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Kramer BJ, Turk-Kubo K, Zehr JP, Gobler CJ. Intensification of harmful cyanobacterial blooms in a eutrophic, temperate lake caused by nitrogen, temperature, and CO 2. Sci Total Environ 2024; 915:169885. [PMID: 38190910 DOI: 10.1016/j.scitotenv.2024.169885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 01/01/2024] [Accepted: 01/01/2024] [Indexed: 01/10/2024]
Abstract
Warmer temperatures can significantly increase the intensity of cyanobacterial harmful algal blooms (CHABs) in eutrophic freshwater ecosystems. However, few studies have examined the effects of CO2 enrichment in tandem with elevated temperature and/or nutrients on cyanobacterial taxa in freshwater ecosystems. Here, we observed changes in the biomass of cyanobacteria, nutrients, pH, and carbonate chemistry over a two-year period in a shallow, eutrophic freshwater lake and performed experiments to examine the effects and co-effects of CO2, temperature, and nutrient enrichment on cyanobacterial and N2-fixing (diazotrophic) communities assessed via high throughput sequencing of the 16S rRNA and nifH genes, respectively. During both years, there were significant CHABs (50-500 μg cyanobacterial chlorophyll-a L-1) and lake CO2 levels were undersaturated (≤300 μatm pCO2). NH4+ significantly increased the net growth rates of cyanobacteria as well as the biomass of the diazotrophic cyanobacterial order Nostocales under elevated and ambient CO2 conditions. In a fall experiment, the N2 fixation rates of Nostocales were significantly higher when populations were enriched with CO2 and P, relative to CO2-enriched populations that were not amended with P. During a summer experiment, N2 fixation rates increased significantly under N and CO2 - enriched conditions relative to N-enriched and ambient CO2 conditions. Nostocales dominated the diazotrophic communities of both experiments, achieving the highest relative abundance under CO2-enriched conditions when N was added in the first experiment and when CO2 and temperature were elevated in the second experiment, when N2 fixation rates also increased significantly. Collectively, this study indicates that N promotes cyanobacterial blooms including those formed by Dolichospermum and that the biomass and N2 fixation rates of diazotrophic cyanobacterial taxa may benefit from enhanced CO2 levels in eutrophic lakes.
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Affiliation(s)
- Benjamin J Kramer
- School of Marine and Atmospheric Sciences, Stony Brook University, Southampton, NY, United States
| | - Kendra Turk-Kubo
- Oceans Sciences Department, University of California at Santa Cruz, CA, United States
| | - Jonathan P Zehr
- Oceans Sciences Department, University of California at Santa Cruz, CA, United States
| | - Christopher J Gobler
- School of Marine and Atmospheric Sciences, Stony Brook University, Southampton, NY, United States.
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2
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Kilner CL, Carrell AA, Wieczynski DJ, Votzke S, DeWitt K, Yammine A, Shaw J, Pelletier DA, Weston DJ, Gibert JP. Temperature and CO 2 interactively drive shifts in the compositional and functional structure of peatland protist communities. Glob Chang Biol 2024; 30:e17203. [PMID: 38433341 DOI: 10.1111/gcb.17203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 01/20/2024] [Accepted: 01/26/2024] [Indexed: 03/05/2024]
Abstract
Microbes affect the global carbon cycle that influences climate change and are in turn influenced by environmental change. Here, we use data from a long-term whole-ecosystem warming experiment at a boreal peatland to answer how temperature and CO2 jointly influence communities of abundant, diverse, yet poorly understood, non-fungi microbial Eukaryotes (protists). These microbes influence ecosystem function directly through photosynthesis and respiration, and indirectly, through predation on decomposers (bacteria and fungi). Using a combination of high-throughput fluid imaging and 18S amplicon sequencing, we report large climate-induced, community-wide shifts in the community functional composition of these microbes (size, shape, and metabolism) that could alter overall function in peatlands. Importantly, we demonstrate a taxonomic convergence but a functional divergence in response to warming and elevated CO2 with most environmental responses being contingent on organismal size: warming effects on functional composition are reversed by elevated CO2 and amplified in larger microbes but not smaller ones. These findings show how the interactive effects of warming and rising CO2 levels could alter the structure and function of peatland microbial food webs-a fragile ecosystem that stores upwards of 25% of all terrestrial carbon and is increasingly threatened by human exploitation.
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Affiliation(s)
- Christopher L Kilner
- Department of Biology, Duke University, Durham, North Carolina, USA
- Bird Conservancy of the Rockies, Fort Collins, Colorado, USA
| | - Alyssa A Carrell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | | | - Samantha Votzke
- Department of Biology, Duke University, Durham, North Carolina, USA
| | - Katrina DeWitt
- Department of Biology, Duke University, Durham, North Carolina, USA
| | - Andrea Yammine
- Department of Biology, Duke University, Durham, North Carolina, USA
| | - Jonathan Shaw
- Department of Biology, Duke University, Durham, North Carolina, USA
| | - Dale A Pelletier
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Jean P Gibert
- Department of Biology, Duke University, Durham, North Carolina, USA
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3
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Wang Y, Xue D, Chen X, Qiu Q, Chen H. Structure and Functions of Endophytic Bacterial Communities Associated with Sphagnum Mosses and Their Drivers in Two Different Nutrient Types of Peatlands. Microb Ecol 2024; 87:47. [PMID: 38407642 PMCID: PMC10896819 DOI: 10.1007/s00248-024-02355-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 01/29/2024] [Indexed: 02/27/2024]
Abstract
Sphagnum mosses are keystone plant species in the peatland ecosystems that play a crucial role in the formation of peat, which shelters a broad diversity of endophytic bacteria with important ecological functions. In particular, methanotrophic and nitrogen-fixing endophytic bacteria benefit Sphagnum moss hosts by providing both carbon and nitrogen. However, the composition and abundance of endophytic bacteria from different species of Sphagnum moss in peatlands of different nutrient statuses and their drivers remain unclear. This study used 16S rRNA gene amplicon sequencing to examine endophytic bacterial communities in Sphagnum mosses and measured the activity of methanotrophic microbial by the 13C-CH4 oxidation rate. According to the results, the endophytic bacterial community structure varied among Sphagnum moss species and Sphagnum capillifolium had the highest endophytic bacterial alpha diversity. Moreover, chlorophyll, phenol oxidase, carbon contents, and water retention capacity strongly shaped the communities of endophytic bacteria. Finally, Sphagnum palustre in Hani (SP) had a higher methane oxidation rate than S. palustre in Taishanmiao. This result is associated with the higher average relative abundance of Methyloferula an obligate methanotroph in SP. In summary, this work highlights the effects of Sphagnum moss characteristics on the endophytic bacteriome. The endophytic bacteriome is important for Sphagnum moss productivity, as well as for carbon and nitrogen cycles in Sphagnum moss peatlands.
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Affiliation(s)
- Yue Wang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9, Section 4, South Renmin Road, Chengdu, 610041, China
- Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan, 624400, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dan Xue
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9, Section 4, South Renmin Road, Chengdu, 610041, China.
- Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan, 624400, China.
| | - Xuhui Chen
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9, Section 4, South Renmin Road, Chengdu, 610041, China
- Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan, 624400, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qing Qiu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9, Section 4, South Renmin Road, Chengdu, 610041, China
| | - Huai Chen
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9, Section 4, South Renmin Road, Chengdu, 610041, China.
- Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan, 624400, China.
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Metze D, Schnecker J, de Carlan CLN, Bhattarai B, Verbruggen E, Ostonen I, Janssens IA, Sigurdsson BD, Hausmann B, Kaiser C, Richter A. Soil warming increases the number of growing bacterial taxa but not their growth rates. Sci Adv 2024; 10:eadk6295. [PMID: 38394199 PMCID: PMC10889357 DOI: 10.1126/sciadv.adk6295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 01/22/2024] [Indexed: 02/25/2024]
Abstract
Soil microorganisms control the fate of soil organic carbon. Warming may accelerate their activities putting large carbon stocks at risk of decomposition. Existing knowledge about microbial responses to warming is based on community-level measurements, leaving the underlying mechanisms unexplored and hindering predictions. In a long-term soil warming experiment in a Subarctic grassland, we investigated how active populations of bacteria and archaea responded to elevated soil temperatures (+6°C) and the influence of plant roots, by measuring taxon-specific growth rates using quantitative stable isotope probing and 18O water vapor equilibration. Contrary to prior assumptions, increased community growth was associated with a greater number of active bacterial taxa rather than generally faster-growing populations. We also found that root presence enhanced bacterial growth at ambient temperatures but not at elevated temperatures, indicating a shift in plant-microbe interactions. Our results, thus, reveal a mechanism of how soil bacteria respond to warming that cannot be inferred from community-level measurements.
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Affiliation(s)
- Dennis Metze
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria
| | - Jörg Schnecker
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | | | - Biplabi Bhattarai
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Erik Verbruggen
- Research Group Plants and Ecosystems, University of Antwerp, Antwerp, Belgium
| | - Ivika Ostonen
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Ivan A. Janssens
- Research Group Plants and Ecosystems, University of Antwerp, Antwerp, Belgium
| | - Bjarni D. Sigurdsson
- Faculty of Environmental and Forest Sciences, Agricultural University of Iceland, Hvanneyri, Borgarnes, Iceland
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Christina Kaiser
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- International Institute for Applied Systems Analysis, Advancing Systems Analysis Program, Laxenburg, Austria
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5
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Berg G, Dorador C, Egamberdieva D, Kostka JE, Ryu CM, Wassermann B. Shared governance in the plant holobiont and implications for one health. FEMS Microbiol Ecol 2024; 100:fiae004. [PMID: 38364305 PMCID: PMC10876113 DOI: 10.1093/femsec/fiae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/30/2023] [Accepted: 02/12/2024] [Indexed: 02/18/2024] Open
Abstract
The holobiont Holobiont theory is more than 80 years old, while the importance of microbial communities for plant holobionts was already identified by Lorenz Hiltner more than a century ago. Both concepts are strongly supported by results from the new field of microbiome research. Here, we present ecological and genetic features of the plant holobiont that underpin principles of a shared governance between hosts and microbes and summarize the relevance of plant holobionts in the context of global change. Moreover, we uncover knowledge gaps that arise when integrating plant holobionts in the broader perspective of the holobiome as well as one and planetary health concepts. Action is needed to consider interacting holobionts at the holobiome scale, for prediction and control of microbiome function to improve human and environmental health outcomes.
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Affiliation(s)
- Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, 8010 Graz, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Cristina Dorador
- Department of Biotechnology, Universidad de Antofagasta & Centre for Biotechnology and Bioengineering (CeBiB), Angamos 601, Antofagasta, Chile
| | - Dilfuza Egamberdieva
- Institute of Fundamental and Applied Research, National Research University, TIIAME, Kari Niyazi street 39, Tashkent 100000, Uzbekistan
- Medical School, Central Asian University, Milliy bog street 264, Tashkent 111221, Uzbekistan
| | - Joel E Kostka
- Schools of Biological Sciences and Earth & Atmospheric Sciences, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30332, United States
| | - Choong-Min Ryu
- Biosystems and Bioengineering, University of Science and Technology KRIBB School, 125 Gwahangro, Yuseong, Daejeon 34141, South Korea
- Molecular Phytobacteriology Laboratory, Infectious Disease Research Center, KRIBB, 125 Gwahangro, Yuseong, Daejeon 34141, South Korea
| | - Birgit Wassermann
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, 8010 Graz, Austria
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Zhang H, Adalibieke W, Ba W, Butterbach-Bahl K, Yu L, Cai A, Fu J, Yu H, Zhang W, Huang W, Jian Y, Jiang W, Zhao Z, Luo J, Deng J, Zhou F. Modeling denitrification nitrogen losses in China's rice fields based on multiscale field-experiment constraints. Glob Chang Biol 2024; 30:e17199. [PMID: 38385944 DOI: 10.1111/gcb.17199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 02/23/2024]
Abstract
Denitrification plays a critical role in soil nitrogen (N) cycling, affecting N availability in agroecosystems. However, the challenges in direct measurement of denitrification products (NO, N2 O, and N2 ) hinder our understanding of denitrification N losses patterns across the spatial scale. To address this gap, we constructed a data-model fusion method to map the county-scale denitrification N losses from China's rice fields over the past decade. The estimated denitrification N losses as a percentage of N application from 2009 to 2018 were 11.8 ± 4.0% for single rice, 12.4 ± 3.7% for early rice, and 11.6 ± 3.1% for late rice. The model results showed that the spatial heterogeneity of denitrification N losses is primarily driven by edaphic and climatic factors rather than by management practices. In particular, diffusion and production rates emerged as key contributors to the variation of denitrification N losses. These findings humanize a 38.9 ± 4.8 kg N ha-1 N loss by denitrification and challenge the common hypothesis that substrate availability drives the pattern of N losses by denitrification in rice fields.
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Affiliation(s)
- Huayan Zhang
- Institute of Carbon Neutrality, Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Wulahati Adalibieke
- Institute of Carbon Neutrality, Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Wenxin Ba
- Institute of Carbon Neutrality, Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing, China
| | | | - Longfei Yu
- Institute of Environment and Ecology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong, China
| | - Andong Cai
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jin Fu
- College of Geography and Remote Sensing, Hohai University, Nanjing, China
| | - Haoming Yu
- Institute of Carbon Neutrality, Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Wantong Zhang
- Institute of Carbon Neutrality, Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Weichen Huang
- Institute of Carbon Neutrality, Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Yiwei Jian
- Institute of Carbon Neutrality, Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Wenjun Jiang
- Institute of Carbon Neutrality, Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Zheng Zhao
- Institute of Ecological Environment Protection Research, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jiafa Luo
- AgResearch Ruakura, Hamilton, New Zealand
| | - Jia Deng
- Earth Systems Research Center, Institute for the Study of Earth, Oceans and Space, University of New Hampshire, Durham, New Hampshire, USA
| | - Feng Zhou
- Institute of Carbon Neutrality, Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing, China
- College of Geography and Remote Sensing, Hohai University, Nanjing, China
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7
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Groß C, Hossen S, Dittrich S, Knorr KH, Borken W, Noll M. Biological nitrogen fixation, diversity and community structure of diazotrophs in two mosses in 25 temperate forests. Environ Microbiol 2024; 26:e16555. [PMID: 38148519 DOI: 10.1111/1462-2920.16555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 11/27/2023] [Indexed: 12/28/2023]
Abstract
Many moss species are associated with nitrogen (N)-fixing bacteria (diazotrophs) that support the N supply of mosses. Our knowledge relates primarily to pristine ecosystems with low atmospheric N input, but knowledge of biological N fixation (BNF) and diazotrophic communities in mosses in temperate forests with high N deposition is limited. We measured BNF rates using the direct stable isotope method and studied the total and potentially active diazotrophic communities in two abundant mosses, Brachythecium rutabulum and Hypnum cupressiforme, both growing on lying deadwood trunks in 25 temperate forest sites. BNF rates in both mosses were similar to those observed in moss species of pristine ecosystems. H. cupressiforme fixed three times more N2 and exhibited lower diazotrophic richness than B. rutabulum. Frankia was the most prominent diazotroph followed by cyanobacteria Nostoc. Manganese, iron, and molybdenum contents in mosses were positively correlated with BNF and diazotrophic communities. Frankia maintained high BNF rates in H. cupressiforme and B. rutabulum even under high chronic N deposition in Central European forests. Moss N concentration and 15 N abundance indicate a rather minor contribution of BNF to the N nutrition of these mosses.
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Affiliation(s)
- Christina Groß
- Department of Soil Ecology, University of Bayreuth, Bayreuth, Germany
| | - Shakhawat Hossen
- Institute for Bioanalysis, Coburg University of Applied Sciences and Arts, Coburg, Germany
| | - Sebastian Dittrich
- Biodiversity and Conservation, Technical University of Dresden, Tharandt, Germany
| | - Klaus-Holger Knorr
- Institute of Landscape Ecology, Ecohydrology and Biogeochemistry Group, University of Münster, Münster, Germany
| | - Werner Borken
- Department of Soil Ecology, University of Bayreuth, Bayreuth, Germany
| | - Matthias Noll
- Institute for Bioanalysis, Coburg University of Applied Sciences and Arts, Coburg, Germany
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Yang Q, Liu Z, Bai E. Comparison of carbon and nitrogen accumulation rate between bog and fen phases in a pristine peatland with the fen-bog transition. Glob Chang Biol 2023; 29:6350-6366. [PMID: 37602716 DOI: 10.1111/gcb.16915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 07/17/2023] [Indexed: 08/22/2023]
Abstract
Long-term carbon and nitrogen dynamics in peatlands are affected by both vegetation production and decomposition processes. Here, we examined the carbon accumulation rate (CAR), nitrogen accumulation rate (NAR) and δ13 C, δ15 N of plant residuals in a peat core dated back to ~8500 cal year BP in a temperate peatland in Northeast China. Impacted by the tephra during 1160 and 789 cal year BP and climate change, the peatland changed from a fen dominated by vascular plants to a bog dominated by Sphagnum mosses. We used the Clymo model to quantify peat addition rate and decay constant for acrotelm and catotelm layers during both bog and fen phases. Our studied peatland was dominated by Sphagnum fuscum during the bog phase (789 to -59 cal year BP) and lower accumulation rates in the acrotelm layer was found during this phase, suggesting the dominant role of volcanic eruption in the CAR of the peat core. Both mean CAR and NAR were higher during the bog phase than during the fen phase in our study, consistent with the results of the only one similar study in the literature. Because the input rate of organic matter was considered to be lower during the bog phase, the decomposition process must have been much lower during the bog phase than during the fen phase and potentially controlled CAR and NAR. During the fen phase, CAR was also lower under higher temperature and summer insolation, conditions beneficial for decomposition. δ15 N of Sphagnum hinted that nitrogen fixation had a positive effect on nitrogen accumulation, particular in recent decades. Our study suggested that decomposition is more important for carbon and nitrogen sequestration than production in peatlands in most conditions and if future climate changes or human disturbance increase decomposition rate, carbon sequestration in peatlands will be jeopardized.
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Affiliation(s)
- Qiannan Yang
- Key Laboratory of Geographical Processes and Ecological Security of Changbai Mountains, Ministry of Education, School of Geographical Sciences, Northeast Normal University, Changchun, China
| | - Ziping Liu
- Key Laboratory of Geographical Processes and Ecological Security of Changbai Mountains, Ministry of Education, School of Geographical Sciences, Northeast Normal University, Changchun, China
- Key Laboratory of Vegetation Ecology, Ministry of Education, Northeast Normal University, Changchun, China
| | - Edith Bai
- Key Laboratory of Geographical Processes and Ecological Security of Changbai Mountains, Ministry of Education, School of Geographical Sciences, Northeast Normal University, Changchun, China
- Key Laboratory of Vegetation Ecology, Ministry of Education, Northeast Normal University, Changchun, China
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9
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Huang S, Zha X, Fu G. Affecting Factors of Plant Phyllosphere Microbial Community and Their Responses to Climatic Warming-A Review. Plants (Basel) 2023; 12:2891. [PMID: 37631103 PMCID: PMC10458011 DOI: 10.3390/plants12162891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 08/02/2023] [Accepted: 08/06/2023] [Indexed: 08/27/2023]
Abstract
Phyllosphere microorganisms are not only an important part of plants, but also an important part of microorganisms. In this review, the function of phyllosphere microorganisms, the assembly mechanism of phyllosphere microorganisms, the driving factors of phyllosphere microbial community structure, and the effects of climate warming on phyllosphere microbial community structure were reviewed. Generally, phyllosphere microorganisms have a variety of functions (e.g., fixing nitrogen, promoting plant growth). Although selection and dispersal processes together regulate the assembly of phyllospheric microbial communities, which one of the ecological processes is dominant and how external disturbances alter the relative contributions of each ecological process remains controversial. Abiotic factors (e.g., climatic conditions, geographical location and physical and chemical properties of soil) and biological factors (e.g., phyllosphere morphological structure, physiological and biochemical characteristics, and plant species and varieties) can affect phyllosphere microbial community structure. However, the predominant factors affecting phyllosphere microbial community structure are controversial. Moreover, how climate warming affects the phyllosphere microbial community structure and its driving mechanism have not been fully resolved, and further relevant studies are needed.
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Affiliation(s)
- Shaolin Huang
- Lhasa Plateau Ecosystem Research Station, Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China;
| | - Xinjie Zha
- Xi’an University of Finance and Economics, Xi’an 710100, China;
| | - Gang Fu
- Lhasa Plateau Ecosystem Research Station, Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China;
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10
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Tang K, Liang Y, Yuan B, Meng J, Feng F. Spatial distribution and core community of diazotrophs in Biological soil crusts and subsoils in temperate semi-arid and arid deserts of China. Front Microbiol 2023; 14:1074855. [PMID: 37608942 PMCID: PMC10440438 DOI: 10.3389/fmicb.2023.1074855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 07/25/2023] [Indexed: 08/24/2023] Open
Abstract
Introduction Biological soil crusts (BSCs) are distributed in arid and semiarid regions, and they function as important microhabitats for nitrogen fixation. The diazotroph community is critical for nitrogen fixation in BSCs and their subsoils. However, little is known about the key groups in different types of BSCs and subsoils in temperate semi-arid or arid deserts. Methods Here, we sampled three types of BSCs and their subsoils from the Inner Mongolian plateau, investigated the distribution characteristics of the diazotroph community by high-throughput sequencing, predicted keystone species using the molecular ecological network analyses pipeline (MENAP), and verified their close relationship with the available nitrogen (AN) content. Results The results showed that available nitrogen content in BSCs was higher than that in subsoils in three different types of BSCs, and there were differences among seasons and according to the mean annual precipitation. The abundance of diazotrophs was higher in Cyano-BSCs, while diversity had no significant difference among BSCs and subsoils. Cyanobacteria and Proteobacteria, Nostocaceae and Scytonemataceae, Skermanella, Scytonema, Azohydromonas, Nostoc and Trichormus were the dominant phyla, families, and genera, respectively. The dominant groups belong to Skermanella, Scytonema, and Nostoc formed the core diazotroph community in the three types of BSCs and subsoils, and each had a close relationship with AN. Discussion These results indicate that diazotrophs in BSCs and subsoils had high diversity, and the core diazotroph communities have a close relationship with nitrogen fixation and that they may be the main contributor to nitrogen fixing in BSCs and subsoils in temperate deserts.
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Affiliation(s)
- Kai Tang
- Laboratory for Environmental Microbiology and Biotechnology in Arid and Cold Regions, College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, China
| | - Yungang Liang
- Laboratory for Environmental Microbiology and Biotechnology in Arid and Cold Regions, College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, China
| | - Bo Yuan
- Laboratory for Environmental Microbiology and Biotechnology in Arid and Cold Regions, College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, China
- College of Life Science, Inner Mongolia Normal University, Hohhot, China
| | - Jianyu Meng
- Laboratory for Environmental Microbiology and Biotechnology in Arid and Cold Regions, College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, China
| | - Fuying Feng
- Laboratory for Environmental Microbiology and Biotechnology in Arid and Cold Regions, College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, China
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11
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Song T, Liu Y, Kolton M, Wilson RM, Keller JK, Rolando JL, Chanton JP, Kostka JE. Porewater constituents inhibit microbially mediated greenhouse gas production (GHG) and regulate the response of soil organic matter decomposition to warming in anoxic peat from a Sphagnum-dominated bog. FEMS Microbiol Ecol 2023; 99:fiad060. [PMID: 37280172 DOI: 10.1093/femsec/fiad060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 05/16/2023] [Accepted: 06/05/2023] [Indexed: 06/08/2023] Open
Abstract
Northern peatlands store approximately one-third of terrestrial soil carbon. Climate warming is expected to stimulate the microbially mediated degradation of peat soil organic matter (SOM), leading to increasing greenhouse gas (GHG; carbon dioxide, CO2; methane, CH4) production and emission. Porewater dissolved organic matter (DOM) plays a key role in SOM decomposition; however, the mechanisms controlling SOM decomposition and its response to warming remain unclear. The temperature dependence of GHG production and microbial community dynamics were investigated in anoxic peat from a Sphagnum-dominated peatland. In this study, peat decomposition, which was quantified by GHG production and carbon substrate utilization is limited by terminal electron acceptors (TEA) and DOM, and these controls of microbially mediated SOM degradation are temperature-dependent. Elevated temperature led to a slight decrease in microbial diversity, and stimulated the growth of specific methanotrophic and syntrophic taxa. These results confirm that DOM is a major driver of decomposition in peatland soils contains inhibitory compounds, but the inhibitory effect is alleviated by warming.
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Affiliation(s)
- Tianze Song
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Yutong Liu
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, United States
- Department of Civil & Environmental Engineering, Pennsylvania State University, University Park, University Park, PA 16802, United States
| | - Max Kolton
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, United States
- French Associates Institute for Agriculture and Biotechnology of Drylands, Ben-Gurion, University of the Negev, Beer Sheva, 8499000, Israel
| | - Rachel M Wilson
- Department of Earth, Ocean & Atmospheric Science, Florida State University, Tallahassee, FL 32304, United States
| | - Jason K Keller
- Schmid College of Science and Technology, Chapman University, 1 University Dr, Orange, CA 92866, United States
| | - Jose L Rolando
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Jeffrey P Chanton
- Department of Earth, Ocean & Atmospheric Science, Florida State University, Tallahassee, FL 32304, United States
| | - Joel E Kostka
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, United States
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA 30318, United States
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30332, United States
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12
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Petro C, Carrell AA, Wilson RM, Duchesneau K, Noble-Kuchera S, Song T, Iversen CM, Childs J, Schwaner G, Chanton JP, Norby RJ, Hanson PJ, Glass JB, Weston DJ, Kostka JE. Climate drivers alter nitrogen availability in surface peat and decouple N 2 fixation from CH 4 oxidation in the Sphagnum moss microbiome. Glob Chang Biol 2023; 29:3159-3176. [PMID: 36999440 DOI: 10.1111/gcb.16651] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 12/20/2022] [Indexed: 05/03/2023]
Abstract
Peat mosses (Sphagnum spp.) are keystone species in boreal peatlands, where they dominate net primary productivity and facilitate the accumulation of carbon in thick peat deposits. Sphagnum mosses harbor a diverse assemblage of microbial partners, including N2 -fixing (diazotrophic) and CH4 -oxidizing (methanotrophic) taxa that support ecosystem function by regulating transformations of carbon and nitrogen. Here, we investigate the response of the Sphagnum phytobiome (plant + constituent microbiome + environment) to a gradient of experimental warming (+0°C to +9°C) and elevated CO2 (+500 ppm) in an ombrotrophic peatland in northern Minnesota (USA). By tracking changes in carbon (CH4 , CO2 ) and nitrogen (NH4 -N) cycling from the belowground environment up to Sphagnum and its associated microbiome, we identified a series of cascading impacts to the Sphagnum phytobiome triggered by warming and elevated CO2 . Under ambient CO2 , warming increased plant-available NH4 -N in surface peat, excess N accumulated in Sphagnum tissue, and N2 fixation activity decreased. Elevated CO2 offset the effects of warming, disrupting the accumulation of N in peat and Sphagnum tissue. Methane concentrations in porewater increased with warming irrespective of CO2 treatment, resulting in a ~10× rise in methanotrophic activity within Sphagnum from the +9°C enclosures. Warming's divergent impacts on diazotrophy and methanotrophy caused these processes to become decoupled at warmer temperatures, as evidenced by declining rates of methane-induced N2 fixation and significant losses of keystone microbial taxa. In addition to changes in the Sphagnum microbiome, we observed ~94% mortality of Sphagnum between the +0°C and +9°C treatments, possibly due to the interactive effects of warming on N-availability and competition from vascular plant species. Collectively, these results highlight the vulnerability of the Sphagnum phytobiome to rising temperatures and atmospheric CO2 concentrations, with significant implications for carbon and nitrogen cycling in boreal peatlands.
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Affiliation(s)
- Caitlin Petro
- Center for Microbial Dynamics and Infection, School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Alyssa A Carrell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Rachel M Wilson
- Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, Florida, USA
| | - Katherine Duchesneau
- Center for Microbial Dynamics and Infection, School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Sekou Noble-Kuchera
- Center for Microbial Dynamics and Infection, School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Tianze Song
- Center for Microbial Dynamics and Infection, School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Colleen M Iversen
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Joanne Childs
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Geoff Schwaner
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Jeffrey P Chanton
- Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, Florida, USA
| | - Richard J Norby
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Department of Ecology & Evolutionary Biology, University of Tennessee, Knoxville, Tennessee, USA
| | - Paul J Hanson
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Jennifer B Glass
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Joel E Kostka
- Center for Microbial Dynamics and Infection, School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
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13
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Adomako MO, Yu FH. Potential effects of micro- and nanoplastics on phyllosphere microorganisms and their evolutionary and ecological responses. Sci Total Environ 2023; 884:163760. [PMID: 37120023 DOI: 10.1016/j.scitotenv.2023.163760] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/22/2023] [Accepted: 04/23/2023] [Indexed: 05/05/2023]
Abstract
Plastic pollution is among the most urgent environmental and social challenges of the 21st century, and their influxes in the environment have altered critical growth drivers in all biomes, attracting global concerns. In particular, the consequences of microplastics on plants and their associated soil microorganisms have gained a large audience. On the contrary, how microplastics and nanoplastics (M/NPs) may influence the plant-associated microorganisms in the phyllosphere (i.e., the aboveground portion of plants) is nearly unknown. We, therefore, summarize evidence that may potentially connect M/NPs, plants, and phyllosphere microorganisms based on studies on other analogous contaminants such as heavy metals, pesticides, and nanoparticles. We show seven pathways that may link M/NPs into the phyllosphere environment, and provide a conceptual framework explaining the direct and indirect (soil legacy) effects of M/NPs on phyllosphere microbial communities. We also discuss the adaptive evolutionary and ecological responses, such as acquiring novel resistance genes via horizontal gene transfer and microbial degradation of plastics of the phyllosphere microbial communities, to M/NPs-induced threats. Finally, we highlight the global consequences (e.g., disruption of ecosystem biogeochemical cycling and impaired host-pathogen defense chemistry that can lead to reduced agricultural productivity) of altered plant-microbiome interactions in the phyllosphere in the context of a predicted surge of plastic production and conclude with pending questions for future research priorities. In conclusion, M/NPs are very likely to produce significant effects on phyllosphere microorganisms and mediate their evolutionary and ecological responses.
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Affiliation(s)
- Michael Opoku Adomako
- Institute of Wetland Ecology & Clone Ecology/Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou 318000, Zhejiang, China
| | - Fei-Hai Yu
- Institute of Wetland Ecology & Clone Ecology/Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou 318000, Zhejiang, China.
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14
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Porada P, Bader MY, Berdugo MB, Colesie C, Ellis CJ, Giordani P, Herzschuh U, Ma Y, Launiainen S, Nascimbene J, Petersen I, Raggio Quílez J, Rodríguez-Caballero E, Rousk K, Sancho LG, Scheidegger C, Seitz S, Van Stan JT, Veste M, Weber B, Weston DJ. A research agenda for nonvascular photoautotrophs under climate change. New Phytol 2023; 237:1495-1504. [PMID: 36511294 DOI: 10.1111/nph.18631] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
Nonvascular photoautotrophs (NVP), including bryophytes, lichens, terrestrial algae, and cyanobacteria, are increasingly recognized as being essential to ecosystem functioning in many regions of the world. Current research suggests that climate change may pose a substantial threat to NVP, but the extent to which this will affect the associated ecosystem functions and services is highly uncertain. Here, we propose a research agenda to address this urgent question, focusing on physiological and ecological processes that link NVP to ecosystem functions while also taking into account the substantial taxonomic diversity across multiple ecosystem types. Accordingly, we developed a new categorization scheme, based on microclimatic gradients, which simplifies the high physiological and morphological diversity of NVP and world-wide distribution with respect to several broad habitat types. We found that habitat-specific ecosystem functions of NVP will likely be substantially affected by climate change, and more quantitative process understanding is required on: (1) potential for acclimation; (2) response to elevated CO2 ; (3) role of the microbiome; and (4) feedback to (micro)climate. We suggest an integrative approach of innovative, multimethod laboratory and field experiments and ecophysiological modelling, for which sustained scientific collaboration on NVP research will be essential.
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Affiliation(s)
- Philipp Porada
- Ecological Modelling, Universität Hamburg, Ohnhorststr. 18, 22609, Hamburg, Germany
| | - Maaike Y Bader
- Ecological Plant Geography, University of Marburg, Deutschhausstr. 10, 35032, Marburg, Germany
| | - Monica B Berdugo
- Ecological Plant Geography, University of Marburg, Deutschhausstr. 10, 35032, Marburg, Germany
| | - Claudia Colesie
- School of Geosciences, University of Edinburgh, Edinburgh, EH9 3JW, UK
| | | | | | - Ulrike Herzschuh
- Polar Terrestrial Environmental Systems, Alfred Wegener Institute, Telegrafenberg A45, 14473, Potsdam, Germany
| | - Yunyao Ma
- Ecological Modelling, Universität Hamburg, Ohnhorststr. 18, 22609, Hamburg, Germany
| | - Samuli Launiainen
- Ecosystems and Modeling, Natural Resources Institute Finland (Luke), Latokartanonkaari 9, 00790, Helsinki, Finland
| | - Juri Nascimbene
- BIOME Lab, Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum University of Bologna, 40126, Bologna, Italy
| | - Imke Petersen
- Ecological Modelling, Universität Hamburg, Ohnhorststr. 18, 22609, Hamburg, Germany
| | - José Raggio Quílez
- Department of Pharmacology, Pharmacognosy and Botany, Universidad Complutense de Madrid, E-28040, Madrid, Spain
| | | | - Kathrin Rousk
- Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, København, Denmark
| | - Leopoldo G Sancho
- Department of Pharmacology, Pharmacognosy and Botany, Universidad Complutense de Madrid, E-28040, Madrid, Spain
| | - Christoph Scheidegger
- Biodiversity and Conservation Biology, Eidg. Forschungsanstalt WSL, Zürcherstr. 111, 8903, Birmensdorf, Switzerland
| | - Steffen Seitz
- Soil Science and Geomorphology, University of Tübingen, Rümelinstr. 19-23, 72070, Tübingen, Germany
| | - John T Van Stan
- Department of Biological, Geological, and Environmental Sciences, Cleveland State University, 2121 Euclid Ave., Cleveland, OH, 44115, USA
| | - Maik Veste
- Institute of Environmental Sciences, Brandenburgische Technische Universität Cottbus-Senftenberg, Konrad-Wachsmann-Allee 6, 03046, Cottbus, Germany
| | - Bettina Weber
- Division of Plant Sciences, Institute for Biology, University of Graz, Holteigasse 6, A-8010, Graz, Austria
- Multiphase Chemistry Department, Max Planck Institute for Chemistry, Hahn-Meitner-Weg 1, 55128, Mainz, Germany
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
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15
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Berg G, Schweitzer M, Abdelfattah A, Cernava T, Wassermann B. Missing symbionts – emerging pathogens? Microbiome management for sustainable agriculture. Symbiosis 2023. [DOI: 10.1007/s13199-023-00903-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
AbstractPlant diversification and co-evolution shaped the plant microbiome and vice versa. This resulted in a specific composition of the plant microbiome and a strong connection with the host in terms of functional interplay. Symbionts are part of the microbiota, and important for the plant’s germination and growth, nutrition, as well as stress protection. However, human activities in the Anthropocene are linked to a significant shift of diversity, evenness and specificity of the plant microbiota. In addition, and very importantly, many plant symbionts are missing or no longer functional. It will require targeted microbiome management to support and reintroduce them. In future agriculture, we should aim at replacing harmful chemicals in the field, as well as post-harvest, by using precision microbiome engineering. This is because the plant microbiome is connected across systems and crucial for human and planetary health. This commentary aims to inspire holistic studies for the development of solutions for sustainable agriculture in framework of the One Health and the Planetary Health concepts.
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16
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Li JT, Zhang Y, Chen H, Sun H, Tian W, Li J, Liu X, Zhou S, Fang C, Li B, Nie M. Low soil moisture suppresses the thermal compensatory response of microbial respiration. Glob Chang Biol 2023; 29:874-889. [PMID: 36177515 DOI: 10.1111/gcb.16448] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 09/14/2022] [Indexed: 06/16/2023]
Abstract
The thermal compensatory response of microbial respiration contributes to a decrease in warming-induced enhancement of soil respiration over time, which could weaken the positive feedback between the carbon cycle and climate warming. Climate warming is also predicted to cause a worldwide decrease in soil moisture, which has an effect on the microbial metabolism of soil carbon. However, whether and how changes in moisture affect the thermal compensatory response of microbial respiration are unexplored. Here, using soils from an 8-year warming experiment in an alpine grassland, we assayed the thermal response of microbial respiration rates at different soil moisture levels. The results showed that relatively low soil moisture suppressed the thermal compensatory response of microbial respiration, leading to an enhanced response to warming. A subsequent moisture incubation experiment involving off-plot soils also showed that the response of microbial respiration to 100 d warming shifted from a slight compensatory response to an enhanced response with decreasing incubation moisture. Further analysis revealed that such respiration regulation by moisture was associated with shifts in enzymatic activities and carbon use efficiency. Our findings suggest that future drought induced by climate warming might weaken the thermal compensatory capacity of microbial respiration, with important consequences for carbon-climate feedback.
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Affiliation(s)
- Jin-Tao Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Yan Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Hongyang Chen
- Research Centre for Northeast Asia Carbon Sink, Centre for Ecological Research, Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, School of Forestry, Northeast Forestry University, Harbin, China
| | - Huiming Sun
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Weitao Tian
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Jinquan Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Xiang Liu
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
| | - Shurong Zhou
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, China
| | - Changming Fang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Bo Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
- Centre for Invasion Biology, Institute of Biodiversity, Yunnan University, Kunming, China
| | - Ming Nie
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
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17
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Cleveland CC, Reis CRG, Perakis SS, Dynarski KA, Batterman SA, Crews TE, Gei M, Gundale MJ, Menge DNL, Peoples MB, Reed SC, Salmon VG, Soper FM, Taylor BN, Turner MG, Wurzburger N. Exploring the Role of Cryptic Nitrogen Fixers in Terrestrial Ecosystems: A Frontier in Nitrogen Cycling Research. Ecosystems 2022. [DOI: 10.1007/s10021-022-00804-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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18
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Ma XY, Xu H, Cao ZY, Shu L, Zhu RL. Will climate change cause the global peatland to expand or contract? Evidence from the habitat shift pattern of Sphagnum mosses. Glob Chang Biol 2022; 28:6419-6432. [PMID: 35900846 DOI: 10.1111/gcb.16354] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
Peatlands play a crucial role in the global carbon cycle. Sphagnum mosses (peat mosses) are considered to be the peatland ecosystem engineers and contribute to the carbon accumulation in the peatland ecosystems. As cold-adapted species, the dominance of Sphagnum mosses in peatlands will be threatened by climate warming. The response of Sphagnum mosses to climate change is closely related to the future trajectory of carbon fluxes in peatlands. However, the impact of climate change on the habitat suitability of Sphagnum mosses on a global scale is poorly understood. To predict the potential impact of climate change on the global distribution of Sphagnum mosses, we used the MaxEnt model to predict the potential geographic distribution of six Sphagnum species that dominate peatlands in the future (2050 and 2070) under two greenhouse gas emission scenarios (SSP1-2.6 and SSP5-8.5). The results show that the mean temperature of the coldest quarter, precipitation of the driest month, and topsoil calcium carbonate are the main factors affecting the habitat availability of Sphagnum mosses. As the climate warms, Sphagnum mosses tend to migrate northward. The suitable habitat and abundance of Sphagnum mosses increase extensively in the high-latitude boreal peatland (north of 50°N) and decrease on a large scale beyond the high-latitude boreal peatland. The southern edge of boreal peatlands would experience the greatest decline in the suitable habitat and richness of Sphagnum mosses with the temperature rising and would be a risk area for the transition from carbon sink to carbon source. The spatial-temporal pattern changes of Sphagnum mosses simulated in this study provide a reference for the development of management and conservation strategies for Sphagnum bogs.
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Affiliation(s)
- Xiao-Ying Ma
- Bryology Laboratory, School of Life Sciences, East China Normal University, Shanghai, China
| | - Hao Xu
- Bryology Laboratory, School of Life Sciences, East China Normal University, Shanghai, China
| | - Zi-Yin Cao
- Bryology Laboratory, School of Life Sciences, East China Normal University, Shanghai, China
| | - Lei Shu
- Bryology Laboratory, School of Life Sciences, East China Normal University, Shanghai, China
| | - Rui-Liang Zhu
- Bryology Laboratory, School of Life Sciences, East China Normal University, Shanghai, China
- Tiantong National Station of Forest Ecosystem, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, East China Normal University, Shanghai, China
- Technology Innovation Center for Land Spatial Eco-restoration in Metropolitan Area, Ministry of Natural Resources, Shanghai, China
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19
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Man B, Xiang X, Zhang J, Cheng G, Zhang C, Luo Y, Qin Y. Keystone Taxa and Predictive Functional Analysis of Sphagnum palustre Tank Microbiomes in Erxianyan Peatland, Central China. Biology (Basel) 2022; 11:1436. [PMID: 36290340 PMCID: PMC9598613 DOI: 10.3390/biology11101436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/23/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
Sphagnum is a fundamental ecosystem of engineers, including more than 300 species around the world. These species host diverse microbes, either endosymbiotic or ectosymbiotic, and are key to carbon sequestration in peatland ecosystems. However, the linkages between different types of Sphagnum and the diversity and ecological functions of Sphagnum-associated microbiomes are poorly known, and so are their joint responses to ecological functions. Here, we systematically investigated endophytes in Sphagnum palustre via next-generation sequencing (NGS) techniques in the Erxianyan peatland, central China. The total bacterial microbiome was classified into 38 phyla and 55 classes, 122 orders and 490 genera. The top 8 phyla of Proteobacteria (33.69%), Firmicutes (11.94%), Bacteroidetes (9.42%), Actinobacteria (6.53%), Planctomycetes (6.37%), Gemmatimonadetes (3.05%), Acidobacteria (5.59%) and Cyanobacteria (1.71%) occupied 78.31% of total OTUs. The core microbiome of S. palustre was mainly distributed mainly in 7 phyla, 9 classes, 15 orders, 22 families and 43 known genera. There were many differences in core microbiomes compared to those in the common higher plants. We further demonstrate that the abundant functional groups have a substantial potential for nitrogen fixation, carbon cycle, nitrate metabolism, sulfate respiration and chitinolysis. These results indicate that potential ecological function of Sphagnum palustre in peatlands is partially rooted in its microbiomes, and that incorporating into functional groups of Sphagnum-associated microbiomes can promote mechanistic understanding of Sphagnum ecology in subalpine peatlands.
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Affiliation(s)
- Baiying Man
- College of Life Science, Shangrao Normal University, Shangrao 334001, China
| | - Xing Xiang
- College of Life Science, Shangrao Normal University, Shangrao 334001, China
| | - Junzhong Zhang
- Key Laboratory of Forest Disaster Warning and Control in Yunnan Higher Education Institutions, South West Forestry University, Kunming 650224, China
| | - Gang Cheng
- College of Life Science, Shangrao Normal University, Shangrao 334001, China
| | - Chao Zhang
- College of Life Science, Shangrao Normal University, Shangrao 334001, China
| | - Yang Luo
- College of Life Science, Shangrao Normal University, Shangrao 334001, China
| | - Yangmin Qin
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
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20
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Groß-Schmölders M, Klein K, Emsens WJ, van Diggelen R, Aggenbach CJS, Liczner Y, Frouz J, Leifeld J, Alewell C. Stable isotopes (δ 13C, δ 15N) and biomarkers as indicators of the hydrological regime of fens in a European east-west transect. Sci Total Environ 2022; 838:156603. [PMID: 35690201 DOI: 10.1016/j.scitotenv.2022.156603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/30/2022] [Accepted: 06/06/2022] [Indexed: 06/15/2023]
Abstract
Peatland degradation is tightly connected to hydrological changes and microbial metabolism. To better understand these metabolism processes, more information is needed on how microbial communities and substrate cycling are affected by changing hydrological regimes. These activities should be imprinted in stable isotope bulk values (δ 15N, δ 13C) due to specific isotopic fractionation by different microbial communities, their metabolic pathways and nutrient sources. We hypothesize that stable isotope values and microbial abundance are correlated and act as indicators of different hydrological regimes. We sampled an East-West transect across European fens in 14 areas and conducted a stable isotope (δ 13C, δ 15N) and membrane fatty acid (mFA) analysis. Within each area an undrained, drained and rewetted site was selected. Rewetted sites were separated based on when rewetting occurred. We found differences in the upper layers of all sites in microbial-derived mFAs and stable isotope values corresponding to hydrological regimes. The highest and lowest quantities of microbial-derived mFAs were measured in undrained and drained sites, respectively. Fungal-derived mFAs were especially lower in drained sites. Simultaneously, δ15N stable isotope values were highest in drained sites. In addition, stable isotope values and microbial-derived mFAs showed distinct depth trends. In undrained sites stable isotopes values slightly increased with depth. In drained sites, δ15N values decreased downwards, whereas δ13C values increased. Overall microbial-derived mFAs decreased with depth. These patterns presumably result from anoxic conditions and high peat recalcitrance in the deeper layers. In sites with short time of rewetting, the microbial-derived mFAs and stable isotope values were similar to values of drained sites, while with increasing rewetting time values shifted to those of undrained sites. We conclude that biomarkers indicate that stable isotope values reflect specific microbial metabolic processes, which differ with hydrological regimes, and thus could indicate both drainage and rewetting in fens.
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Affiliation(s)
- Miriam Groß-Schmölders
- Environmental Geosciences, University of Basel, Bernoullistrasse 32, CH-4056 Basel, Switzerland; Agroscope, Climate and Agriculture Group, Reckenholzstraße 191, CH-8046 Zürich, Switzerland.
| | - Kristy Klein
- Environmental Geosciences, University of Basel, Bernoullistrasse 32, CH-4056 Basel, Switzerland; Agroscope, Climate and Agriculture Group, Reckenholzstraße 191, CH-8046 Zürich, Switzerland.
| | - Willem-Jan Emsens
- Department of Biology, University of Antwerp, Universiteitsplein 1, BE - 2610 Wilrijk, Belgium.
| | - Rudy van Diggelen
- Department of Biology, University of Antwerp, Universiteitsplein 1, BE - 2610 Wilrijk, Belgium.
| | - Camiel J S Aggenbach
- KWR Water cycle Research Institute, Post Box 1072, NL-3430 BB, Nieuwegein, Netherlands.
| | - Yvonne Liczner
- Department of Biology, University of Antwerp, Universiteitsplein 1, BE - 2610 Wilrijk, Belgium.
| | - Jan Frouz
- Institute for Environmental Studies, Charles University Benátská 2, CZ-128282801, Prague, Czech Republic.
| | - Jens Leifeld
- Environmental Geosciences, University of Basel, Bernoullistrasse 32, CH-4056 Basel, Switzerland; Agroscope, Climate and Agriculture Group, Reckenholzstraße 191, CH-8046 Zürich, Switzerland.
| | - Christine Alewell
- Environmental Geosciences, University of Basel, Bernoullistrasse 32, CH-4056 Basel, Switzerland.
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21
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Renaudin M, Laforest-Lapointe I, Bellenger JP. Unraveling global and diazotrophic bacteriomes of boreal forest floor feather mosses and their environmental drivers at the ecosystem and at the plant scale in North America. Sci Total Environ 2022; 837:155761. [PMID: 35533858 DOI: 10.1016/j.scitotenv.2022.155761] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 04/29/2022] [Accepted: 05/03/2022] [Indexed: 06/14/2023]
Abstract
Feather mosses are abundant cryptogams of the boreal forest floor and shelter a broad diversity of bacteria who have important ecological functions (e.g., decomposition, nutrient cycling). In particular, nitrogen (N2-) fixation performed by feather moss-associated diazotrophs constitutes an important entry of nitrogen in the boreal forest ecosystem. However, the composition of the feather moss bacteriome and its environmental drivers are still unclear. Using cDNA amplicon sequencing of the 16S rRNA and nifH genes and cyanobacterial biomass quantification, we explored the active global and diazotrophic bacterial communities of two dominant feather moss species (i) at the ecosystem scale, along a 500-km climatic and nutrient deposition gradient in the North American boreal forest, and (ii) at the plant scale, along the moss shoot senescence gradient. We found that cyanobacteria were major actors of the feather moss bacteriome, accounting for 33% of global bacterial communities and 65% of diazotrophic communities, and that several cyanobacterial and methanotrophic genera were contributing to N2-fixation. Moreover, we showed that bacteria were occupying ecological niches along the moss shoot, with phototrophs being dominant in the apical part and methanotrophs being dominant in the basal part. Finally, climate (temperature, precipitation), environmental variables (moss species, month, tree density) and nutrients (nitrogen, phosphorus, molybdenum, vanadium, iron) strongly shaped global and diazotrophic bacteriomes. In summary, this work presents evidence that the feather moss bacteriome plays crucial roles in supporting moss growth, health, and decomposition, as well as in the boreal forest carbon and nitrogen cycles. This study also highlights the substantial effects of climate and nutrients on the feather moss bacteriome, suggesting the importance of understanding the impacts of global change on moss-associated bacterial growth and activity.
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Affiliation(s)
- Marie Renaudin
- Centre Sève, Département de Chimie, Université de Sherbrooke, J1K 2R1 Sherbrooke, QC, Canada.
| | | | - Jean-Philippe Bellenger
- Centre Sève, Département de Chimie, Université de Sherbrooke, J1K 2R1 Sherbrooke, QC, Canada.
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22
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Rousk K. Biotic and abiotic controls of nitrogen fixation in cyanobacteria-moss associations. New Phytol 2022; 235:1330-1335. [PMID: 35687087 DOI: 10.1111/nph.18264] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
Most mosses are colonized by nitrogen (N)-fixing cyanobacteria. This discovery is relatively recent, which can explain the large knowledge gaps the field is now tackling. For instance, while we have a good understanding of the abiotic controls (e.g. nutrient availability, increased temperature), we still do not know much about the biotic controls of N2 fixation in mosses. I propose here that we should endeavour to position moss-cyanobacteria associations along the mutualism-parasitism continuum under varying abiotic conditions (e.g. nutrient availability). This would finally unravel the nature of the relationship between the partners and will be a big leap in our understanding of the evolution of plant-bacteria interactions using moss-cyanobacteria associations as a model system.
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Affiliation(s)
- Kathrin Rousk
- Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark
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23
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Chen KH, Nelson J. A scoping review of bryophyte microbiota: diverse microbial communities in small plant packages. J Exp Bot 2022; 73:4496-4513. [PMID: 35536989 DOI: 10.1093/jxb/erac191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 05/05/2022] [Indexed: 06/14/2023]
Abstract
Plant health depends not only on the condition of the plant itself but also on its diverse community of microbes, or microbiota. Just like the better-studied angiosperms, bryophytes (mosses, liverworts, and hornworts) harbor diverse communities of bacteria, archaea, fungi, and other microbial eukaryotes. Bryophytes are increasingly recognized as important model systems for understanding plant evolution, development, physiology, and symbiotic interactions. Much of the work on bryophyte microbiota in the past focused on specific symbiont types for each bryophyte group, but more recent studies are taking a broader view acknowledging the coexistence of diverse microbial communities in bryophytes. Therefore, this review integrates studies of bryophyte microbes from both perspectives to provide a holistic view of the existing research for each bryophyte group and on key themes. The systematic search also reveals the taxonomic and geographic biases in this field, including a severe under-representation of the tropics, very few studies on viruses or eukaryotic microbes beyond fungi, and a focus on mycorrhizal fungi studies in liverworts. Such gaps may have led to errors in conclusions about evolutionary patterns in symbiosis. This analysis points to a wealth of future research directions that promise to reveal how the distinct life cycles and physiology of bryophytes interact with their microbiota.
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Affiliation(s)
- Ko-Hsuan Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Jessica Nelson
- Maastricht Science Programme, Maastricht University, Maastricht, The Netherlands
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24
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Alvarenga DO, Rousk K. Unraveling host-microbe interactions and ecosystem functions in moss-bacteria symbioses. J Exp Bot 2022; 73:4473-4486. [PMID: 35728619 DOI: 10.1093/jxb/erac091] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
Abstract
Mosses are non-vascular plants usually found in moist and shaded areas, with great ecological importance in several ecosystems. This is especially true in northern latitudes, where mosses are responsible for up to 100% of primary production in some ecosystems. Mosses establish symbiotic associations with unique bacteria that play key roles in the carbon and nitrogen cycles. For instance, in boreal environments, more than 35% of the nitrogen fixed by diazotrophic symbionts in peatlands is transferred to mosses, directly affecting carbon fixation by the hosts, while moss-associated methanotrophic bacteria contribute 10-30% of moss carbon. Further, half of ecosystem N input may derive from moss-cyanobacteria associations in pristine ecosystems. Moss-bacteria interactions have consequences on a global scale since northern environments sequester 20% of all the carbon generated by forests in the world and stock at least 32% of global terrestrial carbon. Different moss hosts influence bacteria in distinct ways, which suggests that threats to mosses also threaten unique microbial communities with important ecological and biogeochemical consequences. Since their origin ~500 Ma, mosses have interacted with bacteria, making these associations ideal models for understanding the evolution of plant-microbe associations and their contribution to biogeochemical cycles.
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Affiliation(s)
- Danillo O Alvarenga
- Department of Biology, Terrestrial Ecology Section, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark
- Centre for Permafrost, University of Copenhagen, Øster Voldgade 10, DK-1350, Copenhagen, Denmark
| | - Kathrin Rousk
- Department of Biology, Terrestrial Ecology Section, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark
- Centre for Permafrost, University of Copenhagen, Øster Voldgade 10, DK-1350, Copenhagen, Denmark
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25
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Bao T, Jia G, Xu X. Warming enhances dominance of vascular plants over cryptogams across northern wetlands. Glob Chang Biol 2022; 28:4097-4109. [PMID: 35364612 DOI: 10.1111/gcb.16182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 01/13/2022] [Accepted: 03/26/2022] [Indexed: 06/14/2023]
Abstract
Climate warming causes profound effects on structure and function of wetland ecosystem, thus affecting regional and global hydrological cycles and carbon budgets. However, how wetland plants respond to warming is still poorly understood. Here, we synthesized observations from 273 independent sites to explore responses of northern wetland plants to warming. Our results show that warming enhances biomass accumulation for vascular plants including shrubs and graminoids, whereas it reduces biomass accumulation for cryptogams including moss and lichen. This divergent response of vascular plants and cryptogams is particularly pronounced in the high latitudes where permafrost prevails. As warming continues, this divergent response is amplified, however, the reduction in cryptogams is more drastic. Warming leads to declined surface soil moisture and lowered water table, thereby shifting wetlands from a wet system dominated by cryptogams to a drier system with increased cover of vascular plants. Under a high-emission scenario of Shared Socioeconomic Pathways (SSP5), a 4.7-5.1°C mean global temperature rise will cause more than fivefold loss of cryptogams compared with current climate. As cryptogams are largely concentrated at northern high latitudes, where warming will likely be greater than the projected global mean, modification in wetland plant composition and major reduction in cryptogams are expected to occur even much earlier than 2100.
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Affiliation(s)
- Tao Bao
- Key Laboratory of Regional Climate-Environment for Temperate East Asia, Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing, China
| | - Gensuo Jia
- Key Laboratory of Regional Climate-Environment for Temperate East Asia, Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing, China
| | - Xiyan Xu
- Key Laboratory of Regional Climate-Environment for Temperate East Asia, Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing, China
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26
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Carrell AA, Lawrence TJ, Cabugao KGM, Carper DL, Pelletier DA, Lee JH, Jawdy SS, Grimwood J, Schmutz J, Hanson PJ, Shaw AJ, Weston DJ. Habitat-adapted microbial communities mediate Sphagnum peatmoss resilience to warming. New Phytol 2022; 234:2111-2125. [PMID: 35266150 PMCID: PMC9310625 DOI: 10.1111/nph.18072] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 02/21/2022] [Indexed: 05/19/2023]
Abstract
Sphagnum peatmosses are fundamental members of peatland ecosystems, where they contribute to the uptake and long-term storage of atmospheric carbon. Warming threatens Sphagnum mosses and is known to alter the composition of their associated microbiome. Here, we use a microbiome transfer approach to test if microbiome thermal origin influences host plant thermotolerance. We leveraged an experimental whole-ecosystem warming study to collect field-grown Sphagnum, mechanically separate the associated microbiome and then transfer onto germ-free laboratory Sphagnum for temperature experiments. Host and microbiome dynamics were assessed with growth analysis, Chla fluorescence imaging, metagenomics, metatranscriptomics and 16S rDNA profiling. Microbiomes originating from warming field conditions imparted enhanced thermotolerance and growth recovery at elevated temperatures. Metagenome and metatranscriptome analyses revealed that warming altered microbial community structure in a manner that induced the plant heat shock response, especially the HSP70 family and jasmonic acid production. The heat shock response was induced even without warming treatment in the laboratory, suggesting that the warm-microbiome isolated from the field provided the host plant with thermal preconditioning. Our results demonstrate that microbes, which respond rapidly to temperature alterations, can play key roles in host plant growth response to rapidly changing environments.
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Affiliation(s)
- Alyssa A. Carrell
- Biosciences DivisionOak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37831USA
| | - Travis J. Lawrence
- Biosciences DivisionOak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37831USA
| | - Kristine Grace M. Cabugao
- Bredesen Center for Interdisciplinary Research and Graduate EducationUniversity of Tennessee1502 Cumberland Ave.KnoxvilleTN37996USA
| | - Dana L. Carper
- Biosciences DivisionOak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37831USA
| | - Dale A. Pelletier
- Biosciences DivisionOak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37831USA
| | - Jun Hyung Lee
- Biosciences DivisionOak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37831USA
| | - Sara S. Jawdy
- Biosciences DivisionOak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37831USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology601 Genome WayHuntsvilleAL35806USA
- Department of Energy Joint Genome InstituteLawrence Berkeley National Lab1 Cyclotron Rd.BerkeleyCA94720USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology601 Genome WayHuntsvilleAL35806USA
- Department of Energy Joint Genome InstituteLawrence Berkeley National Lab1 Cyclotron Rd.BerkeleyCA94720USA
| | - Paul J. Hanson
- Environmental Sciences DivisionOak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37831USA
| | | | - David J. Weston
- Biosciences DivisionOak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37831USA
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27
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Debray R, Socolar Y, Kaulbach G, Guzman A, Hernandez CA, Curley R, Dhond A, Bowles T, Koskella B. Water stress and disruption of mycorrhizas induce parallel shifts in phyllosphere microbiome composition. New Phytol 2022; 234:2018-2031. [PMID: 34668201 DOI: 10.1111/nph.17817] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 10/06/2021] [Indexed: 06/13/2023]
Abstract
Water and nutrient acquisition are key drivers of plant health and ecosystem function. These factors impact plant physiology directly as well as indirectly through soil- and root-associated microbial responses, but how they in turn affect aboveground plant-microbe interactions are not known. Through experimental manipulations in the field and growth chamber, we examine the interacting effects of water stress, soil fertility, and arbuscular mycorrhizal fungi on bacterial and fungal communities of the tomato (Solanum lycopersicum) phyllosphere. Both water stress and mycorrhizal disruption reduced leaf bacterial richness, homogenized bacterial community composition among plants, and reduced the relative abundance of dominant fungal taxa. We observed striking parallelism in the individual microbial taxa in the phyllosphere affected by irrigation and mycorrhizal associations. Our results show that soil conditions and belowground interactions can shape aboveground microbial communities, with important potential implications for plant health and sustainable agriculture.
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Affiliation(s)
- Reena Debray
- Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Yvonne Socolar
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, 94720, USA
| | - Griffin Kaulbach
- Department of Environmental Studies, Haverford College, Haverford, PA, 19041, USA
| | - Aidee Guzman
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, 94720, USA
| | - Catherine A Hernandez
- Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Rose Curley
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, 94720, USA
| | - Alexander Dhond
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, 94720, USA
| | - Timothy Bowles
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, 94720, USA
| | - Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
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28
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Klarenberg IJ, Keuschnig C, Russi Colmenares AJ, Warshan D, Jungblut AD, Jónsdóttir IS, Vilhelmsson O. Long-term warming effects on the microbiome and nifH gene abundance of a common moss species in sub-Arctic tundra. New Phytol 2022; 234:2044-2056. [PMID: 34719786 DOI: 10.1111/nph.17837] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 10/17/2021] [Indexed: 06/13/2023]
Abstract
Bacterial communities form the basis of biogeochemical processes and determine plant growth and health. Mosses harbour diverse bacterial communities that are involved in nitrogen fixation and carbon cycling. Global climate change is causing changes in aboveground plant biomass and shifting species composition in the Arctic, but little is known about the response of moss microbiomes in these environments. Here, we studied the total and potentially active bacterial communities associated with Racomitrium lanuginosum in response to a 20-yr in situ warming in an Icelandic heathland. We evaluated the effect of warming and warming-induced shrub expansion on the moss bacterial community composition and diversity, and nifH gene abundance. Warming changed both the total and the potentially active bacterial community structure, while litter abundance only affected the total bacterial community structure. The abundance of nifH genes was negatively affected by litter abundance. We also found shifts in the potentially nitrogen-fixing community, with Nostoc decreasing and noncyanobacterial diazotrophs increasing in relative abundance. Our data suggest that the moss microbial community and potentially nitrogen fixing taxa will be sensitive to future warming, partly via changes in litter and shrub abundance.
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Affiliation(s)
- Ingeborg J Klarenberg
- Natural Resource Sciences, University of Akureyri, Borgir i Nordurslod, Akureyri, 600, Iceland
- Faculty of Life and Environmental Sciences, University of Iceland, Sturlugata 7, 102, Reykjavík, Iceland
| | - Christoph Keuschnig
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Avenue Guy de Collongue 36, Écully, 69134, France
| | - Ana J Russi Colmenares
- Faculty of Life and Environmental Sciences, University of Iceland, Sturlugata 7, 102, Reykjavík, Iceland
| | - Denis Warshan
- Faculty of Life and Environmental Sciences, University of Iceland, Sturlugata 7, 102, Reykjavík, Iceland
| | - Anne D Jungblut
- Life Sciences Department, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Ingibjörg S Jónsdóttir
- Faculty of Life and Environmental Sciences, University of Iceland, Sturlugata 7, 102, Reykjavík, Iceland
| | - Oddur Vilhelmsson
- Natural Resource Sciences, University of Akureyri, Borgir i Nordurslod, Akureyri, 600, Iceland
- BioMedical Center, University of Iceland, Vatnsmýrarvegur 16, 101, Reykjavík, Iceland
- School of Biological Sciences, University of Reading, Whiteknights, Reading, RG6 6AJ, UK
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29
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Le TB, Wu J, Gong Y. Vascular plants regulate responses of boreal peatland Sphagnum to climate warming and nitrogen addition. Sci Total Environ 2022; 819:152077. [PMID: 34856288 DOI: 10.1016/j.scitotenv.2021.152077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 06/13/2023]
Abstract
Boreal peatland Sphagnum may be affected by climate warming and elevated nitrogen availability directly and indirectly via altering vascular plant interaction. Here, we used a field experiment of nitrogen addition, warming, and vascular plant removal to investigate the effects of these factors on Sphagnum in a Canadian blanket boreal peatland. We revealed that significant effects of warming and nitrogen addition on Sphagnum were regulated by vascular plant interaction. The intense competition of vascular plants accelerated an adverse effect of warming on Sphagnum, while facilitation of vascular plants reduced detrimental losses of the Sphagnum due to high dose of nitrogen addition and both warming and the nitrogen addition. These findings indicate the crucial role of vascular plants in regulating the effects of environmental changes on existing Sphagnum in boreal peatlands.
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Affiliation(s)
- Thuong Ba Le
- Environment and Sustainability, School of Science and the Environment, Memorial University of Newfoundland, Corner Brook, NL A2H 5G4, Canada; Graduate Program in Environmental Science, Memorial University of Newfoundland, St. John's, NL, Canada; Vietnam National University of Forestry, Hanoi, Viet Nam
| | - Jianghua Wu
- Environment and Sustainability, School of Science and the Environment, Memorial University of Newfoundland, Corner Brook, NL A2H 5G4, Canada; Graduate Program in Environmental Science, Memorial University of Newfoundland, St. John's, NL, Canada.
| | - Yu Gong
- Environment and Sustainability, School of Science and the Environment, Memorial University of Newfoundland, Corner Brook, NL A2H 5G4, Canada; Graduate Program in Environmental Science, Memorial University of Newfoundland, St. John's, NL, Canada
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30
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Carrell AA, Veličković D, Lawrence TJ, Bowen BP, Louie KB, Carper DL, Chu RK, Mitchell HD, Orr G, Markillie LM, Jawdy SS, Grimwood J, Shaw AJ, Schmutz J, Northen TR, Anderton CR, Pelletier DA, Weston DJ. Novel metabolic interactions and environmental conditions mediate the boreal peatmoss-cyanobacteria mutualism. ISME J 2022; 16:1074-85. [PMID: 34845335 DOI: 10.1038/s41396-021-01136-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 09/24/2021] [Accepted: 10/01/2021] [Indexed: 11/18/2022]
Abstract
Interactions between Sphagnum (peat moss) and cyanobacteria play critical roles in terrestrial carbon and nitrogen cycling processes. Knowledge of the metabolites exchanged, the physiological processes involved, and the environmental conditions allowing the formation of symbiosis is important for a better understanding of the mechanisms underlying these interactions. In this study, we used a cross-feeding approach with spatially resolved metabolite profiling and metatranscriptomics to characterize the symbiosis between Sphagnum and Nostoc cyanobacteria. A pH gradient study revealed that the Sphagnum–Nostoc symbiosis was driven by pH, with mutualism occurring only at low pH. Metabolic cross-feeding studies along with spatially resolved matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) identified trehalose as the main carbohydrate source released by Sphagnum, which were depleted by Nostoc along with sulfur-containing choline-O-sulfate, taurine and sulfoacetate. In exchange, Nostoc increased exudation of purines and amino acids. Metatranscriptome analysis indicated that Sphagnum host defense was downregulated when in direct contact with the Nostoc symbiont, but not as a result of chemical contact alone. The observations in this study elucidated environmental, metabolic, and physiological underpinnings of the widespread plant–cyanobacterial symbioses with important implications for predicting carbon and nitrogen cycling in peatland ecosystems as well as the basis of general host-microbe interactions.
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31
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Berg G, Cernava T. The plant microbiota signature of the Anthropocene as a challenge for microbiome research. Microbiome 2022; 10:54. [PMID: 35346369 PMCID: PMC8959079 DOI: 10.1186/s40168-021-01224-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 12/23/2021] [Indexed: 05/21/2023]
Abstract
BACKGROUND One promise of the recently presented microbiome definition suggested that, in combination with unifying concepts and standards, microbiome research could be important for solving new challenges associated with anthropogenic-driven changes in various microbiota. With this commentary we want to further elaborate this suggestion, because we noticed specific signatures in microbiota affected by the Anthropocene. RESULTS Here, we discuss this based on a review of available literature and our own research targeting exemplarily the plant microbiome. It is not only crucial for plants themselves but also linked to planetary health. We suggest that different human activities are commonly linked to a shift of diversity and evenness of the plant microbiota, which is also characterized by a decrease of host specificity, and an increase of r-strategic microbes, pathogens, and hypermutators. The resistome, anchored in the microbiome, follows this shift by an increase of specific antimicrobial resistance (AMR) mechanisms as well as an increase of plasmid-associated resistance genes. This typical microbiome signature of the Anthropocene is often associated with dysbiosis and loss of resilience, and leads to frequent pathogen outbreaks. Although several of these observations are already confirmed by meta-studies, this issue requires more attention in upcoming microbiome studies. CONCLUSIONS Our commentary aims to inspire holistic studies for the development of solutions to restore and save microbial diversity for ecosystem functioning as well as the closely connected planetary health. Video abstract.
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Affiliation(s)
- Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010, Graz, Austria.
- Leibniz-Institute for Agricultural Engineering Potsdam, Max-Eyth-Allee 100, 14469, Potsdam, Germany.
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24/25, 14476, Potsdam, Germany.
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010, Graz, Austria
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Rawat VS, Kaur J, Bhagwat S, Pandit MA, Rawat CD. Deploying Microbes as Drivers and Indicators in Ecological Restoration. Restor Ecol 2022. [DOI: 10.1111/rec.13688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Jasleen Kaur
- Department of Botany, Dyal Singh College University of Delhi New Delhi 110003 India
| | - Sakshi Bhagwat
- Department of Biosciences Faculty of Natural Sciences, Jamia Millia Islamia New Delhi 110025 India
| | - Manisha Arora Pandit
- Department of Zoology, Kalindi College University of Delhi New Delhi 110008 India
| | - Charu Dogra Rawat
- Molecular Biology and Genomics Research Laboratory, Ramjas College University of Delhi Delhi 110007 India
- Department of Zoology, Ramjas College University of Delhi Delhi 110007 India
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Kolton M, Weston DJ, Mayali X, Weber PK, Mcfarlane KJ, Pett-ridge J, Somoza MM, Lietard J, Glass JB, Lilleskov EA, Shaw AJ, Tringe S, Hanson PJ, Kostka JE, Martiny JBH. Defining the Sphagnum Core Microbiome across the North American Continent Reveals a Central Role for Diazotrophic Methanotrophs in the Nitrogen and Carbon Cycles of Boreal Peatland Ecosystems. mBio 2022; 13:e03714-21. [DOI: 10.1128/mbio.03714-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Peat mosses of the genus Sphagnum are ecosystem engineers that frequently predominate over photosynthetic production in boreal peatlands. Sphagnum spp. host diverse microbial communities capable of nitrogen fixation (diazotrophy) and methane oxidation (methanotrophy), thereby potentially supporting plant growth under severely nutrient-limited conditions. Moreover, diazotrophic methanotrophs represent a possible “missing link” between the carbon and nitrogen cycles, but the functional contributions of the Sphagnum-associated microbiome remain in question. A combination of metagenomics, metatranscriptomics, and dual-isotope incorporation assays was applied to investigate Sphagnum microbiome community composition across the North American continent and provide empirical evidence for diazotrophic methanotrophy in Sphagnum-dominated ecosystems. Remarkably consistent prokaryotic communities were detected in over 250 Sphagnum SSU rRNA libraries from peatlands across the United States (5 states, 17 bog/fen sites, 18 Sphagnum species), with 12 genera of the core microbiome comprising 60% of the relative microbial abundance. Additionally, nitrogenase (nifH) and SSU rRNA gene amplicon analysis revealed that nitrogen-fixing populations made up nearly 15% of the prokaryotic communities, predominated by Nostocales cyanobacteria and Rhizobiales methanotrophs. While cyanobacteria comprised the vast majority (>95%) of diazotrophs detected in amplicon and metagenome analyses, obligate methanotrophs of the genus Methyloferula (order Rhizobiales) accounted for one-quarter of transcribed nifH genes. Furthermore, in dual-isotope tracer experiments, members of the Rhizobiales showed substantial incorporation of 13CH4 and 15N2 isotopes into their rRNA. Our study characterizes the core Sphagnum microbiome across large spatial scales and indicates that diazotrophic methanotrophs, here defined as obligate methanotrophs of the rare biosphere (Methyloferula spp. of the Rhizobiales) that also carry out diazotrophy, play a keystone role in coupling of the carbon and nitrogen cycles in nutrient-poor peatlands.
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Pan J, Liu Y, Yang Y, Cheng Z, Lan X, Hu W, Shi G, Zhang Q, Feng H. Slope aspect determines the abundance and composition of nitrogen-cycling microbial communities in an alpine ecosystem. Environ Microbiol 2022; 24:3598-3611. [PMID: 35048487 DOI: 10.1111/1462-2920.15900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 01/11/2022] [Indexed: 11/28/2022]
Abstract
Slope aspect is an important topographic feature that can influence local environmental conditions. While strong effects of slope aspect on aboveground and belowground communities have been frequently elucidated, how slope aspect affects soil nitrogen (N) cycling microbes remains unclear. Here, we characterized the communities of soil N-cycling microbes on south- and north-facing slopes in an alpine ecosystem, by quantifying (qPCR) and high-throughput sequencing six genes involved in N-fixation (nifH), nitrification (archaeal and bacterial amoA) and denitrification (nirK, nirS and nosZ). We found that the abundance, diversity and community composition of major N-cycling microbes differed dramatically between the two slope aspects, and these variances could be well explained by the aspect-driven differences in environmental conditions, especially soil temperature and moisture. The response patterns of different N-cycling groups to slope aspect were much inconsistent, especially for those with similar functions (i.e. ammonia-oxidizing archaea vs. bacteria, nirK- vs. nirS-reducers), indicating strong niche differentiation between these counterparts. We also observed strong preferences and distinct co-occurrence patterns of N-cycling microbial taxa for the two slope aspects. These findings highlight the importance of slope aspect in determining the abundance, species distribution and community structure of N-cycling microbes, and consequently influencing N-cycling processes and ecosystem functioning. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Jianbin Pan
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Yongjun Liu
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.,Center for Grassland Microbiome, Lanzhou University, Lanzhou, 730000, China.,State Key Laboratory of Grassland Agro-ecosystems, Lanzhou University, Lanzhou, 730000, China
| | - Yue Yang
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Zhongxia Cheng
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Xiaomei Lan
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Weigang Hu
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Guoxi Shi
- College of Bioengineering and Biotechnology, Tianshui Normal University, Tianshui, 741000, China
| | - Qi Zhang
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Huyuan Feng
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.,Center for Grassland Microbiome, Lanzhou University, Lanzhou, 730000, China
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ter Horst AM, Santos-Medellín C, Sorensen JW, Zinke LA, Wilson RM, Johnston ER, Trubl G, Pett-Ridge J, Blazewicz SJ, Hanson PJ, Chanton JP, Schadt CW, Kostka JE, Emerson JB. Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations. Microbiome 2021; 9:233. [PMID: 34836550 PMCID: PMC8626947 DOI: 10.1186/s40168-021-01156-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 09/02/2021] [Indexed: 05/31/2023]
Abstract
BACKGROUND Peatlands are expected to experience sustained yet fluctuating higher temperatures due to climate change, leading to increased microbial activity and greenhouse gas emissions. Despite mounting evidence for viral contributions to these processes in peatlands underlain with permafrost, little is known about viruses in other peatlands. More generally, soil viral biogeography and its potential drivers are poorly understood at both local and global scales. Here, 87 metagenomes and five viral size-fraction metagenomes (viromes) from a boreal peatland in northern Minnesota (the SPRUCE whole-ecosystem warming experiment and surrounding bog) were analyzed for dsDNA viral community ecological patterns, and the recovered viral populations (vOTUs) were compared with our curated PIGEON database of 266,125 vOTUs from diverse ecosystems. RESULTS Within the SPRUCE experiment, viral community composition was significantly correlated with peat depth, water content, and carbon chemistry, including CH4 and CO2 concentrations, but not with temperature during the first 2 years of warming treatments. Peat vOTUs with aquatic-like signatures (shared predicted protein content with marine and/or freshwater vOTUs) were significantly enriched in more waterlogged surface peat depths. Predicted host ranges for SPRUCE vOTUs were relatively narrow, generally within a single bacterial genus. Of the 4326 SPRUCE vOTUs, 164 were previously detected in other soils, mostly peatlands. None of the previously identified 202,371 marine and freshwater vOTUs in our PIGEON database were detected in SPRUCE peat, but 0.4% of 80,714 viral clusters (VCs, grouped by predicted protein content) were shared between soil and aquatic environments. On a per-sample basis, vOTU recovery was 32 times higher from viromes compared with total metagenomes. CONCLUSIONS Results suggest strong viral "species" boundaries between terrestrial and aquatic ecosystems and to some extent between peat and other soils, with differences less pronounced at higher taxonomic levels. The significant enrichment of aquatic-like vOTUs in more waterlogged peat suggests that viruses may also exhibit niche partitioning on more local scales. These patterns are presumably driven in part by host ecology, consistent with the predicted narrow host ranges. Although more samples and increased sequencing depth improved vOTU recovery from total metagenomes, the substantially higher per-sample vOTU recovery after viral particle enrichment highlights the utility of soil viromics. Video abstract The importance of Minnesota peat viromes in revealing terrestrial and aquatic niche partitioning for viral populations.
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Affiliation(s)
| | | | - Jackson W. Sorensen
- Department of Plant Pathology, University of California, Davis, Davis, CA USA
| | - Laura A. Zinke
- Department of Plant Pathology, University of California, Davis, Davis, CA USA
| | - Rachel M. Wilson
- Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, FL USA
| | - Eric R. Johnston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Steven J. Blazewicz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Paul J. Hanson
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Jeffrey P. Chanton
- Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, FL USA
| | | | - Joel E. Kostka
- Schools of Biology and Earth & Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30332 USA
| | - Joanne B. Emerson
- Department of Plant Pathology, University of California, Davis, Davis, CA USA
- Genome Center, University of California, Davis, Davis, CA USA
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Hupperts SF, Gerber S, Nilsson MC, Gundale MJ. Empirical and Earth system model estimates of boreal nitrogen fixation often differ: A pathway toward reconciliation. Glob Chang Biol 2021; 27:5711-5725. [PMID: 34382301 DOI: 10.1111/gcb.15836] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 08/06/2021] [Indexed: 06/13/2023]
Abstract
The impacts of global environmental change on productivity in northern latitudes will be contingent on nitrogen (N) availability. In circumpolar boreal ecosystems, nonvascular plants (i.e., bryophytes) and associated N2 -fixing diazotrophs provide one of the largest known N inputs but are rarely accounted for in Earth system models. Instead, most models link N2 -fixation with the functioning of vascular plants. Neglecting nonvascular N2 -fixation may be contributing toward high uncertainty that currently hinders model predictions in northern latitudes, where nonvascular N2 -fixing plants are more common. Adequately accounting for nonvascular N2 -fixation and its drivers could subsequently improve predictions of future N availability and ultimately, productivity, in northern latitudes. Here, we review empirical evidence of boreal nonvascular N2 -fixation responses to global change factors (elevated CO2 , N deposition, warming, precipitation, and shading by vascular plants), and compare empirical findings with model predictions of N2 -fixation using nine Earth system models. The majority of empirical studies found positive effects of CO2 , warming, precipitation, or light on nonvascular N2 -fixation, but N deposition strongly downregulated N2 -fixation in most empirical studies. Furthermore, we found that the responses of N2 -fixation to elevated CO2 were generally consistent between models and very limited empirical data. In contrast, empirical-model comparisons suggest that all models we assessed, and particularly those that scale N2 -fixation with net primary productivity or evapotranspiration, may be overestimating N2 -fixation under increasing N deposition. Overestimations could generate erroneous predictions of future N stocks in boreal ecosystems unless models adequately account for the drivers of nonvascular N2 -fixation. Based on our comparisons, we recommend that models explicitly treat nonvascular N2 -fixation and that field studies include more targeted measurements to improve model structures and parameterization.
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Affiliation(s)
- Stefan F Hupperts
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Stefan Gerber
- Soil and Water Sciences Department, University of Florida, Gainesville, FL, USA
| | - Marie-Charlotte Nilsson
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Michael J Gundale
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Umeå, Sweden
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Wicaksono WA, Cernava T, Berg C, Berg G. Bog ecosystems as a playground for plant-microbe coevolution: bryophytes and vascular plants harbour functionally adapted bacteria. Microbiome 2021; 9:170. [PMID: 34380552 PMCID: PMC8359052 DOI: 10.1186/s40168-021-01117-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 06/21/2021] [Indexed: 05/05/2023]
Abstract
BACKGROUND Bogs are unique ecosystems inhabited by distinctive, coevolved assemblages of organisms, which play a global role for carbon storage, climate stability, water quality and biodiversity. To understand ecology and plant-microbe co-occurrence in bogs, we selected 12 representative species of bryophytes and vascular plants and subjected them to a shotgun metagenomic sequencing approach. We explored specific plant-microbe associations as well as functional implications of the respective communities on their host plants and the bog ecosystem. RESULTS Microbial communities were shown to be functionally adapted to their plant hosts; a higher colonization specificity was found for vascular plants. Bryophytes that commonly constitute the predominant Sphagnum layer in bogs were characterized by a higher bacterial richness and diversity. Each plant group showed an enrichment of distinct phylogenetic and functional bacterial lineages. Detailed analyses of the metabolic potential of 28 metagenome-assembled genomes (MAGs) supported the observed functional specification of prevalent bacteria. We found that novel lineages of Betaproteobacteria and Actinobacteria in the bog environment harboured genes required for carbon fixation via RuBisCo. Interestingly, several of the highly abundant bacteria in both plant types harboured pathogenicity potential and carried similar virulence factors as found with corresponding human pathogens. CONCLUSIONS The unexpectedly high specificity of the plant microbiota reflects intimate plant-microbe interactions and coevolution in bog environments. We assume that the detected pathogenicity factors might be involved in coevolution processes, but the finding also reinforces the role of the natural plant microbiota as a potential reservoir for human pathogens. Overall, the study demonstrates how plant-microbe assemblages can ensure stability, functioning and ecosystem health in bogs. It also highlights the role of bog ecosystems as a playground for plant-microbe coevolution. Video abstract.
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Affiliation(s)
- Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Christian Berg
- Institute of Plant Sciences, University of Graz, Graz, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
- Institute for Biochemistry and Biology, University of Postdam, Postdam, Germany
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Stuart JEM, Holland-Moritz H, Jean M, Miller SN, Ponciano JM, McDaniel SF, Mack MC. The relationship of C and N stable isotopes to high-latitude moss-associated N 2 fixation. Oecologia 2021. [PMID: 34319437 DOI: 10.1007/s00442-021-05005-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 07/23/2021] [Indexed: 10/20/2022]
Abstract
Moss-associated N2 fixation by epiphytic microbes is a key biogeochemical process in nutrient-limited high-latitude ecosystems. Abiotic drivers, such as temperature and moisture, and the identity of host mosses are critical sources of variation in N2 fixation rates. An understanding of the potential interaction between these factors is essential for predicting N inputs as moss communities change with the climate. To further understand the drivers and results of N2 fixation rate variation, we obtained natural abundance values of C and N isotopes and an associated rate of N2 fixation with 15N2 gas incubations in 34 moss species collected in three regions across Alaska, USA. We hypothesized that δ15N values would increase toward 0‰ with higher N2 fixation to reflect the increasing contribution of fixed N2 in moss biomass. Second, we hypothesized that δ13C and N2 fixation would be positively related, as enriched δ13C signatures reflect abiotic conditions favorable to N2 fixation. We expected that the magnitude of these relationships would vary among types of host mosses, reflecting differences in anatomy and habitat. We found little support for our first hypothesis, with only a modest positive relationship between N2 fixation rates and δ15N in a structural equation model. We found a significant positive relationship between δ13C and N2 fixation only in Hypnales, where the probability of N2 fixation activity reached 95% when δ13C values exceeded - 30.4‰. We conclude that moisture and temperature interact strongly with host moss identity in determining the extent to which abiotic conditions impact associated N2 fixation rates.
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Tian L, Yan Z, Wang C, Xu S, Jiang H. Habitat heterogeneity induces regional differences in sediment nitrogen fixation in eutrophic freshwater lake. Sci Total Environ 2021; 772:145594. [PMID: 33770866 DOI: 10.1016/j.scitotenv.2021.145594] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/25/2021] [Accepted: 01/29/2021] [Indexed: 06/12/2023]
Abstract
Biological nitrogen fixation (BNF) in sediments is an important source of bioavailable nitrogen in aquatic systems. However, the effect of habitat change caused by eutrophication on nitrogen fixation within sediments is still unclear. In this study, nitrogen fixation rates and diazotroph diversities in sediments with heterogeneous ecological status in one eutrophic lake were investigated by using an isotope tracer method and sequencing of nitrogen-fixing (nif) genes. The results showed that both nitrogenase activity (NA) and nifH abundance in sediments of blooms area were higher than those in vegetation-dominated habitats. Correlation analysis showed that NA was correlated closely to nifH abundance, dissolved sulfide, and iron. The diazotrophic assemblage contained mainly Proteobacterial sequences belonging to Cluster I and III, and the variations of diazotrophic community could be explained by total nitrogen content, total phosphorus content, organic matters, sulfides, ammonium and iron content. Moreover, the co-occurrence network analysis showed the Alphaproteobacteria shaped the major interactions in diazotrophic community, and sediment properties had stronger effect on diazotrophic community in cyanobacteria-dominated habitat. This study revealed that habitat heterogeneity in eutrophic lakes shaped different succession of BNF in sediments and cyanobacterial blooms significantly improved the nitrogen-fixing activity in sediments, which broadened our understanding of nitrogen cycle and nutrient management in eutrophic freshwater lakes.
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Affiliation(s)
- Linqi Tian
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zaisheng Yan
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Changhui Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Shengqi Xu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Helong Jiang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China.
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Holland-Moritz H, Stuart JEM, Lewis LR, Miller SN, Mack MC, Ponciano JM, McDaniel SF, Fierer N. The bacterial communities of Alaskan mosses and their contributions to N 2-fixation. Microbiome 2021; 9:53. [PMID: 33622403 PMCID: PMC7903681 DOI: 10.1186/s40168-021-01001-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 01/08/2021] [Indexed: 05/14/2023]
Abstract
BACKGROUND Mosses in high-latitude ecosystems harbor diverse bacterial taxa, including N2-fixers which are key contributors to nitrogen dynamics in these systems. Yet the relative importance of moss host species, and environmental factors, in structuring these microbial communities and their N2-fixing potential remains unclear. We studied 26 boreal and tundra moss species across 24 sites in Alaska, USA, from 61 to 69° N. We used cultivation-independent approaches to characterize the variation in moss-associated bacterial communities as a function of host species identity and site characteristics. We also measured N2-fixation rates via 15N2 isotopic enrichment and identified potential N2-fixing bacteria using available literature and genomic information. RESULTS Host species identity and host evolutionary history were both highly predictive of moss microbiome composition, highlighting strong phylogenetic coherence in these microbial communities. Although less important, light availability and temperature also influenced composition of the moss microbiome. Finally, we identified putative N2-fixing bacteria specific to some moss hosts, including potential N2-fixing bacteria outside well-studied cyanobacterial clades. CONCLUSIONS The strong effect of host identity on moss-associated bacterial communities demonstrates mosses' utility for understanding plant-microbe interactions in non-leguminous systems. Our work also highlights the likely importance of novel bacterial taxa to N2-fixation in high-latitude ecosystems. Video Abstract.
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Affiliation(s)
- Hannah Holland-Moritz
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO USA
| | - Julia E. M. Stuart
- Center for Ecosystem Science and Society and the Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ USA
| | - Lily R. Lewis
- Provost’s Office, University of Florida, Gainesville, FL USA
| | - Samantha N. Miller
- Center for Ecosystem Science and Society and the Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ USA
| | - Michelle C. Mack
- Center for Ecosystem Science and Society and the Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ USA
| | | | | | - Noah Fierer
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO USA
- Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder, Boulder, CO USA
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Moler ERV, Page G, Flores-Rentería L, Garms CG, Hull JB, Cooper HF, Swenson J, Perks S, Waring KM, Whipple AV. A method for experimental warming of developing tree seeds with a common garden demonstration of seedling responses. Plant Methods 2021; 17:1. [PMID: 33407638 PMCID: PMC7789486 DOI: 10.1186/s13007-020-00700-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/14/2020] [Indexed: 05/30/2023]
Abstract
BACKGROUND Forest dieback driven by rapid climate warming threatens ecosystems worldwide. The health of forested ecosystems depends on how tree species respond to warming during all life history stages. While it is known that seed development is temperature-sensitive, little is known about possible effects of climate warming on seed development and subsequent seedling performance. Exposure of seeds to high air temperatures may influence subsequent seedling performance negatively, though conversely, warming during seed development may aid acclimation of seedlings to subsequent thermal stress. Technical challenges associated with in-situ warming of developing tree seeds limit understanding of how tree species may respond to seed development in a warmer climate. RESULTS We developed and validated a simple method for passively warming seeds as they develop in tree canopies to enable controlled study of climate warming on seedling performance. We quantified thermal effects of the cone-warming method across individual pine trees and stands by measuring the air temperature surrounding seed cones using thermal loggers and the temperature of seed cone tissue using thermocouples. We then investigated seedling phenotypes in relation to the warming method through a common garden study. We assessed seedling morphology, physiology, and mycorrhizal nodulation in response to experimental cone-warming in 20 seed-source-tree canopies on the San Francisco Peaks in northern Arizona, USA. The warming method increased air temperature surrounding developing seed cones by 2.1 °C, a plausible increase in mean air temperature by 2050 under current climate projections. Notable effect sizes of cone-warming were detected for seedling root length, shoot length, and diameter at root collar using Cohen's Local f2. Root length was affected most by cone-warming, but effect sizes of cone-warming on root length and diameter at root collar became negligible after the first year of growth. Cone-warming had small but significant effects on mycorrhizal fungal richness and seedling multispectral near-infrared indices indicative of plant health. CONCLUSIONS The method was shown to reliably elevate the temperature surrounding seed cones and thereby facilitate experimental in-situ climate warming research on forest trees. The method was furthermore shown to influence plant traits that may affect seedling performance under climate warming.
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Affiliation(s)
- E R V Moler
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA.
- College of Natural Resources, Center for Forest Nursery and Seedling Research, University of Idaho, Moscow, ID, 83843, USA.
| | - G Page
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, 97331, USA
| | - L Flores-Rentería
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA
| | - C G Garms
- Forest Engineering, Resources & Management, Oregon State University, Corvallis, OR, 97331, USA
| | - J B Hull
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - H F Cooper
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - J Swenson
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - S Perks
- USDA Forest Service, Dorena Genetic Resource Center, Cottage Grove, OR, 97424, USA
| | - K M Waring
- School of Forestry, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - A V Whipple
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
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Kolton M, Rolando JL, Kostka JE. Elucidation of the rhizosphere microbiome linked to Spartina alterniflora phenotype in a salt marsh on Skidaway Island, Georgia, USA. FEMS Microbiol Ecol 2020; 96:5813622. [PMID: 32227167 DOI: 10.1093/femsec/fiaa026] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 03/23/2020] [Indexed: 01/04/2023] Open
Abstract
Smooth cordgrass, Spartina alterniflora, dominates salt marshes on the east coast of the United States. While the physicochemical cues affecting S. alterniflora productivity have been studied intensively, the role of plant-microbe interactions in ecosystem functioning remains poorly understood. Thus, in this study, the effects of S. alterniflora phenotype on the composition of archaeal, bacterial, diazotrophic and fungal communities were investigated. Overall, prokaryotic communities were more diverse and bacteria were more abundant in the areas colonized by the tall plant phenotype in comparison to those of short plant phenotype. Diazotrophic methanogens (Methanomicrobia) preferentially colonized the area of the short plant phenotype. Putative iron-oxidizing Zetaproteobacteria and sulfur-oxidizing Campylobacteria were identified as indicator species in the rhizosphere of tall and short plant phenotypes, respectively. Finally, while diazotrophic populations shaped microbial interactions in the areas colonized by the tall plant phenotype, fungal populations filled this role in the areas occupied by the short plant phenotype. The results here demonstrate that S. alterniflora phenotype and proximity to the root zone are selective forces dictating microbial community assembly. Results further reveal that reduction-oxidation chemistry is a major factor driving the selection of belowground microbial populations in salt marsh habitats.
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Affiliation(s)
- Max Kolton
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - José L Rolando
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Joel E Kostka
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA.,School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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Stuart JEM, Holland-Moritz H, Lewis LR, Jean M, Miller SN, McDaniel SF, Fierer N, Ponciano JM, Mack MC. Host Identity as a Driver of Moss-Associated N2 Fixation Rates in Alaska. Ecosystems 2020. [DOI: 10.1007/s10021-020-00534-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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44
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Hassan MM, Yuan G, Chen JG, Tuskan GA, Yang X. Prime Editing Technology and Its Prospects for Future Applications in Plant Biology Research. Biodes Res 2020; 2020:9350905. [PMID: 37849904 PMCID: PMC10530660 DOI: 10.34133/2020/9350905] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/19/2020] [Indexed: 10/19/2023] Open
Abstract
Many applications in plant biology requires editing genomes accurately including correcting point mutations, incorporation of single-nucleotide polymorphisms (SNPs), and introduction of multinucleotide insertion/deletions (indels) into a predetermined position in the genome. These types of modifications are possible using existing genome-editing technologies such as the CRISPR-Cas systems, which require induction of double-stranded breaks in the target DNA site and the supply of a donor DNA molecule that contains the desired edit sequence. However, low frequency of homologous recombination in plants and difficulty of delivering the donor DNA molecules make this process extremely inefficient. Another kind of technology known as base editing can perform precise editing; however, only certain types of modifications can be obtained, e.g., C/G-to-T/A and A/T-to-G/C. Recently, a new type of genome-editing technology, referred to as "prime editing," has been developed, which can achieve various types of editing such as any base-to-base conversion, including both transitions (C→T, G→A, A→G, and T→C) and transversion mutations (C→A, C→G, G→C, G→T, A→C, A→T, T→A, and T→G), as well as small indels without the requirement for inducing double-stranded break in the DNA. Because prime editing has wide flexibility to achieve different types of edits in the genome, it holds a great potential for developing superior crops for various purposes, such as increasing yield, providing resistance to various abiotic and biotic stresses, and improving quality of plant product. In this review, we describe the prime editing technology and discuss its limitations and potential applications in plant biology research.
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Affiliation(s)
- Md. Mahmudul Hassan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge TN 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Genetics and Plant Breeding, Patuakhali Science and Technology University, Dumki, Patuakhali 8602, Bangladesh
| | - Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge TN 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge TN 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge TN 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge TN 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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45
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van den Elzen E, Bengtsson F, Fritz C, Rydin H, Lamers LPM. Variation in symbiotic N2 fixation rates among Sphagnum mosses. PLoS One 2020; 15:e0228383. [PMID: 32017783 PMCID: PMC7001857 DOI: 10.1371/journal.pone.0228383] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 01/14/2020] [Indexed: 11/18/2022] Open
Abstract
Biological nitrogen (N) fixation is an important process supporting primary production in ecosystems, especially in those where N availability is limiting growth, such as peatlands and boreal forests. In many peatlands, peat mosses (genus Sphagnum) are the prime ecosystem engineers, and like feather mosses in boreal forests, they are associated with a diverse community of diazotrophs (N2-fixing microorganisms) that live in and on their tissue. The large variation in N2 fixation rates reported in literature remains, however, to be explained. To assess the potential roles of habitat (including nutrient concentration) and species traits (in particular litter decomposability and photosynthetic capacity) on the variability in N2 fixation rates, we compared rates associated with various Sphagnum moss species in a bog, the surrounding forest and a fen in Sweden. We found appreciable variation in N2 fixation rates among moss species and habitats, and showed that both species and habitat conditions strongly influenced N2 fixation. We here show that higher decomposition rates, as explained by lower levels of decomposition-inhibiting compounds, and higher phosphorous (P) levels, are related with higher diazotrophic activity. Combining our findings with those of other studies, we propose a conceptual model in which both species-specific traits of mosses (as related to the trade-off between rapid photosynthesis and resistance to decomposition) and P availability, explain N2 fixation rates. This is expected to result in a tight coupling between P and N cycling in peatlands.
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Affiliation(s)
- Eva van den Elzen
- Department of Aquatic Ecology and Environmental Biology, Institute for
Water and Wetland Research, Radboud University, AJ Nijmegen, the
Netherlands
| | - Fia Bengtsson
- Department of Plant Ecology and Evolution, Evolutionary Biology Centre,
Uppsala University, Uppsala, Sweden
| | - Christian Fritz
- Department of Aquatic Ecology and Environmental Biology, Institute for
Water and Wetland Research, Radboud University, AJ Nijmegen, the
Netherlands
| | - Håkan Rydin
- Department of Plant Ecology and Evolution, Evolutionary Biology Centre,
Uppsala University, Uppsala, Sweden
| | - Leon P. M. Lamers
- Department of Aquatic Ecology and Environmental Biology, Institute for
Water and Wetland Research, Radboud University, AJ Nijmegen, the
Netherlands
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46
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Shin B, Bociu I, Kolton M, Huettel M, Kostka JE. Succession of microbial populations and nitrogen-fixation associated with the biodegradation of sediment-oil-agglomerates buried in a Florida sandy beach. Sci Rep 2019; 9:19401. [PMID: 31852991 PMCID: PMC6920467 DOI: 10.1038/s41598-019-55625-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 12/02/2019] [Indexed: 01/06/2023] Open
Abstract
The Deepwater Horizon (DWH) oil spill contaminated coastlines from Louisiana to Florida, burying oil up to 70 cm depth in sandy beaches, posing a potential threat to environmental and human health. The dry and nutrient-poor beach sand presents a taxing environment for microbial growth, raising the question how the biodegradation of the buried oil would proceed. Here we report the results of an in-situ experiment that (i) characterized the dominant microbial communities contained in sediment oil agglomerates (SOAs) of DWH oil buried in a North Florida sandy beach, (ii) elucidated the long-term succession of the microbial populations that developed in the SOAs, and (iii) revealed the coupling of SOA degradation to nitrogen fixation. Orders of magnitude higher bacterial abundances in SOAs compared to surrounding sands distinguished SOAs as hotspots of microbial growth. Blooms of bacterial taxa with a demonstrated potential for hydrocarbon degradation (Gammaproteobacteria, Alphaproteobacteria, Actinobacteria) developed in the SOAs, initiating a succession of microbial populations that mirrored the evolution of the petroleum hydrocarbons. Growth of nitrogen-fixing prokaryotes or diazotrophs (Rhizobiales and Frankiales), reflected in increased abundances of nitrogenase genes (nifH), catalyzed biodegradation of the nitrogen-poor petroleum hydrocarbons, emphasizing nitrogen fixation as a central mechanism facilitating the recovery of sandy beaches after oil contamination.
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Affiliation(s)
- Boryoung Shin
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Ioana Bociu
- Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, FL, USA
| | - Max Kolton
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Markus Huettel
- Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, FL, USA
| | - Joel E Kostka
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA. .,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
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47
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Hamard S, Robroek BJM, Allard PM, Signarbieux C, Zhou S, Saesong T, de Baaker F, Buttler A, Chiapusio G, Wolfender JL, Bragazza L, Jassey VEJ. Effects of Sphagnum Leachate on Competitive Sphagnum Microbiome Depend on Species and Time. Front Microbiol 2019; 10:2042. [PMID: 31555245 PMCID: PMC6742715 DOI: 10.3389/fmicb.2019.02042] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 08/20/2019] [Indexed: 12/03/2022] Open
Abstract
Plant specialized metabolites play an important role in soil carbon (C) and nutrient fluxes. Through anti-microbial effects, they can modulate microbial assemblages and associated microbial-driven processes, such as nutrient cycling, so to positively or negatively cascade on plant fitness. As such, plant specialized metabolites can be used as a tool to supplant competitors. These compounds are little studied in bryophytes. This is especially notable in peatlands where Sphagnum mosses can dominate the vegetation and show strong interspecific competition. Sphagnum mosses form carpets where diverse microbial communities live and play a crucial role in Sphagnum fitness by regulating C and nutrient cycling. Here, by means of a microcosm experiment, we assessed to what extent moss metabolites of two Sphagnum species (S. fallax and S. divinum) modulate the competitive Sphagnum microbiome, with particular focus on microbial respiration. Using a reciprocal leachate experiment, we found that interactions between Sphagnum leachates and microbiome are species-specific. We show that both Sphagnum leachates differed in compound richness and compound relative abundance, especially sphagnum acid derivates, and that they include microbial-related metabolites. The addition of S. divinum leachate on the S. fallax microbiome immediately reduced microbial respiration (−95%). Prolonged exposition of S. fallax microbiome to S. divinum leachate destabilized the food web structure due to a modulation of microbial abundance. In particular, leachate addition decreased the biomass of testate amoebae and rotifers but increased that of ciliates. These changes did not influence microbial CO2 respiration, suggesting that the structural plasticity of the food web leads to its functional resistance through the replacement of species that are functionally redundant. In contrast, S. fallax leachate neither affected S. divinum microbial respiration, nor microbial biomass. We, however, found that S. fallax leachate addition stabilized the food web structure associated to S. divinum by changing trophic interactions among species. The differences in allelopathic effects between both Sphagnum leachates might impact their competitiveness and affect species distribution at local scale. Our study further paves the way to better understand the role of moss and microbial specialized metabolites in peatland C dynamics.
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Affiliation(s)
- Samuel Hamard
- ECOLAB, Laboratoire d'Ecologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse, France.,Laboratory of Ecological Systems (ECOS), Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Architecture, Civil and Environmental Engineering, Lausanne, Switzerland.,Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Lausanne, Switzerland.,Laboratoire de Géologie, UMR 8538, CNRS-ENS, Ecole Normale Supérieure, Paris, France
| | - Bjorn J M Robroek
- Laboratory of Ecological Systems (ECOS), Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Architecture, Civil and Environmental Engineering, Lausanne, Switzerland.,School of Biological Sciences, University of Southampton, Southampton, United Kingdom.,Aquatic Ecology and Environmental Biology Group, Faculty of Science, Institute for Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Pierre-Marie Allard
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Constant Signarbieux
- Laboratory of Ecological Systems (ECOS), Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Architecture, Civil and Environmental Engineering, Lausanne, Switzerland.,Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Lausanne, Switzerland
| | - Shuaizhen Zhou
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Tongchai Saesong
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland.,Department of Pharmaceutical Chemistry and Pharmacognosy, Faculty of Pharmaceutical Sciences and Center of Excellence for Innovation in Chemistry, Naresuan University, Phitsanulok, Thailand
| | - Flore de Baaker
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Alexandre Buttler
- Laboratory of Ecological Systems (ECOS), Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Architecture, Civil and Environmental Engineering, Lausanne, Switzerland.,Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Lausanne, Switzerland.,Laboratoire Chrono-Environnement, Université Bourgogne Franche Comté, UMR CNRS 6249 USC INRA, Montbéliard, France
| | - Geneviève Chiapusio
- Laboratoire Chrono-Environnement, Université Bourgogne Franche Comté, UMR CNRS 6249 USC INRA, Montbéliard, France.,Laboratoire Carrtel, Université Savoie Mont Blanc INRA 042, Domaine Universitaire Belledonne, Le Bourget-du-Lac, France
| | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Luca Bragazza
- Laboratory of Ecological Systems (ECOS), Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Architecture, Civil and Environmental Engineering, Lausanne, Switzerland.,Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Lausanne, Switzerland.,Department of Life Science and Biotechnologies, University of Ferrara, Ferrara, Italy
| | - Vincent E J Jassey
- ECOLAB, Laboratoire d'Ecologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse, France.,Laboratory of Ecological Systems (ECOS), Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Architecture, Civil and Environmental Engineering, Lausanne, Switzerland.,Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Lausanne, Switzerland
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