The Plant Holobiont: Integrating Microbiomes into Plant Biology

Submission Deadline: 10 January 2027 View: 30 Submit to Special Issue

Guest Editor(s)

Prof. Dr. Gustavo Santoyo

Email: gustavo.santoyo@umich.mx

Affiliation: Institute of Chemical and Biological Research, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico

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Research Interests: plant holobiont, microbial ecology, PGPR

Prof. Dr. Sergio de los Santos-Villalobos

Email: sergio.delossantos@itson.edu.mx

Affiliation: Laboratorio de Biotecnología del Recurso Microbiano, Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, 5 de Febrero 818 Sur, Col. Centro, Ciudad Obregón, Sonora, Mexico

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Research Interests: microbial ecology, plant-soil-microorganism interactions, PGPR,

Prof. Dr. Ma. del Carmen Orozco-Mosqueda

Email: carmen.orozco@itcelaya.edu.mx

Affiliation: Department of Biochemical and Environmental Engineering, National Technological Institute of Mexico in Celaya, Celaya, Mexico

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Research Interests: environmental microbiology, sustainable agriculture, bioinoculants, PGPR, agroecology, plant-soil-microorganism interactions

Summary

Plants do not function as isolated organisms but rather as complex holobionts, intimately associated with diverse microbial communities inhabiting mainly the rhizosphere, endosphere, phyllosphere. These microbiomes contribute to plant nutrition, development, stress resilience, immune responses, and adaptation to changing environments, making them integral components of plant biology. Advances in microbiome research have transformed our understanding of plants from autonomous individuals to dynamic ecological systems whose performance and evolution are shaped by interactions with diverse groups of microorganisms, including bacteria, fungi, archaea, and protists.

Recent developments in high-throughput sequencing, multi-omics technologies, systems biology, defined microbial communities (DMC), and computational approaches have greatly expanded our ability to characterize plant-associated microbiomes and unravel the molecular mechanisms governing plant-microbe interactions. These approaches are revealing how microbial communities assemble, communicate, and function, and how they influence plant physiology, ecosystem processes, and agricultural sustainability. Integrating microbiome science into plant biology provides unprecedented opportunities to improve crop productivity, enhance resilience to climate change, reduce dependence on agrochemicals, and develop next-generation microbial technologies for sustainable agriculture.

For this Research Topic, we welcome reviews and research articles that advance our understanding of the plant holobiont from molecular to ecosystem scales. We particularly encourage contributions that bridge fundamental plant biology with microbiome science and explore innovative approaches for harnessing beneficial microbial functions in natural and agricultural systems. Potential subjects for this topic include, but are not limited to:
● The plant holobiont concept and its implications for plant biology
● Assembly, structure, and function of plant-associated microbiomes
● Plant-microbe and microbe-microbe interactions
● Rhizosphere, endosphere, phyllosphere microbiomes
● Plant microbiomes under abiotic and biotic stresses
● Multi-omics approaches to study plant holobionts
● Systems biology and network analysis of plant-microbiome interactions
● Defined microbial communities (DMC) and microbial consortia
● Microbiome engineering and microbiome-assisted crop improvement
● Biocontrol and Plant growth-promoting microorganisms
● Microbiome-mediated nutrient cycling and plant nutrition
● Evolution and ecology of plant holobionts
● Microbiome-based biostimulants, biofertilizers, and sustainable agricultural practices

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