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Arend M, Paulitz E, Hsieh YE, Nikoloski Z. Scaling metabolic model reconstruction up to the pan-genome level: A systematic review and prospective applications to photosynthetic organisms. Metab Eng 2025; 90:67-77. [PMID: 40081464 DOI: 10.1016/j.ymben.2025.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2024] [Revised: 02/11/2025] [Accepted: 02/25/2025] [Indexed: 03/16/2025]
Abstract
Advances in genomics technologies have generated large data sets that provide tremendous insights into the genetic diversity of taxonomic groups. However, it remains challenging to pinpoint the effect of genetic diversity on different traits without performing resource-intensive phenotyping experiments. Pan-genome-scale metabolic models (panGEMs) extend traditional genome-scale metabolic models by considering the entire reaction repertoire that enables the prediction and comparison of metabolic capabilities within a taxonomic group. Here, we systematically review the state-of-the-art methodologies for constructing panGEMs, focusing on used tools, databases, experimental datasets, and orthology relationships. We highlight the unique advantages of panGEMs compared to single-species GEMs in predicting metabolic phenotypes and in guiding the experimental validation of genome annotations. In addition, we emphasize the disparity between the available (pan-)genomic data on photosynthetic organisms and their under-representation in current (pan)GEMs. Finally, we propose a perspective for tackling the reconstruction of panGEMs for photosynthetic eukaryotes that can help advance our understanding of the metabolic diversity in this taxonomic group.
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Affiliation(s)
- Marius Arend
- Bioinformatics Department, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany; Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany; Bioinformatics and Mathematical Modeling Department, Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Emilian Paulitz
- Bioinformatics Department, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany; Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Yunli Eric Hsieh
- Bioinformatics Department, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany; Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany; School of BioSciences, The University of Melbourne, Parkville, 3010 VIC, Australia
| | - Zoran Nikoloski
- Bioinformatics Department, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany; Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany; Bioinformatics and Mathematical Modeling Department, Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria.
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2
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Delgado-Baquerizo M, Singh BK, Liu YR, Sáez-Sandino T, Coleine C, Muñoz-Rojas M, Bastida F, Trivedi P. Integrating ecological and evolutionary frameworks for SynCom success. THE NEW PHYTOLOGIST 2025; 246:1922-1933. [PMID: 40177999 DOI: 10.1111/nph.70112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2024] [Accepted: 03/11/2025] [Indexed: 04/05/2025]
Abstract
Use of synthetic microbial communities (SynComs) is a promising approach that harnesses nature-based solutions to support soil fertility and food security, mitigate climate change impacts, and restore terrestrial ecosystems. Several microbial products are in the market, and many others are at different stages of development and commercialization. Yet, we are still far from being able to fully harness the potential and successful applications of such biotechnological tools. The limited field efficiency and efficacy of SynComs have significantly constrained commercial opportunities, resulting in market growth falling below expectations. To overcome these challenges and manage expectations, it is critical to address current limitations, failures, and potential environmental consequences of SynComs. In this Viewpoint, we explore how using multiple eco-evolutionary theories can inform SynCom design and success. We further discuss the current status of SynComs and identify the next steps needed to develop and deploy the next generation of tools to boost their ability to support multiple ecosystem services, including food security and environmental sustainability.
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Affiliation(s)
- Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), Consejo Superior de Investigaciones Científicas (CSIC), Av. Reina Mercedes 10, E-41012, Sevilla, Spain
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, 2751, NSW, Australia
| | - Yu-Rong Liu
- State Key Laboratory of Agricultural Microbiology and College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tadeo Sáez-Sandino
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, 2751, NSW, Australia
| | - Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, 01100, Viterbo, Italy
| | - Miriam Muñoz-Rojas
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), Consejo Superior de Investigaciones Científicas (CSIC), Av. Reina Mercedes 10, E-41012, Sevilla, Spain
| | - Felipe Bastida
- CEBAS-CSIC, Campus Universitario de Espinardo, E-30100, Murcia, Spain
| | - Pankaj Trivedi
- Microbiome Network and Department of Agricultural Biology, Colorado State University, Fort Collins, 80523, CO, USA
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance (IGCAST), Texas Tech University, Lubbock, TX, 79409, USA
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3
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Li D, Li Z, Xu B, Chen T, Sun J, Hou J, Liu S. Microbial denitrification responses to elevated CO 2 in lake-shore sediments under different flooding conditions. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2025; 386:125835. [PMID: 40381298 DOI: 10.1016/j.jenvman.2025.125835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2025] [Revised: 04/25/2025] [Accepted: 05/13/2025] [Indexed: 05/20/2025]
Abstract
The lake-shore zone is a critical site for recognizing the ecological impacts of global climate change, such as persistent elevated CO2 (eCO2). However, the direct effect of eCO2 on functional microorganisms in lake-shore sediments is neglected or confused at previous studies. In this study, the short-term direct effects of eCO2 on microbial denitrification in lake-shore sediments were investigated by simulating four flooding conditions (non-flooding (NF), intermittent flooding (IF), alternating high and low water-level flooding (HLF), and constant water-level flooding (WF)) through incubation experiments in the laboratory. This work demonstrated eCO2 directly increased denitrification in lake-shore sediments under different water-level conditions by different regulatory mechanism within the short term of 24 days. The microbial pentose phosphate pathway (PPP) and glycolysis in HLF and WF sediments were enhanced, while glycolysis in NF and IF sediments were obviously suppressed. Additionally, eCO2 strengthened negative associations of nosZ-type and nirK-type denitrifiers communities in NF, while increased their positive associations in IF, HLF, and WF. The regulation of metabolic pathways in denitrifiers would become more important than their microbial community when denitrifiers adapting eCO2. And the rising CO2 levels shifted sediments hotspots for potential N2O emissions from dry-wet alternation areas in lake-shore zone to the near-lake regions and lake basins. Based on these results, we recommend adjusting water-level management strategies in the lake-shore zone to address the greenhouse effect. For example, increasing the size of intermittently flooded areas and decreasing the proportion of continuously flooded areas in the lake-shore zone to mitigate N2O emissions and optimize sediment denitrification.
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Affiliation(s)
- Dapeng Li
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China
| | - Ziyu Li
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China
| | - Boran Xu
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China
| | - Tianhua Chen
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China
| | - Jingqiu Sun
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China
| | - Jun Hou
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Songqi Liu
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China.
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4
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Song X, Wang Y, Wang Y, Zhao K, Tong D, Gao R, Lv X, Kong D, Ruan Y, Wang M, Tang X, Li F, Luo Y, Zhu Y, Xu J, Ma B. Rhizosphere-triggered viral lysogeny mediates microbial metabolic reprogramming to enhance arsenic oxidation. Nat Commun 2025; 16:4048. [PMID: 40307209 PMCID: PMC12044158 DOI: 10.1038/s41467-025-58695-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2024] [Accepted: 03/26/2025] [Indexed: 05/02/2025] Open
Abstract
The rhizosphere is a critical hotspot for metabolic activities involving arsenic (As). While recent studies indicate many functions for soil viruses, much remains overlooked regarding their quantitative impact on rhizosphere processes. Here, we analyze time-series metagenomes of rice (Oryza sativa L.)rhizosphere and bulk soil to explore how viruses mediate rhizosphere As biogeochemistry. We observe the rhizosphere favors lysogeny in viruses associated with As-oxidizing microbes, with a positive correlation between As oxidation and the prevalence of these microbial hosts. Moreover, results demonstrate these lysogenic viruses enrich both As oxidation and phosphorus co-metabolism genes and mediated horizontal gene transfers (HGTs) of As oxidases. In silico simulation with genome-scale metabolic models (GEMs) and in vitro validation with experiments estimate that rhizosphere lysogenic viruses contribute up to 25% of microbial As oxidation. These findings enhance our comprehension of the plant-microbiome-virome interplay and highlight the potential of rhizosphere viruses for improving soil health in sustainable agriculture.
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Affiliation(s)
- Xinwei Song
- State Key Laboratory of Soil Pollution Control and Safety, Zhejiang University, Hangzhou, 310058, China
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 311200, China
- Zhejiang Provincial Key Laboratory of Agricultural, Resources and Environment, College of Environmental and Resource Science, Zhejiang University, Hangzhou, 310058, China
| | - Yiling Wang
- State Key Laboratory of Soil Pollution Control and Safety, Zhejiang University, Hangzhou, 310058, China
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 311200, China
- Zhejiang Provincial Key Laboratory of Agricultural, Resources and Environment, College of Environmental and Resource Science, Zhejiang University, Hangzhou, 310058, China
| | - Youjing Wang
- Zhejiang Provincial Key Laboratory of Agricultural, Resources and Environment, College of Environmental and Resource Science, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, Hangzhou, 310058, China
| | - Kankan Zhao
- State Key Laboratory of Soil Pollution Control and Safety, Zhejiang University, Hangzhou, 310058, China
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 311200, China
- Zhejiang Provincial Key Laboratory of Agricultural, Resources and Environment, College of Environmental and Resource Science, Zhejiang University, Hangzhou, 310058, China
| | - Di Tong
- Zhejiang Provincial Key Laboratory of Agricultural, Resources and Environment, College of Environmental and Resource Science, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, Hangzhou, 310058, China
| | - Ruichuan Gao
- Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Xiaofei Lv
- Department of Environmental Engineering, China Jiliang University, Hangzhou, 310018, China
| | - Dedong Kong
- Institute of Digital Agriculture, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Yunjie Ruan
- Institute of Agricultural Bio-Environmental Engineering, College of Bio-Systems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
- The Rural Development Academy, Zhejiang University, Hangzhou, 310058, China
| | - Mengcen Wang
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
| | - Xianjin Tang
- State Key Laboratory of Soil Pollution Control and Safety, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural, Resources and Environment, College of Environmental and Resource Science, Zhejiang University, Hangzhou, 310058, China
| | - Fangbai Li
- Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Yongming Luo
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, 210000, Nanjing, China
| | - Yongguan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, 100085, Beijing, China
| | - Jianming Xu
- State Key Laboratory of Soil Pollution Control and Safety, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural, Resources and Environment, College of Environmental and Resource Science, Zhejiang University, Hangzhou, 310058, China
| | - Bin Ma
- State Key Laboratory of Soil Pollution Control and Safety, Zhejiang University, Hangzhou, 310058, China.
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 311200, China.
- Zhejiang Provincial Key Laboratory of Agricultural, Resources and Environment, College of Environmental and Resource Science, Zhejiang University, Hangzhou, 310058, China.
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5
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Chesneau G, Herpell J, Wolf SM, Perin S, Hacquard S. MetaFlowTrain: a highly parallelized and modular fluidic system for studying exometabolite-mediated inter-organismal interactions. Nat Commun 2025; 16:3310. [PMID: 40210863 PMCID: PMC11985495 DOI: 10.1038/s41467-025-58530-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2024] [Accepted: 03/25/2025] [Indexed: 04/12/2025] Open
Abstract
Metabolic fluxes between cells, organisms, or communities drive ecosystem assembly and functioning and explain higher-level biological organization. Exometabolite-mediated inter-organismal interactions, however, remain poorly described due to technical challenges in measuring these interactions. Here, we present MetaFlowTrain, an easy-to-assemble, cheap, semi-high-throughput, and modular fluidic system in which multiple media can be flushed at adjustable flow rates into gnotobiotic microchambers accommodating diverse micro-organisms, ranging from bacteria to small eukaryotes. These microchambers can be used alone or connected in series to create microchamber trains within which metabolites, but not organisms, directionally travel between microchambers to modulate organismal growth. Using MetaFlowTrain, we uncover soil conditioning effects on synthetic community structure and plant growth, and reveal microbial antagonism mediated by exometabolite production. Our study highlights MetaFlowTrain as a versatile system for investigating plant-microbe-microbe metabolic interactions. We also discuss the system´s potential to discover metabolites that function as signaling molecules, drugs, or antimicrobials across various systems.
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Affiliation(s)
- Guillaume Chesneau
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Johannes Herpell
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Sarah Marie Wolf
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Silvina Perin
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Stéphane Hacquard
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
- Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, Cologne, Germany.
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6
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Wang Q, Zhang J, Liang J, Wang Y, Ren C, Chen X, Cheng D, Zhang H, Liu H. Genomic Insights into Selenate Reduction by Anaerobacillus Species. Microorganisms 2025; 13:659. [PMID: 40142551 PMCID: PMC11944866 DOI: 10.3390/microorganisms13030659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2025] [Revised: 03/11/2025] [Accepted: 03/11/2025] [Indexed: 03/28/2025] Open
Abstract
Selenium (Se), a potentially toxic trace element, undergoes complex biogeochemical cycling in the environment, largely driven by microbial activity. The reduction in selenate or selenite to elemental selenium is an environmentally beneficial process, as it decreases both Se toxicity and mobility. This reduction is catalyzed by enzymes encoded by various related genes. The link between Se reduction gene clusters and specific taxonomic groups is significant for elucidating the ecological roles and processes of Se reduction in diverse environments. In this study, a new species of Se-reducing microorganism belonging to the genus Anaerobacillus was isolated from a mining site. A comparative analysis of the growth characteristics reveals that Anaerobacillus species exhibit notable metabolic versatility, particularly in their fermentation abilities and utilization of diverse electron donors and acceptors. Genome analysis identified a diverse array of gene clusters associated with selenate uptake (sul, pst), selenate reduction (ser), and selenite reduction (hig, frd, trx, and bsh). Since selenate reduction is the first crucial step in Se reduction, genes linked to selenate reductase are the focus. The serA gene clusters analysis suggests that the serA gene is highly conserved across Anaerobacillus species. The surrounding genes of serA show significant variability in both presence and gene size. This evolutionary difference in coenzyme utilization and serA regulation suggests distinct survival strategies among Anaerobacillus species. This study offers insights into Se bio-transformations and the adaptive strategies of Se-reducing microorganisms.
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Affiliation(s)
- Qidong Wang
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao 266590, China; (Q.W.); (J.Z.); (Y.W.); (C.R.); (X.C.); (D.C.); (H.L.)
- Institute of Yellow River Delta Earth Surface Processes and Ecological Integrity, Shandong University of Science and Technology, Qingdao 266590, China
| | - Jian Zhang
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao 266590, China; (Q.W.); (J.Z.); (Y.W.); (C.R.); (X.C.); (D.C.); (H.L.)
- Institute of Yellow River Delta Earth Surface Processes and Ecological Integrity, Shandong University of Science and Technology, Qingdao 266590, China
- School of Geographical Environment, Shandong Normal University, Jinan 250358, China
| | - Jinhui Liang
- State Environmental Protection Key Laboratory of Land and Sea Ecological Governance and Systematic Regulation, Jinan 250101, China;
- Shandong Academy for Environmental Planning, Jinan 250101, China
| | - Yanlong Wang
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao 266590, China; (Q.W.); (J.Z.); (Y.W.); (C.R.); (X.C.); (D.C.); (H.L.)
- Institute of Yellow River Delta Earth Surface Processes and Ecological Integrity, Shandong University of Science and Technology, Qingdao 266590, China
| | - Chongyang Ren
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao 266590, China; (Q.W.); (J.Z.); (Y.W.); (C.R.); (X.C.); (D.C.); (H.L.)
- Institute of Yellow River Delta Earth Surface Processes and Ecological Integrity, Shandong University of Science and Technology, Qingdao 266590, China
| | - Xinhan Chen
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao 266590, China; (Q.W.); (J.Z.); (Y.W.); (C.R.); (X.C.); (D.C.); (H.L.)
- Institute of Yellow River Delta Earth Surface Processes and Ecological Integrity, Shandong University of Science and Technology, Qingdao 266590, China
| | - Dongle Cheng
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao 266590, China; (Q.W.); (J.Z.); (Y.W.); (C.R.); (X.C.); (D.C.); (H.L.)
- Institute of Yellow River Delta Earth Surface Processes and Ecological Integrity, Shandong University of Science and Technology, Qingdao 266590, China
| | - Huanxin Zhang
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao 266590, China; (Q.W.); (J.Z.); (Y.W.); (C.R.); (X.C.); (D.C.); (H.L.)
- Institute of Yellow River Delta Earth Surface Processes and Ecological Integrity, Shandong University of Science and Technology, Qingdao 266590, China
| | - Huaqing Liu
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao 266590, China; (Q.W.); (J.Z.); (Y.W.); (C.R.); (X.C.); (D.C.); (H.L.)
- Institute of Yellow River Delta Earth Surface Processes and Ecological Integrity, Shandong University of Science and Technology, Qingdao 266590, China
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7
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Delgado-Baquerizo M, Eldridge DJ, Liu YR, Liu ZW, Coleine C, Trivedi P. Soil biodiversity and function under global change. PLoS Biol 2025; 23:e3003093. [PMID: 40146744 DOI: 10.1371/journal.pbio.3003093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/28/2025] [Indexed: 03/29/2025] Open
Abstract
Soil organisms represent the most abundant and diverse organisms on the planet and support almost every ecosystem function we know, and thus impact our daily lives. Some of these impacts have been well-documented, such as the role of soil organisms in regulating soil fertility and carbon sequestration; processes that have direct implications for essential ecosystem services including food security and climate change mitigation. Moreover, soil biodiversity also plays a critical role in supporting other aspects from One Health-the combined health of humans, animals, and the environment-to the conservation of historic structures such as monuments. Unfortunately, soil biodiversity is also highly vulnerable to a growing number of stressors associated with global environmental change. Understanding how and when soil biodiversity supports these functions, and how it will adapt to changing environmental conditions, is crucial for conserving soils and maintaining soil processes for future generations. In this Essay, we discuss the fundamental importance of soil biodiversity for supporting multiple ecosystem services and One Health, and further highlight essential knowledge gaps that need to be addressed to conserve soil biodiversity for the next generations.
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Affiliation(s)
- Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
| | - David J Eldridge
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Yu-Rong Liu
- State Key Laboratory of Agricultural Microbiology and College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Zhong-Wen Liu
- State Key Laboratory of Agricultural Microbiology and College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Pankaj Trivedi
- Microbiome Network and Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado, United States of America
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance (IGCAST), Texas Tech University, Lubbock, Texas, United States of America
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Zheng X, Li J, Ouyang Y, Wu G, He X, Wang D, Zhang XX. Ecological linkages between top-down designed benzothiazole-degrading consortia and selection strength: From performance to community structure and functional genes. WATER RESEARCH 2024; 267:122491. [PMID: 39353343 DOI: 10.1016/j.watres.2024.122491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2024] [Revised: 08/15/2024] [Accepted: 09/20/2024] [Indexed: 10/04/2024]
Abstract
The inefficient biodegradation and incomplete mineralization of nitrogenous heterocyclic compounds (NHCs) have emerged as a pressing environmental concern. The top-down design offers potential solutions to this issue by targeting improvements in community function, but the ecological linkages between selection strength and the structure and function of desired microbiomes remain elusive. Herein, the integration of metagenomics, culture-based approach, non-targeted metabolite screening and enzymatic verification experiments revealed the effect of enrichment concentration on the top-down designed benzothiazole (BTH, a typical NHC)-degrading consortia. Significant differences were observed for the degradation efficiency and community structure under varying BTH selections. Notably, the enriched consortia at high concentrations of BTH were dominated by genus Rhodococcus, possessing higher degradation rates. Moreover, the isolate Rhodococcus pyridinivorans Rho48 displayed excellent efficiencies in BTH removal (98 %) and mineralization (∼ 60 %) through the hydroxylation and cleavage of thiazole and benzene rings, where cytochrome P450 enzyme was firstly reported to participate in BTH conversion. The functional annotation of 460 recovered genomes from the enriched consortia revealed diverse interspecific cooperation patterns that accounted for the BTH mineralization, particularly Nakamurella and Micropruina under low selection strength, and Rhodococcus and Marmoricola under high selection strength. This study highlights the significance of selection strength in top-down design of synthetic microbiomes for degrading refractory organic pollutants, providing valuable guidance for designing functionally optimized microbiomes used in environmental engineering.
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Affiliation(s)
- Xiulin Zheng
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Jie Li
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Yixin Ouyang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Gang Wu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Xiwei He
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China; School of Environment, Jiangsu Engineering Lab of Water and Soil Eco-Remediation, Nanjing Normal University, Nanjing 210023, China
| | - Depeng Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China.
| | - Xu-Xiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China.
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9
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Li Z, Li D, Liu S, Zhao H, Li B, Shan S, Zhu Y, Sun J, Hou J. Impact of elevated CO 2 on microbial communities and functions in riparian sediments: Role of pollution levels in modulating effects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 954:176481. [PMID: 39341255 DOI: 10.1016/j.scitotenv.2024.176481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 08/14/2024] [Accepted: 09/21/2024] [Indexed: 09/30/2024]
Abstract
The impact of elevated CO2 levels on microorganisms is a focal point in studying the environmental effects of global climate change. A growing number of studies have demonstrated the importance of the direct effects of elevated CO2 on microorganisms, which are confounded by indirect effects that are not easily identified. Riparian zones have become key factor in identifying the environmental effects of global climate change because of their special location. However, the direct effects of elevated CO2 levels on microbial activity and function in riparian zone sediments remain unclear. In this study, three riparian sediments with different pollution risk levels of heavy metals and nutrients were selected to explore the direct response of microbial communities and functions to elevated CO2 excluding plants. The results showed that the short-term effects of elevated CO2 did not change the diversity of the bacterial and fungal communities, but altered the composition of their communities. Additionally, differences were observed in the responses of microbial functions to elevated CO2 levels among the three regions. Elevated CO2 promoted the activities of nitrification and denitrification enzymes and led to significant increases in N2O release in the three sediments, with the greatest increase of 76.09 % observed in the Yuyangshan Bay (YYS). Microbial carbon metabolism was promoted by elevated CO2 in YYS but was significantly inhibited by elevated CO2 in Gonghu Bay and Meiliang Bay. Moreover, TOC, TN, and Pb contents were identified as key factors contributing to the different microbial responses to elevated CO2 in sediments with different heavy metal and nutrient pollution. In conclusion, this study provides in-depth insights into the responses of bacteria and fungi in polluted riparian sediments to elevated CO2, which helps elucidate the complex interactions between microbial activity and environmental stressors.
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Affiliation(s)
- Ziyu Li
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Dapeng Li
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China.
| | - Songqi Liu
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China.
| | - Huilin Zhao
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Boling Li
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Sujie Shan
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Yizhi Zhu
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Jingqiu Sun
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Jun Hou
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
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10
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Peng X, Wang S, Wang M, Feng K, He Q, Yang X, Hou W, Li F, Zhao Y, Hu B, Zou X, Deng Y. Metabolic interdependencies in thermophilic communities are revealed using co-occurrence and complementarity networks. Nat Commun 2024; 15:8166. [PMID: 39289365 PMCID: PMC11408653 DOI: 10.1038/s41467-024-52532-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 09/09/2024] [Indexed: 09/19/2024] Open
Abstract
Microbial communities exhibit intricate interactions underpinned by metabolic dependencies. To elucidate these dependencies, we present a workflow utilizing random matrix theory on metagenome-assembled genomes to construct co-occurrence and metabolic complementarity networks. We apply this approach to a temperature gradient hot spring, unraveling the interplay between thermal stress and metabolic cooperation. Our analysis reveals an increase in the frequency of metabolic interactions with rising temperatures. Amino acids, coenzyme A derivatives, and carbohydrates emerge as key exchange metabolites, forming the foundation for syntrophic dependencies, in which commensalistic interactions take a greater proportion than mutualistic ones. These metabolic exchanges are most prevalent between phylogenetically distant species, especially archaea-bacteria collaborations, as a crucial adaptation to harsh environments. Furthermore, we identify a significant positive correlation between basal metabolite exchange and genome size disparity, potentially signifying a means for streamlined genomes to leverage cooperation with metabolically richer partners. This phenomenon is also confirmed by another composting system which has a similar wide range of temperature fluctuations. Our workflow provides a feasible way to decipher the metabolic complementarity mechanisms underlying microbial interactions, and our findings suggested environmental stress regulates the cooperative strategies of thermophiles, while these dependencies have been potentially hardwired into their genomes during co-evolutions.
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Affiliation(s)
- Xi Peng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Shang Wang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China
| | - Miaoxiao Wang
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
- Department of Environmental Microbiology, Eawag, Dübendorf, Switzerland
| | - Kai Feng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China
| | - Qing He
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China
| | - Xingsheng Yang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Weiguo Hou
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, China
| | - Fangru Li
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, China
| | - Yuxiang Zhao
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Baolan Hu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China
| | - Xiao Zou
- Department of Ecology/Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Guizhou University, Guiyang, China
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China.
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China.
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11
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Berruto CA, Demirer GS. Engineering agricultural soil microbiomes and predicting plant phenotypes. Trends Microbiol 2024; 32:858-873. [PMID: 38429182 DOI: 10.1016/j.tim.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 03/03/2024]
Abstract
Plant growth-promoting rhizobacteria (PGPR) can improve crop yields, nutrient use efficiency, plant tolerance to stressors, and confer benefits to future generations of crops grown in the same soil. Unlocking the potential of microbial communities in the rhizosphere and endosphere is therefore of great interest for sustainable agriculture advancements. Before plant microbiomes can be engineered to confer desirable phenotypic effects on their plant hosts, a deeper understanding of the interacting factors influencing rhizosphere community structure and function is needed. Dealing with this complexity is becoming more feasible using computational approaches. In this review, we discuss recent advances at the intersection of experimental and computational strategies for the investigation of plant-microbiome interactions and the engineering of desirable soil microbiomes.
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Affiliation(s)
- Chiara A Berruto
- Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Gozde S Demirer
- Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
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12
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Poupin MJ, González B. Embracing complexity in plant-microbiome systems. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e70000. [PMID: 39189551 PMCID: PMC11348195 DOI: 10.1111/1758-2229.70000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 07/27/2024] [Indexed: 08/28/2024]
Abstract
Despite recent advances in understanding the role of microorganisms in plant holobiont metabolism, physiology, and fitness, several relevant questions are yet to be answered, with implications for ecology, evolution, and sustainable agriculture. This article explores some of these questions and discusses emerging research areas in plant microbiomes. Firstly, it emphasizes the need to move beyond taxonomic characterization towards understanding microbial functions within plant ecosystems. Secondly, controlling methodological biases and enhancing OMICS technologies' standardization is imperative for a deeper comprehension of plant-microbiota interactions. Furthermore, while plant microbiota research has primarily centred on bacteria and fungi, other microbial players such as archaea, viruses, and microeukaryotes have been largely overlooked. Emerging evidence highlights their presence and potential roles, underscoring the need for thorough assessments. Future research should aim to elucidate the ecological microbial interactions, their impact on plant performance, and how the plant context shapes microbial community dynamics. Finally, a discussion is provided on how the multiple layers of abiotic and biotic factors influencing the spatiotemporal dynamics of plant-microbiome systems require in-depth attention. Examples illustrate how synthetic communities and computational methods such as machine learning and artificial intelligence provide alternatives to tackle these challenges and analyse the plant holobiont as a complex system.
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Affiliation(s)
- María Josefina Poupin
- Laboratorio de Bioingeniería, Facultad de Ingeniería y CienciasUniversidad Adolfo IbáñezSantiagoChile
- Center of Applied Ecology and Sustainability (CAPES)SantiagoChile
- Millennium Nucleus for the Development of Super Adaptable Plants (MN‐SAP)SantiagoChile
| | - Bernardo González
- Laboratorio de Bioingeniería, Facultad de Ingeniería y CienciasUniversidad Adolfo IbáñezSantiagoChile
- Center of Applied Ecology and Sustainability (CAPES)SantiagoChile
- Millennium Nucleus for the Development of Super Adaptable Plants (MN‐SAP)SantiagoChile
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13
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Hsieh YE, Tandon K, Verbruggen H, Nikoloski Z. Comparative analysis of metabolic models of microbial communities reconstructed from automated tools and consensus approaches. NPJ Syst Biol Appl 2024; 10:54. [PMID: 38783065 PMCID: PMC11116368 DOI: 10.1038/s41540-024-00384-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024] Open
Abstract
Genome-scale metabolic models (GEMs) of microbial communities offer valuable insights into the functional capabilities of their members and facilitate the exploration of microbial interactions. These models are generated using different automated reconstruction tools, each relying on different biochemical databases that may affect the conclusions drawn from the in silico analysis. One way to address this problem is to employ a consensus reconstruction method that combines the outcomes of different reconstruction tools. Here, we conducted a comparative analysis of community models reconstructed from three automated tools, i.e. CarveMe, gapseq, and KBase, alongside a consensus approach, utilizing metagenomics data from two marine bacterial communities. Our analysis revealed that these reconstruction approaches, while based on the same genomes, resulted in GEMs with varying numbers of genes and reactions as well as metabolic functionalities, attributed to the different databases employed. Further, our results indicated that the set of exchanged metabolites was more influenced by the reconstruction approach rather than the specific bacterial community investigated. This observation suggests a potential bias in predicting metabolite interactions using community GEMs. We also showed that consensus models encompassed a larger number of reactions and metabolites while concurrently reducing the presence of dead-end metabolites. Therefore, the usage of consensus models allows making full and unbiased use from aggregating genes from the different reconstructions in assessing the functional potential of microbial communities.
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Affiliation(s)
- Yunli Eric Hsieh
- Bioinformatics Department, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
| | - Kshitij Tandon
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
| | - Heroen Verbruggen
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
| | - Zoran Nikoloski
- Bioinformatics Department, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany.
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14
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Williams A, Sinanaj B, Hoysted GA. Plant-microbe interactions through a lens: tales from the mycorrhizosphere. ANNALS OF BOTANY 2024; 133:399-412. [PMID: 38085925 PMCID: PMC11006548 DOI: 10.1093/aob/mcad191] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 12/11/2023] [Indexed: 04/12/2024]
Abstract
BACKGROUND The soil microbiome plays a pivotal role in maintaining ecological balance, supporting food production, preserving water quality and safeguarding human health. Understanding the intricate dynamics within the soil microbiome necessitates unravelling complex bacterial-fungal interactions (BFIs). BFIs occur in diverse habitats, such as the phyllosphere, rhizosphere and bulk soil, where they exert substantial influence on plant-microbe associations, nutrient cycling and overall ecosystem functions. In various symbiotic associations, fungi form mycorrhizal connections with plant roots, enhancing nutrient uptake through the root and mycorrhizal pathways. Concurrently, specific soil bacteria, including mycorrhiza helper bacteria, play a pivotal role in nutrient acquisition and promoting plant growth. Chemical communication and biofilm formation further shape plant-microbial interactions, affecting plant growth, disease resistance and nutrient acquisition processes. SCOPE Promoting synergistic interactions between mycorrhizal fungi and soil microbes holds immense potential for advancing ecological knowledge and conservation. However, despite the significant progress, gaps remain in our understanding of the evolutionary significance, perception, functional traits and ecological relevance of BFIs. Here we review recent findings obtained with respect to complex microbial communities - particularly in the mycorrhizosphere - and include the latest advances in the field, outlining their profound impacts on our understanding of ecosystem dynamics and plant physiology and function. CONCLUSIONS Deepening our understanding of plant BFIs can help assess their capabilities with regard to ecological and agricultural safe-guarding, in particular buffering soil stresses, and ensuring sustainable land management practices. Preserving and enhancing soil biodiversity emerge as critical imperatives in sustaining life on Earth amidst pressures of anthropogenic climate change. A holistic approach integrates scientific knowledge on bacteria and fungi, which includes their potential to foster resilient soil ecosystems for present and future generations.
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Affiliation(s)
- Alex Williams
- Plants, Photosynthesis and Soil, School of Bioscience, University of Sheffield, Sheffield, S10 2TN, UK
| | - Besiana Sinanaj
- Plants, Photosynthesis and Soil, School of Bioscience, University of Sheffield, Sheffield, S10 2TN, UK
| | - Grace A Hoysted
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
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15
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Liu Y, Xu Z, Chen L, Xun W, Shu X, Chen Y, Sun X, Wang Z, Ren Y, Shen Q, Zhang R. Root colonization by beneficial rhizobacteria. FEMS Microbiol Rev 2024; 48:fuad066. [PMID: 38093453 PMCID: PMC10786197 DOI: 10.1093/femsre/fuad066] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 12/07/2023] [Accepted: 12/12/2023] [Indexed: 01/13/2024] Open
Abstract
Rhizosphere microbes play critical roles for plant's growth and health. Among them, the beneficial rhizobacteria have the potential to be developed as the biofertilizer or bioinoculants for sustaining the agricultural development. The efficient rhizosphere colonization of these rhizobacteria is a prerequisite for exerting their plant beneficial functions, but the colonizing process and underlying mechanisms have not been thoroughly reviewed, especially for the nonsymbiotic beneficial rhizobacteria. This review systematically analyzed the root colonizing process of the nonsymbiotic rhizobacteria and compared it with that of the symbiotic and pathogenic bacteria. This review also highlighted the approaches to improve the root colonization efficiency and proposed to study the rhizobacterial colonization from a holistic perspective of the rhizosphere microbiome under more natural conditions.
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Affiliation(s)
- Yunpeng Liu
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P.R. China
| | - Zhihui Xu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, P.R. China
| | - Lin Chen
- Experimental Center of Forestry in North China, Chinese Academy of Forestry, 1 Shuizha West Road, Beijing 102300, P.R. China
| | - Weibing Xun
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, P.R. China
| | - Xia Shu
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P.R. China
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, P.R. China
| | - Yu Chen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, P.R. China
| | - Xinli Sun
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, P.R. China
| | - Zhengqi Wang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, P.R. China
| | - Yi Ren
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, P.R. China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, P.R. China
| | - Ruifu Zhang
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P.R. China
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, P.R. China
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16
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Jing J, Garbeva P, Raaijmakers JM, Medema MH. Strategies for tailoring functional microbial synthetic communities. THE ISME JOURNAL 2024; 18:wrae049. [PMID: 38537571 PMCID: PMC11008692 DOI: 10.1093/ismejo/wrae049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/26/2024] [Indexed: 04/12/2024]
Abstract
Natural ecosystems harbor a huge reservoir of taxonomically diverse microbes that are important for plant growth and health. The vast diversity of soil microorganisms and their complex interactions make it challenging to pinpoint the main players important for the life support functions microbes can provide to plants, including enhanced tolerance to (a)biotic stress factors. Designing simplified microbial synthetic communities (SynComs) helps reduce this complexity to unravel the molecular and chemical basis and interplay of specific microbiome functions. While SynComs have been successfully employed to dissect microbial interactions or reproduce microbiome-associated phenotypes, the assembly and reconstitution of these communities have often been based on generic abundance patterns or taxonomic identities and co-occurrences but have only rarely been informed by functional traits. Here, we review recent studies on designing functional SynComs to reveal common principles and discuss multidimensional approaches for community design. We propose a strategy for tailoring the design of functional SynComs based on integration of high-throughput experimental assays with microbial strains and computational genomic analyses of their functional capabilities.
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Affiliation(s)
- Jiayi Jing
- Bioinformatics Group, Department of Plant Science, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Paolina Garbeva
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Marnix H Medema
- Bioinformatics Group, Department of Plant Science, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
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17
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Vannier N, Mesny F, Getzke F, Chesneau G, Dethier L, Ordon J, Thiergart T, Hacquard S. Genome-resolved metatranscriptomics reveals conserved root colonization determinants in a synthetic microbiota. Nat Commun 2023; 14:8274. [PMID: 38092730 PMCID: PMC10719396 DOI: 10.1038/s41467-023-43688-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 11/16/2023] [Indexed: 12/17/2023] Open
Abstract
The identification of processes activated by specific microbes during microbiota colonization of plant roots has been hampered by technical constraints in metatranscriptomics. These include lack of reference genomes, high representation of host or microbial rRNA sequences in datasets, or difficulty to experimentally validate gene functions. Here, we recolonized germ-free Arabidopsis thaliana with a synthetic, yet representative root microbiota comprising 106 genome-sequenced bacterial and fungal isolates. We used multi-kingdom rRNA depletion, deep RNA-sequencing and read mapping against reference microbial genomes to analyse the in planta metatranscriptome of abundant colonizers. We identified over 3,000 microbial genes that were differentially regulated at the soil-root interface. Translation and energy production processes were consistently activated in planta, and their induction correlated with bacterial strains' abundance in roots. Finally, we used targeted mutagenesis to show that several genes consistently induced by multiple bacteria are required for root colonization in one of the abundant bacterial strains (a genetically tractable Rhodanobacter). Our results indicate that microbiota members activate strain-specific processes but also common gene sets to colonize plant roots.
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Affiliation(s)
- Nathan Vannier
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
| | - Fantin Mesny
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- Institute for Plant Sciences, University of Cologne, 50923, Cologne, Germany
| | - Felix Getzke
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Guillaume Chesneau
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Laura Dethier
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Jana Ordon
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Thorsten Thiergart
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Stéphane Hacquard
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany.
- Cluster of Excellence on Plant Sciences, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany.
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18
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Gonçalves OS, Creevey CJ, Santana MF. Designing a synthetic microbial community through genome metabolic modeling to enhance plant-microbe interaction. ENVIRONMENTAL MICROBIOME 2023; 18:81. [PMID: 37974247 PMCID: PMC10655421 DOI: 10.1186/s40793-023-00536-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 10/30/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND Manipulating the rhizosphere microbial community through beneficial microorganism inoculation has gained interest in improving crop productivity and stress resistance. Synthetic microbial communities, known as SynComs, mimic natural microbial compositions while reducing the number of components. However, achieving this goal requires a comprehensive understanding of natural microbial communities and carefully selecting compatible microorganisms with colonization traits, which still pose challenges. In this study, we employed multi-genome metabolic modeling of 270 previously described metagenome-assembled genomes from Campos rupestres to design a synthetic microbial community to improve the yield of important crop plants. RESULTS We used a targeted approach to select a minimal community (MinCom) encompassing essential compounds for microbial metabolism and compounds relevant to plant interactions. This resulted in a reduction of the initial community size by approximately 4.5-fold. Notably, the MinCom retained crucial genes associated with essential plant growth-promoting traits, such as iron acquisition, exopolysaccharide production, potassium solubilization, nitrogen fixation, GABA production, and IAA-related tryptophan metabolism. Furthermore, our in-silico selection for the SymComs, based on a comprehensive understanding of microbe-microbe-plant interactions, yielded a set of six hub species that displayed notable taxonomic novelty, including members of the Eremiobacterota and Verrucomicrobiota phyla. CONCLUSION Overall, the study contributes to the growing body of research on synthetic microbial communities and their potential to enhance agricultural practices. The insights gained from our in-silico approach and the selection of hub species pave the way for further investigations into the development of tailored microbial communities that can optimize crop productivity and improve stress resilience in agricultural systems.
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Affiliation(s)
- Osiel S Gonçalves
- Grupo de Genômica Eco-evolutiva Microbiana, Laboratório de Genética Molecular de Microrganismos, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Christopher J Creevey
- School of Biological Sciences, Institute for Global Food Security, Queen's University Belfast, Belfast, BT9 5DL, UK
| | - Mateus F Santana
- Grupo de Genômica Eco-evolutiva Microbiana, Laboratório de Genética Molecular de Microrganismos, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.
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19
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Tian Y, Liu Y, Uwaremwe C, Zhao X, Yue L, Zhou Q, Wang Y, Tran LSP, Li W, Chen G, Sha Y, Wang R. Characterization of three new plant growth-promoting microbes and effects of the interkingdom interactions on plant growth and disease prevention. PLANT CELL REPORTS 2023; 42:1757-1776. [PMID: 37674059 DOI: 10.1007/s00299-023-03060-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 08/12/2023] [Indexed: 09/08/2023]
Abstract
KEY MESSAGE The novel interkingdom PGPM consortia enhanced the ability of plant growth promotion and disease resistance, which would be beneficial to improve plant growth in sustainable agriculture through engineering microbiome. Plant growth-promoting microbes (PGPMs) play important roles in promoting plant growth and bio-controlling of pathogens. Much information reveals that the plant growth-promoting ability of individual PGPM affects plant growth. However, the effects of the PGPM consortia properties on plant growth remain largely unexplored. Here, we characterized three new PGPM strains including Rhodotorula graminis JJ10.1 (termed as J), Pseudomonas psychrotolerans YY7 (termed as Y) and P. chlororaphis T8 (termed as T), and assessed their effects in combination with Bacillus amyloliquefaciens FZB42 (termed as F) on plant growth promotion and disease prevention in Arabidopsis thaliana and tomato (Solanum lycopersicum) plants by investigating morphological changes, whole-genome sequencing and plant growth promoting (PGP) characterization. Results revealed that the three new strains R. graminis JJ10.1, P. psychrotolerans YY7 and P. chlororaphis T8 had the potential for being combined with B. amyloliquefaciens FZB42 to form interkingdom PGPM consortia. The combinations of R. graminis JJ10.1, B. amyloliquefaciens FZB42, and P. psychrotolerans YY7, i. e. JF and JYF, exhibited the strongest ability of synergetic biofilm production. Furthermore, the growth-promotion abilities of the consortia were significantly enhanced compared with those of individual strains under both inoculation and volatile organic compounds (VOCs) treatment. Importantly, the consortia showed stronger abilities of in planta disease prevention than individual strains. Findings of our study may provide future guidance for engineering the minimal microbiome communities to improve plant growth and/or disease resistance in sustainable agriculture.
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Affiliation(s)
- Yuan Tian
- Gansu Gaolan Field Scientific Observation and Research Station for Agricultural Ecosystem, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
- State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, 730000, People's Republic of China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yang Liu
- Gansu Gaolan Field Scientific Observation and Research Station for Agricultural Ecosystem, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Constantine Uwaremwe
- Gansu Gaolan Field Scientific Observation and Research Station for Agricultural Ecosystem, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Xia Zhao
- Gansu Gaolan Field Scientific Observation and Research Station for Agricultural Ecosystem, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Liang Yue
- Gansu Gaolan Field Scientific Observation and Research Station for Agricultural Ecosystem, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Qin Zhou
- Gansu Gaolan Field Scientific Observation and Research Station for Agricultural Ecosystem, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yun Wang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
| | - Lam-Son Phan Tran
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
| | - Weiqiang Li
- Jilin Da'an Agro-Ecosystem National Observation Research Station, Changchun Jingyuetan Remote Sensing Experiment Station, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Science, Changchun, 130102, People's Republic of China
| | - Gaofeng Chen
- Gansu Shangnong Biotechnology Co. Ltd, Baiyin, 730900, People's Republic of China
| | - Yuexia Sha
- Institute of Plant Protection, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, People's Republic of China
| | - Ruoyu Wang
- Gansu Gaolan Field Scientific Observation and Research Station for Agricultural Ecosystem, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China.
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
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Yuan J, Zhao K, Tan X, Xue R, Zeng Y, Ratti C, Trivedi P. Perspective on the development of synthetic microbial community (SynCom) biosensors. Trends Biotechnol 2023; 41:1227-1236. [PMID: 37183053 DOI: 10.1016/j.tibtech.2023.04.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 04/10/2023] [Accepted: 04/20/2023] [Indexed: 05/16/2023]
Abstract
Synthetic microbial community (SynCom) biosensors are a promising technology for detecting and responding to environmental cues and target molecules. SynCom biosensors use engineered microorganisms to create a more complex and diverse sensing system, enabling them to respond to stimuli with enhanced sensitivity and accuracy. Here, we give a definition of SynCom biosensors, outline their construction workflow, and discuss current biosensing technology. We also highlight the challenges and future for developing and optimizing SynCom biosensors and the potential applications in agriculture and food management, biotherapeutic development, home sensing, urban and environmental monitoring, and the One Health foundation. We believe SynCom biosensors could be used in a real-time and remote-controlled manner to sense the chaos of constantly dynamic environments.
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Affiliation(s)
- Jing Yuan
- Microbiome Network and Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80524, USA; Senseable City Lab, Department of Urban Studies and Planning, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Kankan Zhao
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiangfeng Tan
- Institute of Digital Agriculture, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, 310021, China
| | - Ran Xue
- Hangzhou Innovation Center, Zhejiang University, Hangzhou 311200, China
| | - Yuan Zeng
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA; Southern Piedmont Agricultural Research and Extension Center, Virginia Tech, Blackstone, VA 23824, USA
| | - Carlo Ratti
- Senseable City Lab, Department of Urban Studies and Planning, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Pankaj Trivedi
- Microbiome Network and Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80524, USA
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Mesny F, Hacquard S, Thomma BPHJ. Co-evolution within the plant holobiont drives host performance. EMBO Rep 2023; 24:e57455. [PMID: 37471099 PMCID: PMC10481671 DOI: 10.15252/embr.202357455] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/28/2023] [Accepted: 07/06/2023] [Indexed: 07/21/2023] Open
Abstract
Plants interact with a diversity of microorganisms that influence their growth and resilience, and they can therefore be considered as ecological entities, namely "plant holobionts," rather than as singular organisms. In a plant holobiont, the assembly of above- and belowground microbiota is ruled by host, microbial, and environmental factors. Upon microorganism perception, plants activate immune signaling resulting in the secretion of factors that modulate microbiota composition. Additionally, metabolic interdependencies and antagonism between microbes are driving forces for community assemblies. We argue that complex plant-microbe and intermicrobial interactions have been selected for during evolution and may promote the survival and fitness of plants and their associated microorganisms as holobionts. As part of this process, plants evolved metabolite-mediated strategies to selectively recruit beneficial microorganisms in their microbiota. Some of these microbiota members show host-adaptation, from which mutualism may rapidly arise. In the holobiont, microbiota members also co-evolved antagonistic activities that restrict proliferation of microbes with high pathogenic potential and can therefore prevent disease development. Co-evolution within holobionts thus ultimately drives plant performance.
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Affiliation(s)
- Fantin Mesny
- Institute for Plant SciencesUniversity of CologneCologneGermany
| | - Stéphane Hacquard
- Department of Plant Microbe InteractionsMax Planck Institute for Plant Breeding ResearchCologneGermany
- Cluster of Excellence on Plant Sciences (CEPLAS)CologneGermany
| | - Bart PHJ Thomma
- Institute for Plant SciencesUniversity of CologneCologneGermany
- Cluster of Excellence on Plant Sciences (CEPLAS)CologneGermany
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Cao Y, Du P, Zhang J, Ji J, Xu J, Liang B. Dopamine alleviates cadmium stress in apple trees by recruiting beneficial microorganisms to enhance the physiological resilience revealed by high-throughput sequencing and soil metabolomics. HORTICULTURE RESEARCH 2023; 10:uhad112. [PMID: 37577402 PMCID: PMC10419553 DOI: 10.1093/hr/uhad112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/16/2023] [Indexed: 08/15/2023]
Abstract
Dopamine has demonstrated promise as a stress-relief substance. However, the function of dopamine in Cd tolerance and its mechanism remains largely unknown. The current study was performed to investigate the mechanism of dopamine on alleviating apple Cd stress through regular application of CdCl2 and dopamine solution to potting soil. The results indicated that dopamine significantly reduced reactive oxygen species (ROS) and Cd accumulation and alleviated the inhibitory effect of Cd stress on the growth of apple plants through activation of the antioxidant system, enhancement of photosynthetic capacity, and regulation of gene expression related to Cd absorption and detoxification. The richness of the rhizosphere microbial community increased, and community composition and assembly were affected by dopamine treatment. Network analysis of microbial communities showed that the numbers of nodes and total links increased significantly after dopamine treatment, while the keystone species shifted. Linear discriminant analysis effect size indicated that some biomarkers were significantly enriched after dopamine treatment, suggesting that dopamine induced plants to recruit potentially beneficial microorganisms (Pseudoxanthomonas, Aeromicrobium, Bradyrhizobium, Frankia, Saccharimonadales, Novosphingobium, and Streptomyces) to resist Cd stress. The co-occurrence network showed several metabolites that were positively correlated with relative growth rate and negatively correlated with Cd accumulation, suggesting that potentially beneficial microorganisms may be attracted by several metabolites (L-threonic acid, profenamine, juniperic acid and (3β,5ξ,9ξ)-3,6,19-trihydroxyurs-12-en-28-oic acid). Our results demonstrate that dopamine alleviates Cd stress in apple trees by recruiting beneficial microorganisms to enhance the physiological resilience revealed. This study provides an effective means to reduce the harm to agricultural production caused by heavy metals.
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Affiliation(s)
- Yang Cao
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Peihua Du
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Jiran Zhang
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Jiahao Ji
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Jizhong Xu
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Bowen Liang
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
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23
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Poupin MJ, Ledger T, Roselló-Móra R, González B. The Arabidopsis holobiont: a (re)source of insights to understand the amazing world of plant-microbe interactions. ENVIRONMENTAL MICROBIOME 2023; 18:9. [PMID: 36803555 PMCID: PMC9938593 DOI: 10.1186/s40793-023-00466-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
As holobiont, a plant is intrinsically connected to its microbiomes. However, some characteristics of these microbiomes, such as their taxonomic composition, biological and evolutionary role, and especially the drivers that shape them, are not entirely elucidated. Reports on the microbiota of Arabidopsis thaliana first appeared more than ten years ago. However, there is still a lack of a comprehensive understanding of the vast amount of information that has been generated using this holobiont. The main goal of this review was to perform an in-depth, exhaustive, and systematic analysis of the literature regarding the Arabidopsis-microbiome interaction. A core microbiota was identified as composed of a few bacterial and non-bacterial taxa. The soil (and, to a lesser degree, air) were detected as primary microorganism sources. From the plant perspective, the species, ecotype, circadian cycle, developmental stage, environmental responses, and the exudation of metabolites were crucial factors shaping the plant-microbe interaction. From the microbial perspective, the microbe-microbe interactions, the type of microorganisms belonging to the microbiota (i.e., beneficial or detrimental), and the microbial metabolic responses were also key drivers. The underlying mechanisms are just beginning to be unveiled, but relevant future research needs were identified. Thus, this review provides valuable information and novel analyses that will shed light to deepen our understanding of this plant holobiont and its interaction with the environment.
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Affiliation(s)
- M J Poupin
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, 7941169, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
- Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile
| | - T Ledger
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, 7941169, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
- Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile
| | - R Roselló-Móra
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA UIB-CSIC), Illes Balears, Majorca, Spain
| | - B González
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, 7941169, Santiago, Chile.
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile.
- Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile.
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