m2 d-1 and 2.98 mmol CH4 m2 d-1 when wet, and 124.01 mmol CO2 m2 d-1 and -0.41 mmol CH4 m2 d-1 when dry. Soil microbial community richness was nearly 2-fold higher during the wet phase than the dry phase, including relative increases in Nitrososphaerales, Myxococcales and Koribacteraceae and methanogens Methanobacteriales. Vegetation type significantly influenced soil carbon, aboveground carbon, and greenhouse gas emissions. Overall, our results suggest that passive rehabilitation of rain-filled wetlands, while valuable for biodiversity and habitat provisioning, is ineffective for increasing carbon gains within 20 years. Carbon offsetting opportunities may be better in systems with faster sediment accretion. Active rehabilitation methods, particularly that reinstate the natural hydrology of drained wetlands, should also be considered.
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Affiliation(s)
- Sarah Treby
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia.
| | - Paul E Carnell
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
| | - Stacey M Trevathan-Tackett
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
| | - Giuditta Bonetti
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
| | - Peter I Macreadie
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
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12
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Rodríguez E, López JC, Prieto P, Merchán L, García-Encina PA, Lebrero R, Muñoz R. A rapid regulation with different response intensities of the pmoA gene guarantees process robustness towards methane surges in continuous and feast-famine bioreactors. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.01.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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13
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Bodelier PLE, Pérez G, Veraart AJ, Krause SMB. Methanotroph Ecology, Environmental Distribution and Functioning. METHANOTROPHS 2019. [DOI: 10.1007/978-3-030-23261-0_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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14
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Meisner A, de Boer W. Strategies to Maintain Natural Biocontrol of Soil-Borne Crop Diseases During Severe Drought and Rainfall Events. Front Microbiol 2018; 9:2279. [PMID: 30450083 PMCID: PMC6225574 DOI: 10.3389/fmicb.2018.02279] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 09/06/2018] [Indexed: 11/13/2022] Open
Abstract
In many parts of the world, agricultural ecosystems are increasingly exposed to severe drought, and rainfall events due to climate changes. This coincides with a higher vulnerability of crops to soil-borne diseases, which is mostly ascribed to decreased resistance to pathogen attacks. However, loss of the natural capacity of soil microbes to suppress soil-borne plant pathogens may also contribute to increased disease outbreaks. In this perspectives paper, we will discuss the effect of extreme weather events on pathogen-antagonist interactions during drought and rainfall events and upon recovery. We will focus on diseases caused by root-infecting fungi and oomycetes. In addition, we will explore factors that affect restoration of the balance between pathogens and other soil microbes. Finally, we will indicate potential future avenues to improve the resistance and/or recovery of natural biocontrol during, and after water stresses. As such, our perspective paper will highlight a knowledge gap that needs to be bridged to adapt agricultural ecosystems to changing climate scenarios.
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Affiliation(s)
- Annelein Meisner
- Microbial Ecology Group, Department of Biology, Lund University, Lund, Sweden
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
- Department of Soil Quality, Wageningen University and Research Centre, Wageningen, Netherlands
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