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Ishizawa H, Tada M, Tashiro Y, Kuroda M, Inoue D, Dohra H, Futamata H, Ike M. Complete genome sequences of six duckweed-associated bacterial strains for studying community assembly in synthetic plant microbiome. Microbiol Resour Announc 2024; 13:e0128023. [PMID: 38426728 PMCID: PMC11008219 DOI: 10.1128/mra.01280-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 02/19/2024] [Indexed: 03/02/2024] Open
Abstract
We report the complete genome sequences of six bacterial strains isolated from a floating macrophyte, duckweed. These six strains, representing the six dominant families of the natural duckweed microbiome, establish a simple model ecosystem when inoculated onto sterilized duckweed. Their genomes would provide insights into community assembly in plant microbiome.
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Affiliation(s)
- Hidehiro Ishizawa
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Hyogo, Japan
- Division of Sustainable Energy and Environmental Engineering, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
- Research Institute of Green Science and Technology, Shizuoka University, Suruga-ku, Shizuoka, Japan
| | - Minami Tada
- Division of Sustainable Energy and Environmental Engineering, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
| | - Yosuke Tashiro
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Hamamatsu, Japan
- Graduate School of Science and Technology, Shizuoka University, Hamamatsu, Japan
| | - Masashi Kuroda
- Division of Sustainable Energy and Environmental Engineering, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
- Faculty of Social and Environmental Studies, Tokoha University, Shizuoka, Japan
| | - Daisuke Inoue
- Division of Sustainable Energy and Environmental Engineering, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
| | - Hideo Dohra
- Research Institute of Green Science and Technology, Shizuoka University, Suruga-ku, Shizuoka, Japan
- Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Hiroyuki Futamata
- Research Institute of Green Science and Technology, Shizuoka University, Suruga-ku, Shizuoka, Japan
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Hamamatsu, Japan
- Graduate School of Science and Technology, Shizuoka University, Hamamatsu, Japan
| | - Michihiko Ike
- Division of Sustainable Energy and Environmental Engineering, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
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Ishizawa H, Tashiro Y, Inoue D, Ike M, Futamata H. Learning beyond-pairwise interactions enables the bottom-up prediction of microbial community structure. Proc Natl Acad Sci U S A 2024; 121:e2312396121. [PMID: 38315845 PMCID: PMC10873592 DOI: 10.1073/pnas.2312396121] [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: 08/04/2023] [Accepted: 12/20/2023] [Indexed: 02/07/2024] Open
Abstract
Understanding the assembly of multispecies microbial communities represents a significant challenge in ecology and has wide applications in agriculture, wastewater treatment, and human healthcare domains. Traditionally, studies on the microbial community assembly focused on analyzing pairwise relationships among species; however, neglecting higher-order interactions, i.e., the change of pairwise relationships in the community context, may lead to substantial deviation from reality. Herein, we have proposed a simple framework that incorporates higher-order interactions into a bottom-up prediction of the microbial community assembly and examined its accuracy using a seven-member synthetic bacterial community on a host plant, duckweed. Although the synthetic community exhibited emergent properties that cannot be predicted from pairwise coculturing results, our results demonstrated that incorporating information from three-member combinations allows the acceptable prediction of the community structure and actual interaction forces within it. This reflects that the occurrence of higher-order effects follows consistent patterns, which can be predicted even from trio combinations, the smallest unit of higher-order interactions. These results highlight the possibility of predicting, explaining, and understanding the microbial community structure from the bottom-up by learning interspecies interactions from simple beyond-pairwise combinations.
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Affiliation(s)
- Hidehiro Ishizawa
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji671-2280, Japan
- Research Institute of Green Science and Technology, Shizuoka University, Hamamatsu432-8561, Japan
| | - Yosuke Tashiro
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Hamamatsu432-8561, Japan
- Graduate School of Science and Technology, Shizuoka University, Hamamatsu432-8561, Japan
| | - Daisuke Inoue
- Division of Sustainable Energy and Environmental Engineering, Graduate School of Engineering, Osaka University, Suita565-0821, Japan
| | - Michihiko Ike
- Division of Sustainable Energy and Environmental Engineering, Graduate School of Engineering, Osaka University, Suita565-0821, Japan
| | - Hiroyuki Futamata
- Research Institute of Green Science and Technology, Shizuoka University, Hamamatsu432-8561, Japan
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Hamamatsu432-8561, Japan
- Graduate School of Science and Technology, Shizuoka University, Hamamatsu432-8561, Japan
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Ziegler P, Appenroth KJ, Sree KS. Survival Strategies of Duckweeds, the World's Smallest Angiosperms. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12112215. [PMID: 37299193 DOI: 10.3390/plants12112215] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/26/2023] [Accepted: 05/31/2023] [Indexed: 06/12/2023]
Abstract
Duckweeds (Lemnaceae) are small, simply constructed aquatic higher plants that grow on or just below the surface of quiet waters. They consist primarily of leaf-like assimilatory organs, or fronds, that reproduce mainly by vegetative replication. Despite their diminutive size and inornate habit, duckweeds have been able to colonize and maintain themselves in almost all of the world's climate zones. They are thereby subject to multiple adverse influences during the growing season, such as high temperatures, extremes of light intensity and pH, nutrient shortage, damage by microorganisms and herbivores, the presence of harmful substances in the water, and competition from other aquatic plants, and they must also be able to withstand winter cold and drought that can be lethal to the fronds. This review discusses the means by which duckweeds come to grips with these adverse influences to ensure their survival. Important duckweed attributes in this regard are a pronounced potential for rapid growth and frond replication, a juvenile developmental status facilitating adventitious organ formation, and clonal diversity. Duckweeds have specific features at their disposal for coping with particular environmental difficulties and can also cooperate with other organisms of their surroundings to improve their survival chances.
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Affiliation(s)
- Paul Ziegler
- Department of Plant Physiology, University of Bayreuth, 95440 Bayreuth, Germany
| | - Klaus J Appenroth
- Matthias Schleiden Institute-Plant Physiology, University of Jena, 07743 Jena, Germany
| | - K Sowjanya Sree
- Department of Environmental Science, Central University of Kerala, Periye 671320, India
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Inoue D, Nakamura S, Sugiyama T, Ike M. Potential of Predatory Bacteria to Colonize the Duckweed Microbiome and Change Its Structure: A Model Study Using the Obligate Predatory Bacterium, Bacteriovorax sp. HI3. Microbes Environ 2023; 38:ME23040. [PMID: 37690850 PMCID: PMC10522839 DOI: 10.1264/jsme2.me23040] [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: 04/26/2023] [Accepted: 08/09/2023] [Indexed: 09/12/2023] Open
Abstract
Modifying the duckweed microbiome is a major challenge for enhancing the effectiveness of duckweed-based wastewater treatment and biomass production technologies. We herein examined the potential of the exogenous introduction of predatory bacteria to change the duckweed microbiome. Bacteriovorax sp. HI3, a model predatory bacterium, colonized the core of the Lemna microbiome, and its predatory behavior changed the microbiome structure, which correlated with colonization density. These results reveal that bacterial predatory interactions may be important drivers that shape the duckweed microbiome, suggesting their potential usefulness in modifying the microbiome.
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Affiliation(s)
- Daisuke Inoue
- Division of Sustainable Energy and Environmental Engineering, Osaka University, 2–1 Yamadaoka, Suita, Osaka 565–0871, Japan
| | - So Nakamura
- Division of Sustainable Energy and Environmental Engineering, Osaka University, 2–1 Yamadaoka, Suita, Osaka 565–0871, Japan
| | - Tomomi Sugiyama
- Division of Sustainable Energy and Environmental Engineering, Osaka University, 2–1 Yamadaoka, Suita, Osaka 565–0871, Japan
| | - Michihiko Ike
- Division of Sustainable Energy and Environmental Engineering, Osaka University, 2–1 Yamadaoka, Suita, Osaka 565–0871, Japan
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Gilbert S, Poulev A, Chrisler W, Acosta K, Orr G, Lebeis S, Lam E. Auxin-Producing Bacteria from Duckweeds Have Different Colonization Patterns and Effects on Plant Morphology. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11060721. [PMID: 35336603 PMCID: PMC8950272 DOI: 10.3390/plants11060721] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 01/30/2022] [Accepted: 02/20/2022] [Indexed: 05/30/2023]
Abstract
The role of auxin in plant-microbe interaction has primarily been studied using indole-3-acetic acid (IAA)-producing pathogenic or plant-growth-promoting bacteria. However, the IAA biosynthesis pathway in bacteria involves indole-related compounds (IRCs) and intermediates with less known functions. Here, we seek to understand changes in plant response to multiple plant-associated bacteria taxa and strains that differ in their ability to produce IRCs. We had previously studied 47 bacterial strains isolated from several duckweed species and determined that 79% of these strains produced IRCs in culture, such as IAA, indole lactic acid (ILA), and indole. Using Arabidopsis thaliana as our model plant with excellent genetic tools, we performed binary association assays on a subset of these strains to evaluate morphological responses in the plant host and the mode of bacterial colonization. Of the 21 tested strains, only four high-quantity IAA-producing Microbacterium strains caused an auxin root phenotype. Compared to the commonly used colorimetric Salkowski assay, auxin concentration determined by LC-MS was a superior indicator of a bacteria's ability to cause an auxin root phenotype. Studies with the auxin response mutant axr1-3 provided further genetic support for the role of auxin signaling in mediating the root morphology response to IAA-producing bacteria strains. Interestingly, our microscopy results also revealed new evidence for the role of the conserved AXR1 gene in endophytic colonization of IAA-producing Azospirillum baldaniorum Sp245 via the guard cells.
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Affiliation(s)
- Sarah Gilbert
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA; (S.G.); (A.P.); (K.A.)
| | - Alexander Poulev
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA; (S.G.); (A.P.); (K.A.)
| | - William Chrisler
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA; (W.C.); (G.O.)
| | - Kenneth Acosta
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA; (S.G.); (A.P.); (K.A.)
| | - Galya Orr
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA; (W.C.); (G.O.)
| | - Sarah Lebeis
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA;
| | - Eric Lam
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA; (S.G.); (A.P.); (K.A.)
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Genome-wide identification of bacterial colonization and fitness determinants on the floating macrophyte, duckweed. Commun Biol 2022; 5:68. [PMID: 35046504 PMCID: PMC8770550 DOI: 10.1038/s42003-022-03014-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 12/23/2021] [Indexed: 11/08/2022] Open
Abstract
AbstractBacterial communities associated with aquatic macrophytes largely influence host primary production and nutrient cycling in freshwater environments; however, little is known about how specific bacteria migrate to and proliferate at this unique habitat. Here, we separately identified bacterial genes involved in the initial colonization and overall fitness on plant surface, using the genome-wide transposon sequencing (Tn-seq) of Aquitalea magnusonii H3, a plant growth-promoting bacterium of the floating macrophyte, duckweed. Functional annotation of identified genes indicated that initial colonization efficiency might be simply explained by motility and cell surface structure, while overall fitness was associated with diverse metabolic and regulatory functions. Genes involved in lipopolysaccharides and type-IV pili biosynthesis showed different contributions to colonization and fitness, reflecting their metabolic cost and profound roles in host association. These results provide a comprehensive genetic perspective on aquatic-plant-bacterial interactions, and highlight the potential trade-off between bacterial colonization and proliferation abilities on plant surface.
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Beck AE, Kleiner M, Garrell AK. Elucidating Plant-Microbe-Environment Interactions Through Omics-Enabled Metabolic Modelling Using Synthetic Communities. FRONTIERS IN PLANT SCIENCE 2022; 13:910377. [PMID: 35795346 PMCID: PMC9251461 DOI: 10.3389/fpls.2022.910377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/16/2022] [Indexed: 05/10/2023]
Abstract
With a growing world population and increasing frequency of climate disturbance events, we are in dire need of methods to improve plant productivity, resilience, and resistance to both abiotic and biotic stressors, both for agriculture and conservation efforts. Microorganisms play an essential role in supporting plant growth, environmental response, and susceptibility to disease. However, understanding the specific mechanisms by which microbes interact with each other and with plants to influence plant phenotypes is a major challenge due to the complexity of natural communities, simultaneous competition and cooperation effects, signalling interactions, and environmental impacts. Synthetic communities are a major asset in reducing the complexity of these systems by simplifying to dominant components and isolating specific variables for controlled experiments, yet there still remains a large gap in our understanding of plant microbiome interactions. This perspectives article presents a brief review discussing ways in which metabolic modelling can be used in combination with synthetic communities to continue progress toward understanding the complexity of plant-microbe-environment interactions. We highlight the utility of metabolic models as applied to a community setting, identify different applications for both flux balance and elementary flux mode simulation approaches, emphasize the importance of ecological theory in guiding data interpretation, and provide ideas for how the integration of metabolic modelling techniques with big data may bridge the gap between simplified synthetic communities and the complexity of natural plant-microbe systems.
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Affiliation(s)
- Ashley E. Beck
- Department of Biological and Environmental Sciences, Carroll College, Helena, MT, United States
- *Correspondence: Ashley E. Beck,
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Anna-Katharina Garrell
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
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