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Song HS, Lee NR, Kessell AK, McCullough HC, Park SY, Zhou K, Lee DY. Kinetics-based inference of environment-dependent microbial interactions and their dynamic variation. mSystems 2024; 9:e0130523. [PMID: 38682902 PMCID: PMC11097648 DOI: 10.1128/msystems.01305-23] [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: 12/05/2023] [Accepted: 03/28/2024] [Indexed: 05/01/2024] Open
Abstract
Microbial communities in nature are dynamically evolving as member species change their interactions subject to environmental variations. Accounting for such context-dependent dynamic variations in interspecies interactions is critical for predictive ecological modeling. In the absence of generalizable theoretical foundations, we lack a fundamental understanding of how microbial interactions are driven by environmental factors, significantly limiting our capability to predict and engineer community dynamics and function. To address this issue, we propose a novel theoretical framework that allows us to represent interspecies interactions as an explicit function of environmental variables (such as substrate concentrations) by combining growth kinetics and a generalized Lotka-Volterra model. A synergistic integration of these two complementary models leads to the prediction of alterations in interspecies interactions as the outcome of dynamic balances between positive and negative influences of microbial species in mixed relationships. The effectiveness of our method was experimentally demonstrated using a synthetic consortium of two Escherichia coli mutants that are metabolically dependent (due to an inability to synthesize essential amino acids) but competitively grow on a shared substrate. The analysis of the E. coli binary consortium using our model not only showed how interactions between the two amino acid auxotrophic mutants are controlled by the dynamic shifts in limiting substrates but also enabled quantifying previously uncharacterizable complex aspects of microbial interactions, such as asymmetry in interactions. Our approach can be extended to other ecological systems to model their environment-dependent interspecies interactions from growth kinetics.IMPORTANCEModeling environment-controlled interspecies interactions through separate identification of positive and negative influences of microbes in mixed relationships is a new capability that can significantly improve our ability to understand, predict, and engineer the complex dynamics of microbial communities. Moreover, the prediction of microbial interactions as a function of environmental variables can serve as valuable benchmark data to validate modeling and network inference tools in microbial ecology, the development of which has often been impeded due to the lack of ground truth information on interactions. While demonstrated against microbial data, the theory developed in this work is readily applicable to general community ecology to predict interactions among macroorganisms, such as plants and animals, as well as microorganisms.
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Affiliation(s)
- Hyun-Seob Song
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Food Science and Technology, Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Na-Rae Lee
- Research Institute for Bioactive-Metabolome Network, Konkuk University, Seoul, South Korea
| | - Aimee K. Kessell
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Hugh C. McCullough
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Seo-Young Park
- School of Chemical Engineering, Sungkyunkwan University, Suwon-si, Gyeonggi-do, South Korea
| | - Kang Zhou
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, Singapore
| | - Dong-Yup Lee
- School of Chemical Engineering, Sungkyunkwan University, Suwon-si, Gyeonggi-do, South Korea
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2
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Berruto CA, Demirer GS. Engineering agricultural soil microbiomes and predicting plant phenotypes. Trends Microbiol 2024:S0966-842X(24)00043-X. [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] [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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3
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Kimotho RN, Maina S. Unraveling plant-microbe interactions: can integrated omics approaches offer concrete answers? JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1289-1313. [PMID: 37950741 PMCID: PMC10901211 DOI: 10.1093/jxb/erad448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 11/08/2023] [Indexed: 11/13/2023]
Abstract
Advances in high throughput omics techniques provide avenues to decipher plant microbiomes. However, there is limited information on how integrated informatics can help provide deeper insights into plant-microbe interactions in a concerted way. Integrating multi-omics datasets can transform our understanding of the plant microbiome from unspecified genetic influences on interacting species to specific gene-by-gene interactions. Here, we highlight recent progress and emerging strategies in crop microbiome omics research and review key aspects of how the integration of host and microbial omics-based datasets can be used to provide a comprehensive outline of complex crop-microbe interactions. We describe how these technological advances have helped unravel crucial plant and microbial genes and pathways that control beneficial, pathogenic, and commensal plant-microbe interactions. We identify crucial knowledge gaps and synthesize current limitations in our understanding of crop microbiome omics approaches. We highlight recent studies in which multi-omics-based approaches have led to improved models of crop microbial community structure and function. Finally, we recommend holistic approaches in integrating host and microbial omics datasets to achieve precision and efficiency in data analysis, which is crucial for biotic and abiotic stress control and in understanding the contribution of the microbiota in shaping plant fitness.
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Affiliation(s)
- Roy Njoroge Kimotho
- Hebei Key Laboratory of Soil Ecology, Key Laboratory of Agricultural Water Resources, Centre for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Solomon Maina
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, New South Wales 2568, Australia
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4
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Benmrid B, Ghoulam C, Zeroual Y, Kouisni L, Bargaz A. Bioinoculants as a means of increasing crop tolerance to drought and phosphorus deficiency in legume-cereal intercropping systems. Commun Biol 2023; 6:1016. [PMID: 37803170 PMCID: PMC10558546 DOI: 10.1038/s42003-023-05399-5] [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: 05/12/2023] [Accepted: 09/28/2023] [Indexed: 10/08/2023] Open
Abstract
Ensuring plant resilience to drought and phosphorus (P) stresses is crucial to support global food security. The phytobiome, shaped by selective pressures, harbors stress-adapted microorganisms that confer host benefits like enhanced growth and stress tolerance. Intercropping systems also offer benefits through facilitative interactions, improving plant growth in water- and P-deficient soils. Application of microbial consortia can boost the benefits of intercropping, although questions remain about the establishment, persistence, and legacy effects within resident soil microbiomes. Understanding microbe- and plant-microbe dynamics in drought-prone soils is key. This review highlights the beneficial effects of rhizobacterial consortia-based inoculants in legume-cereal intercropping systems, discusses challenges, proposes a roadmap for development of P-solubilizing drought-adapted consortia, and identifies research gaps in crop-microbe interactions.
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Affiliation(s)
- Bouchra Benmrid
- Plant-Microbe Interactions Laboratory, AgroBiosciences Program, College for Sustainable Agriculture and Environmental Sciences, Mohammed VI Polytechnic University, Ben Guerir, 43150, Morocco.
| | - Cherki Ghoulam
- Plant-Microbe Interactions Laboratory, AgroBiosciences Program, College for Sustainable Agriculture and Environmental Sciences, Mohammed VI Polytechnic University, Ben Guerir, 43150, Morocco
- Agrobiotechnology & Bioengineering Center, Research Unit CNRST labeled, Cadi Ayyad University, Faculty of Sciences and Techniques, 40000, Marrakech, Morocco
| | - Youssef Zeroual
- Situation Innovation - OCP Group, Jorf Lasfar, 24025, Morocco
| | - Lamfeddal Kouisni
- African Sustainable Agriculture Research Institute, Mohammed VI Polytechnic University, Laayoune, Morocco
| | - Adnane Bargaz
- Plant-Microbe Interactions Laboratory, AgroBiosciences Program, College for Sustainable Agriculture and Environmental Sciences, Mohammed VI Polytechnic University, Ben Guerir, 43150, Morocco.
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5
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Ferrocino I, Rantsiou K, McClure R, Kostic T, de Souza RSC, Lange L, FitzGerald J, Kriaa A, Cotter P, Maguin E, Schelkle B, Schloter M, Berg G, Sessitsch A, Cocolin L. The need for an integrated multi-OMICs approach in microbiome science in the food system. Compr Rev Food Sci Food Saf 2023; 22:1082-1103. [PMID: 36636774 DOI: 10.1111/1541-4337.13103] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 12/05/2022] [Accepted: 12/19/2022] [Indexed: 01/14/2023]
Abstract
Microbiome science as an interdisciplinary research field has evolved rapidly over the past two decades, becoming a popular topic not only in the scientific community and among the general public, but also in the food industry due to the growing demand for microbiome-based technologies that provide added-value solutions. Microbiome research has expanded in the context of food systems, strongly driven by methodological advances in different -omics fields that leverage our understanding of microbial diversity and function. However, managing and integrating different complex -omics layers are still challenging. Within the Coordinated Support Action MicrobiomeSupport (https://www.microbiomesupport.eu/), a project supported by the European Commission, the workshop "Metagenomics, Metaproteomics and Metabolomics: the need for data integration in microbiome research" gathered 70 participants from different microbiome research fields relevant to food systems, to discuss challenges in microbiome research and to promote a switch from microbiome-based descriptive studies to functional studies, elucidating the biology and interactive roles of microbiomes in food systems. A combination of technologies is proposed. This will reduce the biases resulting from each individual technology and result in a more comprehensive view of the biological system as a whole. Although combinations of different datasets are still rare, advanced bioinformatics tools and artificial intelligence approaches can contribute to understanding, prediction, and management of the microbiome, thereby providing the basis for the improvement of food quality and safety.
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Affiliation(s)
- Ilario Ferrocino
- Department of Agriculture, Forest and Food Science, University of Turin, Grugliasco, Italy
| | - Kalliopi Rantsiou
- Department of Agriculture, Forest and Food Science, University of Turin, Grugliasco, Italy
| | - Ryan McClure
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Tanja Kostic
- AIT Austrian Institute of Technology GmbH, Bioresources Unit, Tulln, Austria
| | - Rafael Soares Correa de Souza
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Lene Lange
- BioEconomy, Research & Advisory, Valby, Denmark
| | - Jamie FitzGerald
- Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
| | - Aicha Kriaa
- MICALIS, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Paul Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
| | - Emmanuelle Maguin
- MICALIS, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | | | | | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Angela Sessitsch
- AIT Austrian Institute of Technology GmbH, Bioresources Unit, Tulln, Austria
| | - Luca Cocolin
- Department of Agriculture, Forest and Food Science, University of Turin, Grugliasco, Italy
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6
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Nelson AR, Toyoda J, Chu RK, Tolić N, Garayburu-Caruso VA, Saup CM, Renteria L, Wells JR, Stegen JC, Wilkins MJ, Danczak RE. Implications of sample treatment on characterization of riverine dissolved organic matter. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2022; 24:773-782. [PMID: 35416230 DOI: 10.1039/d2em00044j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
High-resolution mass spectrometry techniques are widely used in the environmental sciences to characterize natural organic matter and, when utilizing these instruments, researchers must make multiple decisions regarding sample pre-treatment and the instrument ionization mode. To identify how these choices alter organic matter characterization and resulting conclusions, we analyzed a collection of 17 riverine samples from East River, CO (USA) under four PPL-based Solid Phase Extraction (SPE) treatment and electrospray ionization polarity (e.g., positive and negative) combinations: SPE (+), SPE (-), non-SPE (-), and non-SPE (+). The greatest number of formula assignments were achieved with SPE-treated samples due to the removal of compounds that could interfere with ionization. Furthermore, the SPE (-) treatment captured the most formulas across the widest chemical compound diversity. In addition to a reduced number of assigned formulas, the non-SPE datasets resulted in altered thermodynamic interpretations that could cascade into incomplete assumptions about the availability of organic matter pools for heterotrophic microbial respiration. Thus, we infer that the SPE (-) treatment is the best single method for characterizing environmental organic matter pools unless the focus is on lipid-like compounds, in which case we recommend a combination of SPE (-) and SPE (+) to adequately characterize these molecules.
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Affiliation(s)
| | - Jason Toyoda
- School of Earth Sciences, The Ohio State University, USA
| | - Rosalie K Chu
- School of Earth Sciences, The Ohio State University, USA
| | - Nikola Tolić
- School of Earth Sciences, The Ohio State University, USA
| | | | | | - Lupita Renteria
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, USA
| | - Jacqueline R Wells
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, USA
| | - James C Stegen
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, USA
| | | | - Robert E Danczak
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, USA
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7
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Abbà S, Rossi M, Vallino M, Galetto L, Marzachì C, Turina M. Metatranscriptomic Assessment of the Microbial Community Associated With the Flavescence dorée Phytoplasma Insect Vector Scaphoideus titanus. Front Microbiol 2022; 13:866523. [PMID: 35516423 PMCID: PMC9063733 DOI: 10.3389/fmicb.2022.866523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
Phytoplasmas are insect-borne pathogenic bacteria that cause major economic losses to several crops worldwide. The dynamic microbial community associated with insect vectors influences several aspects of their biology, including their vector competence for pathogens. Unraveling the diversity of the microbiome of phytoplasma insect vectors is gaining increasing importance in the quest to develop novel microbe-based pest control strategies that can minimize the use of insecticides for better environmental quality. The leafhopper Scaphoideus titanus is the primary vector of the Flavescence dorée phytoplasma, a quarantine pest which is dramatically affecting the main grape-growing European countries. In this study, the RNA-Seq data, which were previously used for insect virus discovery, were further explored to assess the composition of the whole microbial community associated with insects caught in the wild in both its native (the United States) and invasive (Europe) areas. The first de novo assembly of the insect transcriptome was used to filter the host sequencing reads. The remaining ones were assembled into contigs and analyzed by blastx to provide the taxonomic identification of the microorganisms associated with S. titanus, including the non-bacterial components. By comparing the transcriptomic libraries, we could differentiate the stable and consistent associations from the more ephemeral and flexible ones. Two species appeared to be universal to the core microbiome of S. titanus: the obligate bacterial symbiont Candidatus Sulcia muelleri and an Ophiocordyceps-allied fungus distantly related to yeast-like symbionts described from other hemipterans. Bacteria of the genus Cardinium have been identified as another dominant member of the microbiome, but only in the European specimens. Although we are yet to witness how the interplay among the microorganisms influences the vector competence of S. titanus, this unbiased in silico characterization of its microbiome is paramount for identifying the naturally occurring targets for new biocontrol strategies to counteract Flavescence dorée spread in Europe.
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8
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Shoubridge AP, Choo JM, Martin AM, Keating DJ, Wong ML, Licinio J, Rogers GB. The gut microbiome and mental health: advances in research and emerging priorities. Mol Psychiatry 2022; 27:1908-1919. [PMID: 35236957 DOI: 10.1038/s41380-022-01479-w] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 01/17/2022] [Accepted: 02/08/2022] [Indexed: 12/19/2022]
Abstract
The gut microbiome exerts a considerable influence on human neurophysiology and mental health. Interactions between intestinal microbiology and host regulatory systems have now been implicated both in the development of psychiatric conditions and in the efficacy of many common therapies. With the growing acceptance of the role played by the gut microbiome in mental health outcomes, the focus of research is now beginning to shift from identifying relationships between intestinal microbiology and pathophysiology, and towards using this newfound insight to improve clinical outcomes. Here, we review recent advances in our understanding of gut microbiome-brain interactions, the mechanistic underpinnings of these relationships, and the ongoing challenge of distinguishing association and causation. We set out an overarching model of the evolution of microbiome-CNS interaction and examine how a growing knowledge of these complex systems can be used to determine disease susceptibility and reduce risk in a targeted manner.
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Affiliation(s)
- Andrew P Shoubridge
- Microbiome and Host Health, South Australian Health and Medical Research Institute, Adelaide, SA, 5001, Australia.,Infection and Immunity, Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Australia
| | - Jocelyn M Choo
- Microbiome and Host Health, South Australian Health and Medical Research Institute, Adelaide, SA, 5001, Australia.,Infection and Immunity, Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Australia
| | - Alyce M Martin
- Neuroscience, Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Australia
| | - Damien J Keating
- Neuroscience, Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Australia
| | - Ma-Li Wong
- Department of Psychiatry and Behavioral Sciences and Department of Neuroscience and Physiology, State University of New York Upstate Medical University, Syracuse, NY, 13210, USA
| | - Julio Licinio
- Department of Psychiatry and Behavioral Sciences and Department of Neuroscience and Physiology, State University of New York Upstate Medical University, Syracuse, NY, 13210, USA.,Department of Psychiatry, Flinders University College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Australia
| | - Geraint B Rogers
- Microbiome and Host Health, South Australian Health and Medical Research Institute, Adelaide, SA, 5001, Australia. .,Infection and Immunity, Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Australia.
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9
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Song HS, Lindemann SR, Lee DY. Editorial: Predictive Modeling of Human Microbiota and Their Role in Health and Disease. Front Microbiol 2021; 12:782871. [PMID: 34917060 PMCID: PMC8668940 DOI: 10.3389/fmicb.2021.782871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/11/2021] [Indexed: 12/23/2022] Open
Affiliation(s)
- Hyun-Seob Song
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, Lincoln, NE, United States.,Department of Food Science and Technology, Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Stephen R Lindemann
- Department of Food Science, Whistler Center for Carbohydrate Research, Purdue University, West Lafayette, IN, United States.,Department of Nutrition Science, Purdue University, West Lafayette, IN, United States
| | - Dong-Yup Lee
- School of Chemical Engineering, Sungkyunkwan University, Suwon, South Korea
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10
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Kaul S, Choudhary M, Gupta S, Dhar MK. Engineering Host Microbiome for Crop Improvement and Sustainable Agriculture. Front Microbiol 2021; 12:635917. [PMID: 34122359 PMCID: PMC8193672 DOI: 10.3389/fmicb.2021.635917] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 04/16/2021] [Indexed: 12/27/2022] Open
Abstract
Dynamic consortium of microbial communities (bacteria, fungi, protists, viruses, and nematodes) colonizing multiple tissue types and coevolving conclusively with the host plant is designated as a plant microbiome. The interplay between plant and its microbial mutualists supports several agronomic functions, establishing its crucial role in plant beneficial activities. Deeper functional and mechanistic understanding of plant-microbial ecosystems will render many "ecosystem services" by emulating symbiotic interactions between plants, soil, and microbes for enhanced productivity and sustainability. Therefore, microbiome engineering represents an emerging biotechnological tool to directly add, remove, or modify properties of microbial communities for higher specificity and efficacy. The main goal of microbiome engineering is enhancement of plant functions such as biotic/abiotic stresses, plant fitness and productivities, etc. Various ecological-, biochemical-, and molecular-based approaches have come up as a new paradigm for disentangling many microbiome-based agromanagement hurdles. Furthermore, multidisciplinary approaches provide a predictive framework in achieving a reliable and sustainably engineered plant-microbiome for stress physiology, nutrient recycling, and high-yielding disease-resistant genotypes.
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Affiliation(s)
- Sanjana Kaul
- School of Biotechnology, University of Jammu, Jammu, India
| | | | - Suruchi Gupta
- School of Biotechnology, University of Jammu, Jammu, India
| | - Manoj K Dhar
- School of Biotechnology, University of Jammu, Jammu, India
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