1
|
Chodkowski JL, Shade A. Bioactive exometabolites drive maintenance competition in simple bacterial communities. mSystems 2024; 9:e0006424. [PMID: 38470039 PMCID: PMC11019792 DOI: 10.1128/msystems.00064-24] [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: 01/18/2024] [Accepted: 02/19/2024] [Indexed: 03/13/2024] Open
Abstract
During prolonged resource limitation, bacterial cells can persist in metabolically active states of non-growth. These maintenance periods, such as those experienced in stationary phase, can include upregulation of secondary metabolism and release of exometabolites into the local environment. As resource limitation is common in many environmental microbial habitats, we hypothesized that neighboring bacterial populations employ exometabolites to compete or cooperate during maintenance and that these exometabolite-facilitated interactions can drive community outcomes. Here, we evaluated the consequences of exometabolite interactions over the stationary phase among three environmental strains: Burkholderia thailandensis E264, Chromobacterium subtsugae ATCC 31532, and Pseudomonas syringae pv. tomato DC3000. We assembled them into synthetic communities that only permitted chemical interactions. We compared the responses (transcripts) and outputs (exometabolites) of each member with and without neighbors. We found that transcriptional dynamics were changed with different neighbors and that some of these changes were coordinated between members. The dominant competitor B. thailandensis consistently upregulated biosynthetic gene clusters to produce bioactive exometabolites for both exploitative and interference competition. These results demonstrate that competition strategies during maintenance can contribute to community-level outcomes. It also suggests that the traditional concept of defining competitiveness by growth outcomes may be narrow and that maintenance competition could be an additional or alternative measure. IMPORTANCE Free-living microbial populations often persist and engage in environments that offer few or inconsistently available resources. Thus, it is important to investigate microbial interactions in this common and ecologically relevant condition of non-growth. This work investigates the consequences of resource limitation for community metabolic output and for population interactions in simple synthetic bacterial communities. Despite non-growth, we observed active, exometabolite-mediated competition among the bacterial populations. Many of these interactions and produced exometabolites were dependent on the community composition but we also observed that one dominant competitor consistently produced interfering exometabolites regardless. These results are important for predicting and understanding microbial interactions in resource-limited environments.
Collapse
Affiliation(s)
- John L. Chodkowski
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Ashley Shade
- Universite Claude Bernard Lyon 1, Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, Villeurbanne, France
| |
Collapse
|
2
|
Parnell JJ, Vintila S, Tang C, Wagner MR, Kleiner M. Evaluation of ready-to-use freezer stocks of a synthetic microbial community for maize root colonization. Microbiol Spectr 2024; 12:e0240123. [PMID: 38084978 PMCID: PMC10783020 DOI: 10.1128/spectrum.02401-23] [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: 06/07/2023] [Accepted: 11/06/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE Synthetic communities (SynComs) are an invaluable tool to characterize and model plant-microbe interactions. Multimember SynComs approximate intricate real-world interactions between plants and their microbiome, but the complexity and time required for their construction increase enormously for each additional member added to the SynCom. Therefore, researchers who study a diversity of microbiomes using SynComs are looking for ways to simplify the use of SynComs. In this manuscript, we evaluate the feasibility of creating ready-to-use freezer stocks of a well-studied seven-member SynCom for maize roots. The frozen ready-to-use SynCom stocks work according to the principle of "just add buffer and apply to sterilized seeds or seedlings" and thus can save time applied in multiple days of laborious growing and combining of multiple microorganisms. We show that ready-to-use SynCom stocks provide comparable results to those of freshly constructed SynComs and thus allow for significant time savings when working with SynComs.
Collapse
Affiliation(s)
- J. Jacob Parnell
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Simina Vintila
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Clara Tang
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Maggie R. Wagner
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
- Kansas Biological Survey & Center for Ecological Research, University of Kansas, Lawrence, Kansas, USA
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| |
Collapse
|
3
|
Frascella A, Sarrocco S, Jona Lasinio G, Pollice A, Emiliani G, Danti R, Barberini S, Della Rocca G. Characterization of Trichoderma species from forest ecosystems by high-throughput phenotypic microarray. Fungal Biol 2023; 127:1376-1383. [PMID: 37993248 DOI: 10.1016/j.funbio.2023.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/18/2023] [Accepted: 09/21/2023] [Indexed: 11/24/2023]
Abstract
The use of beneficial organisms for the biocontrol of soil-borne pathogens in forestry is still poor explored. In this work, the nutritional demands of 10 previously selected isolates of Trichoderma for the biocontrol of forest soil-borne pathogens have been tested by Phenotype Microarray technology, to investigate about their C-source utilization and exploring the possibility to obtain a microbial consortia (SynCom), an innovative strategy for the biocontrol of plant disease. All Trichoderma isolates tested in this study showed a high spore germination percentage within 3 d and evidenced nutritional preference regardless of the species they belong to, and unrelated to their soil of origin. Results of growth curve analysis and MANOVA test revealed that all isolates assimilate a broad range of substrates, generally preferring complex compounds such as monosaccharides related compounds, nitrogen compounds, carboxylic acids and esters. No evidence of competition for nutritional resources have been observed among isolates of this study. As a result, a combination of different isolates could be proposed to obtain a SynCom useful for the practice of phytopathogen biocontrol in forestry. The addition of i-erythritol, adenosine and turanose to a growth substrate could be suggested as stimulating compounds for the growth of the selected Trichoderma isolates.
Collapse
Affiliation(s)
- Arcangela Frascella
- Institute of BioEconomy, National Research Council, Via Madonna Del Piano, 10, Sesto Fiorentino (Florence) 50019, Italy
| | - Sabrina Sarrocco
- Department of Agriculture, Food and Environment, University of Pisa, Via Del Borghetto 80, Pisa 50124, Italy.
| | - Giovanna Jona Lasinio
- Department of Statistical Sciences, University of Rome "Sapienza", Piazzale Aldo Moro 5, Rome, Italy
| | - Alessio Pollice
- Department of Economics and Finance, University of Bari Aldo Moro, Largo Abbazia Santa Scolastica, Bari, Italy
| | - Giovanni Emiliani
- Institute of Sustainable Plant Protection, National Research Council, Via Madonna Del Piano, 10, Sesto Fiorentino (Florence) 50019, Italy
| | - Roberto Danti
- Institute of Sustainable Plant Protection, National Research Council, Via Madonna Del Piano, 10, Sesto Fiorentino (Florence) 50019, Italy
| | - Sara Barberini
- Institute of Sustainable Plant Protection, National Research Council, Via Madonna Del Piano, 10, Sesto Fiorentino (Florence) 50019, Italy
| | - Gianni Della Rocca
- Institute of Sustainable Plant Protection, National Research Council, Via Madonna Del Piano, 10, Sesto Fiorentino (Florence) 50019, Italy
| |
Collapse
|
4
|
Flores-Duarte NJ, Navarro-Torre S, Mateos-Naranjo E, Redondo-Gómez S, Pajuelo E, Rodríguez-Llorente ID. Nodule Synthetic Bacterial Community as Legume Biofertilizer under Abiotic Stress in Estuarine Soils. Plants (Basel) 2023; 12:plants12112083. [PMID: 37299063 DOI: 10.3390/plants12112083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/17/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023]
Abstract
Estuaries are ecologically important ecosystems particularly affected by climate change and human activities. Our interest is focused on the use of legumes to fight against the degradation of estuarine soils and loss of fertility under adverse conditions. This work was aimed to determine the potential of a nodule synthetic bacterial community (SynCom), including two Ensifer sp. and two Pseudomonas sp. strains isolated from Medicago spp. nodules, to promote M. sativa growth and nodulation in degraded estuarine soils under several abiotic stresses, including high metal contamination, salinity, drought and high temperature. These plant growth promoting (PGP) endophytes were able to maintain and even increase their PGP properties in the presence of metals. Inoculation with the SynCom in pots containing soil enhanced plant growth parameters (from 3- to 12-fold increase in dry weight), nodulation (from 1.5- to 3-fold increase in nodules number), photosynthesis and nitrogen content (up to 4-fold under metal stress) under all the controlled conditions tested. The increase in plant antioxidant enzymatic activities seems to be a common and important mechanism of plant protection induced by the SynCom under abiotic stress conditions. The SynCom increased M. sativa metals accumulation in roots, with low levels of metals translocation to shoots. Results indicated that the SynCom used in this work is an appropriate ecological and safe tool to improve Medicago growth and adaptation to degraded estuarine soils under climate change conditions.
Collapse
Affiliation(s)
- Noris J Flores-Duarte
- Departamento de Microbiología y Parasitología, Universidad de Sevilla, 41012 Seville, Spain
| | | | - Enrique Mateos-Naranjo
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, 41012 Seville, Spain
| | - Susana Redondo-Gómez
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, 41012 Seville, Spain
| | - Eloísa Pajuelo
- Departamento de Microbiología y Parasitología, Universidad de Sevilla, 41012 Seville, Spain
| | | |
Collapse
|
5
|
Singha LP, Shukla P. Microbiome engineering for bioremediation of emerging pollutants. Bioprocess Biosyst Eng 2023; 46:323-39. [PMID: 36029349 DOI: 10.1007/s00449-022-02777-x] [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: 06/12/2022] [Accepted: 08/12/2022] [Indexed: 11/02/2022]
Abstract
Axenic microbial applications in the open environment are unrealistic and may not be always practically viable. Therefore, it is important to use mixed microbial cultures and their interactions with the microbiome in the targeted ecosystem to perform robust functions towards their sustainability in harsh environmental conditions. Emerging pollutants like phthalates and hydrocarbons that are toxic to several aquatic and terrestrial life forms in the water bodies and lands are an alarming situation. The present review explores the possibility of devising an inclusive eco-friendly strategy like microbiome engineering which proves to be a unique and crucial technology involving the power of microbial communication through quorum sensing. This review discusses the interspecies and intra-species communications between different microbial groups with their respective environments. Moreover, this review also envisages the efforts for designing the next level of microbiome-host engineering concept (MHEC). The focus of the review also extended toward using omics and metabolic network analysis-based tools for effective microbiome engineering. These approaches might be quite helpful in the future to understand such microbial interactions but it will be challenging to implement in the real environment to get the desired functions. Finally, the review also discusses multiple approaches for the bioremediation of toxic chemicals from the soil environment.
Collapse
|
6
|
Armanhi JSL, de Souza RSC, Biazotti BB, Yassitepe JEDCT, Arruda P. Modulating Drought Stress Response of Maize by a Synthetic Bacterial Community. Front Microbiol 2021; 12:747541. [PMID: 34745050 PMCID: PMC8566980 DOI: 10.3389/fmicb.2021.747541] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 07/26/2021] [Accepted: 09/20/2021] [Indexed: 01/21/2023] Open
Abstract
Plant perception and responses to environmental stresses are known to encompass a complex set of mechanisms in which the microbiome is involved. Knowledge about plant physiological responses is therefore critical for understanding the contribution of the microbiome to plant resilience. However, as plant growth is a dynamic process, a major hurdle is to find appropriate tools to effectively measure temporal variations of different plant physiological parameters. Here, we used a non-invasive real-time phenotyping platform in a one-to-one (plant–sensors) set up to investigate the impact of a synthetic community (SynCom) harboring plant-beneficial bacteria on the physiology and response of three commercial maize hybrids to drought stress (DS). SynCom inoculation significantly reduced yield loss and modulated vital physiological traits. SynCom-inoculated plants displayed lower leaf temperature, reduced turgor loss under severe DS and a faster recovery upon rehydration, likely as a result of sap flow modulation and better water usage. Microbiome profiling revealed that SynCom bacterial members were able to robustly colonize mature plants and recruit soil/seed-borne beneficial microbes. The high-resolution temporal data allowed us to record instant plant responses to daily environmental fluctuations, thus revealing the impact of the microbiome in modulating maize physiology, resilience to drought, and crop productivity.
Collapse
Affiliation(s)
- Jaderson Silveira Leite Armanhi
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil.,Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Rafael Soares Correa de Souza
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil.,Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Bárbara Bort Biazotti
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil.,Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil.,Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | | | - Paulo Arruda
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil.,Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil.,Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| |
Collapse
|
7
|
Minchev Z, Kostenko O, Soler R, Pozo MJ. Microbial Consortia for Effective Biocontrol of Root and Foliar Diseases in Tomato. Front Plant Sci 2021; 12:756368. [PMID: 34804094 PMCID: PMC8602810 DOI: 10.3389/fpls.2021.756368] [Citation(s) in RCA: 15] [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: 08/10/2021] [Accepted: 10/04/2021] [Indexed: 05/26/2023]
Abstract
The use of beneficial microorganisms for the biological control of plant diseases and pests has emerged as a viable alternative to chemical pesticides in agriculture. Traditionally, microbe-based biocontrol strategies for crop protection relied on the application of single microorganisms. However, the design of microbial consortia for improving the reliability of current biological control practices is now a major trend in biotechnology, and it is already being exploited commercially in the context of sustainable agriculture. In the present study, exploiting the microbial library of the biocontrol company Koppert Biological Systems, we designed microbial consortia composed of carefully selected, well-characterized beneficial bacteria and fungi displaying diverse biocontrol modes of action. We compared their ability to control shoot and root pathogens when applied separately or in combination as microbial consortia, and across different application strategies that imply direct microbial antagonism or induced systemic plant resistance. We hypothesized that consortia will be more versatile than the single strains, displaying an extended functionality, as they will be able to control a wider range of plant diseases through diverse mechanisms and application methods. Our results confirmed our hypothesis, revealing that while different individual microorganisms were the most effective in controlling the root pathogen Fusarium oxysporum or the foliar pathogen Botrytis cinerea in tomato, the consortia showed an extended functionality, effectively controlling both pathogens under any of the application schemes, always reaching the same protection levels as the best performing single strains. Our findings illustrate the potential of microbial consortia, composed of carefully selected and compatible beneficial microorganisms, including bacteria and fungi, for the development of stable and versatile biological control products for plant protection against a wider range of diseases.
Collapse
Affiliation(s)
- Zhivko Minchev
- Business Unit Microbiology, Agronomical Development Department, Koppert Biological Systems, Berkel en Rodenrijs, Netherlands
| | - Olga Kostenko
- Business Unit Microbiology, Agronomical Development Department, Koppert Biological Systems, Berkel en Rodenrijs, Netherlands
| | - Roxina Soler
- Business Unit Microbiology, Agronomical Development Department, Koppert Biological Systems, Berkel en Rodenrijs, Netherlands
| | - María J. Pozo
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, CSIC, Granada, Spain
| |
Collapse
|
8
|
You C, Qin D, Wang Y, Lan W, Li Y, Yu B, Peng Y, Xu J, Dong J. Plant Triterpenoids Regulate Endophyte Community to Promote Medicinal Plant Schisandra sphenanthera Growth and Metabolites Accumulation. J Fungi (Basel) 2021; 7:jof7100788. [PMID: 34682210 PMCID: PMC8539763 DOI: 10.3390/jof7100788] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 09/14/2021] [Accepted: 09/16/2021] [Indexed: 11/16/2022] Open
Abstract
Beneficial interactions between endophytes and plants are critical for plant growth and metabolite accumulation. Nevertheless, the secondary metabolites controlling the feedback between the host plant and the endophytic microbial community remain elusive in medicinal plants. In this report, we demonstrate that plant-derived triterpenoids predominantly promote the growth of endophytic bacteria and fungi, which in turn promote host plant growth and secondary metabolite productions. From culturable bacterial and fungal microbial strains isolated from the medicinal plant Schisandra sphenanthera, through triterpenoid-mediated screens, we constructed six synthetic communities (SynComs). By using a binary interaction method in plates, we revealed that triterpenoid-promoted bacterial and fungal strains (TPB and TPF) played more positive roles in the microbial community. The functional screening of representative strains suggested that TPB and TPF provide more beneficial abilities to the host. Moreover, pot experiments in a sterilized system further demonstrated that TPB and TPF play important roles in host growth and metabolite accumulation. In summary, these experiments revealed a role of triterpenoids in endophytic microbiome assembly and indicated a strategy for constructing SynComs on the basis of the screening of secondary metabolites, in which bacteria and fungi join forces to promote plant health. These findings may open new avenues towards the breeding of high yielding and high metabolite-accumulating medicinal plants by exploiting their interaction with beneficial endophytes.
Collapse
Affiliation(s)
- Chuan You
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing 400715, China; (C.Y.); (D.Q.); (Y.W.); (W.L.); (Y.L.); (B.Y.); (Y.P.); (J.X.)
| | - Dan Qin
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing 400715, China; (C.Y.); (D.Q.); (Y.W.); (W.L.); (Y.L.); (B.Y.); (Y.P.); (J.X.)
- Key Scientific Research Base of Pest and Mold Control of Heritage Collection (Chongqing China Three Gorges Museum), State Administration of Cultural Heritage, Chongqing 400015, China
| | - Yumeng Wang
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing 400715, China; (C.Y.); (D.Q.); (Y.W.); (W.L.); (Y.L.); (B.Y.); (Y.P.); (J.X.)
| | - Wenyi Lan
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing 400715, China; (C.Y.); (D.Q.); (Y.W.); (W.L.); (Y.L.); (B.Y.); (Y.P.); (J.X.)
| | - Yehong Li
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing 400715, China; (C.Y.); (D.Q.); (Y.W.); (W.L.); (Y.L.); (B.Y.); (Y.P.); (J.X.)
| | - Baohong Yu
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing 400715, China; (C.Y.); (D.Q.); (Y.W.); (W.L.); (Y.L.); (B.Y.); (Y.P.); (J.X.)
| | - Yajun Peng
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing 400715, China; (C.Y.); (D.Q.); (Y.W.); (W.L.); (Y.L.); (B.Y.); (Y.P.); (J.X.)
| | - Jieru Xu
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing 400715, China; (C.Y.); (D.Q.); (Y.W.); (W.L.); (Y.L.); (B.Y.); (Y.P.); (J.X.)
| | - Jinyan Dong
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing 400715, China; (C.Y.); (D.Q.); (Y.W.); (W.L.); (Y.L.); (B.Y.); (Y.P.); (J.X.)
- Correspondence:
| |
Collapse
|
9
|
Wang C, Li Y, Li M, Zhang K, Ma W, Zheng L, Xu H, Cui B, Liu R, Yang Y, Zhong Y, Liao H. Functional assembly of root-associated microbial consortia improves nutrient efficiency and yield in soybean. J Integr Plant Biol 2021; 63:1021-1035. [PMID: 33491865 DOI: 10.1111/jipb.13073] [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: 12/18/2020] [Accepted: 01/20/2021] [Indexed: 06/12/2023]
Abstract
Root-associated microbes are critical for plant growth and nutrient acquisition. However, scant information exists on optimizing communities of beneficial root-associated microbes or the mechanisms underlying their interactions with host plants. In this report, we demonstrate that root-associated microbes are critical influencers of host plant growth and nutrient acquisition. Three synthetic communities (SynComs) were constructed based on functional screening of 1,893 microbial strains isolated from root-associated compartments of soybean plants. Functional assemblage of SynComs promoted significant plant growth and nutrient acquisition under both N/P nutrient deficiency and sufficiency conditions. Field trials further revealed that application of SynComs stably and significantly promoted plant growth, facilitated N and P acquisition, and subsequently increased soybean yield. Among the tested communities, SynCom1 exhibited the greatest promotion effect, with yield increases of up to 36.1% observed in two field sites. Further RNA-seq implied that SynCom application systemically regulates N and P signaling networks at the transcriptional level, which leads to increased representation of important growth pathways, especially those related to auxin responses. Overall, this study details a promising strategy for constructing SynComs based on functional screening, which are capable of enhancing nutrient acquisition and crop yield through the activities of beneficial root-associated microbes.
Collapse
Affiliation(s)
- Cunhu Wang
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yanjun Li
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Mingjia Li
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Kefei Zhang
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wenjing Ma
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lei Zheng
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hanyu Xu
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Baofeng Cui
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ran Liu
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yongqing Yang
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yongjia Zhong
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hong Liao
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| |
Collapse
|
10
|
Ishizawa H, Tada M, Kuroda M, Inoue D, Futamata H, Ike M. Synthetic Bacterial Community of Duckweed: A Simple and Stable System to Study Plant-microbe Interactions. Microbes Environ 2021; 35. [PMID: 33268659 PMCID: PMC7734406 DOI: 10.1264/jsme2.me20112] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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] [Indexed: 01/04/2023] Open
Abstract
A complete understanding of the plant microbiome has not yet been achieved due to its complexity and temporal shifts in the community structure. To overcome these issues, we created a synthetic bacterial community of the aquatic plant, duckweed. The synthetic community established with six bacterial strains showed a stable composition for 50 days, which may have been because duckweed maintains a similar physiological status through its clonal reproduction. Additionally, the synthetic community reflected the taxonomic structure of the natural duckweed microbiome at the family level. These results suggest the potential of a duckweed-based synthetic community as a useful model system for examining the community assembly mechanisms of the plant microbiome.
Collapse
Affiliation(s)
- Hidehiro Ishizawa
- Division of Sustainable Energy and Environmental Engineering, Graduate School of Engineering, Osaka University.,Research Institute of Green Science and Technology, Shizuoka University
| | - Minami Tada
- Division of Sustainable Energy and Environmental Engineering, Graduate School of Engineering, Osaka University
| | - Masashi Kuroda
- Division of Sustainable Energy and Environmental Engineering, Graduate School of Engineering, Osaka University.,Faculty of Social and Environmental Studies, Tokoha University
| | - Daisuke Inoue
- Division of Sustainable Energy and Environmental Engineering, Graduate School of Engineering, Osaka University
| | - Hiroyuki Futamata
- Research Institute of Green Science and Technology, Shizuoka University
| | - Michihiko Ike
- Division of Sustainable Energy and Environmental Engineering, Graduate School of Engineering, Osaka University
| |
Collapse
|
11
|
Teixeira PJPL, Colaianni NR, Law TF, Conway JM, Gilbert S, Li H, Salas-González I, Panda D, Del Risco NM, Finkel OM, Castrillo G, Mieczkowski P, Jones CD, Dangl JL. Specific modulation of the root immune system by a community of commensal bacteria. Proc Natl Acad Sci U S A 2021; 118:e2100678118. [PMID: 33879573 PMCID: PMC8072228 DOI: 10.1073/pnas.2100678118] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [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] [Indexed: 12/22/2022] Open
Abstract
Plants have an innate immune system to fight off potential invaders that is based on the perception of nonself or modified-self molecules. Microbe-associated molecular patterns (MAMPs) are evolutionarily conserved microbial molecules whose extracellular detection by specific cell surface receptors initiates an array of biochemical responses collectively known as MAMP-triggered immunity (MTI). Well-characterized MAMPs include chitin, peptidoglycan, and flg22, a 22-amino acid epitope found in the major building block of the bacterial flagellum, FliC. The importance of MAMP detection by the plant immune system is underscored by the large diversity of strategies used by pathogens to interfere with MTI and that failure to do so is often associated with loss of virulence. Yet, whether or how MTI functions beyond pathogenic interactions is not well understood. Here we demonstrate that a community of root commensal bacteria modulates a specific and evolutionarily conserved sector of the Arabidopsis immune system. We identify a set of robust, taxonomically diverse MTI suppressor strains that are efficient root colonizers and, notably, can enhance the colonization capacity of other tested commensal bacteria. We highlight the importance of extracellular strategies for MTI suppression by showing that the type 2, not the type 3, secretion system is required for the immunomodulatory activity of one robust MTI suppressor. Our findings reveal that root colonization by commensals is controlled by MTI, which, in turn, can be selectively modulated by specific members of a representative bacterial root microbiota.
Collapse
Affiliation(s)
- Paulo J P L Teixeira
- HHMI, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Nicholas R Colaianni
- HHMI, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Theresa F Law
- HHMI, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Jonathan M Conway
- HHMI, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Sarah Gilbert
- HHMI, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Haofan Li
- Department of Biology, Kenyon College, Gambier, OH 43022
| | - Isai Salas-González
- HHMI, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Darshana Panda
- HHMI, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Nicole M Del Risco
- HHMI, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Omri M Finkel
- HHMI, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Gabriel Castrillo
- HHMI, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Piotr Mieczkowski
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Corbin D Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Jeffery L Dangl
- HHMI, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599;
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| |
Collapse
|
12
|
Pang Z, Chen J, Wang T, Gao C, Li Z, Guo L, Xu J, Cheng Y. Linking Plant Secondary Metabolites and Plant Microbiomes: A Review. Front Plant Sci 2021; 12:621276. [PMID: 33737943 PMCID: PMC7961088 DOI: 10.3389/fpls.2021.621276] [Citation(s) in RCA: 172] [Impact Index Per Article: 57.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 02/08/2021] [Indexed: 05/09/2023]
Abstract
Plant secondary metabolites (PSMs) play many roles including defense against pathogens, pests, and herbivores; response to environmental stresses, and mediating organismal interactions. Similarly, plant microbiomes participate in many of the above-mentioned processes directly or indirectly by regulating plant metabolism. Studies have shown that plants can influence their microbiome by secreting various metabolites and, in turn, the microbiome may also impact the metabolome of the host plant. However, not much is known about the communications between the interacting partners to impact their phenotypic changes. In this article, we review the patterns and potential underlying mechanisms of interactions between PSMs and plant microbiomes. We describe the recent developments in analytical approaches and methods in this field. The applications of these new methods and approaches have increased our understanding of the relationships between PSMs and plant microbiomes. Though the current studies have primarily focused on model organisms, the methods and results obtained so far should help future studies of agriculturally important plants and facilitate the development of methods to manipulate PSMs-microbiome interactions with predictive outcomes for sustainable crop productions.
Collapse
Affiliation(s)
- Zhiqiang Pang
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jia Chen
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Tuhong Wang
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Chunsheng Gao
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Zhimin Li
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Litao Guo
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Jianping Xu
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Yi Cheng
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| |
Collapse
|
13
|
Marín O, González B, Poupin MJ. From Microbial Dynamics to Functionality in the Rhizosphere: A Systematic Review of the Opportunities With Synthetic Microbial Communities. Front Plant Sci 2021; 12:650609. [PMID: 34149752 PMCID: PMC8210828 DOI: 10.3389/fpls.2021.650609] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 04/15/2021] [Indexed: 05/07/2023]
Abstract
Synthetic microbial communities (SynComs) are a useful tool for a more realistic understanding of the outcomes of multiple biotic interactions where microbes, plants, and the environment are players in time and space of a multidimensional and complex system. Toward a more in-depth overview of the knowledge that has been achieved using SynComs in the rhizosphere, a systematic review of the literature on SynComs was performed to identify the overall rationale, design criteria, experimental procedures, and outcomes of in vitro or in planta tests using this strategy. After an extensive bibliography search and a specific selection process, a total of 30 articles were chosen for further analysis, grouping them by their reported SynCom size. The reported SynComs were constituted with a highly variable number of members, ranging from 3 to 190 strains, with a total of 1,393 bacterial isolates, where the three most represented phyla were Proteobacteria, Actinobacteria, and Firmicutes. Only four articles did not reference experiments with SynCom on plants, as they considered only microbial in vitro studies, whereas the others chose different plant models and plant-growth systems; some of them are described and reviewed in this article. Besides, a discussion on different approaches (bottom-up and top-down) to study the microbiome role in the rhizosphere is provided, highlighting how SynComs are an effective system to connect and fill some knowledge gaps and to have a better understanding of the mechanisms governing these multiple interactions. Although the SynCom approach is already helpful and has a promising future, more systematic and standardized studies are needed to harness its full potential.
Collapse
Affiliation(s)
- Olga Marín
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
| | - Bernardo González
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
| | - María Josefina Poupin
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
- *Correspondence: María Josefina Poupin
| |
Collapse
|