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ARS Home » Pacific West Area » Albany, California » Plant Gene Expression Center » Research » Publications at this Location » Publication #382539

Research Project: Discovery of Plant Genetic Mechanisms Controlling Microbial Recruitment to the Root Microbiome

Location: Plant Gene Expression Center

Title: Holo-omics for deciphering plant-microbiome interactions

item XU, LING - University Of California
item PIERROZ, GRADY - University Of California
item WIPF, EDI - University Of California
item GAO, CHENG - University Of California
item TAYLOR, JOHN - University Of California
item LEMAUX, PEGGY - University Of California
item Coleman-Derr, Devin

Submitted to: Microbiome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/2/2021
Publication Date: 3/24/2021
Citation: Xu, L., Pierroz, G., Wipf, E., Gao, C., Taylor, J., Lemaux, P., Coleman-Derr, D.A. 2021. Holo-omics for deciphering plant-microbiome interactions. Microbiome. 9:69.

Interpretive Summary: Host-microbiome interactions are recognized for their importance to host health. An improved understanding of the molecular underpinnings of host-microbiome relationships will advance our capacity to accurately predict host fitness and manipulate interaction outcomes. Within the plant microbiome research field, unlocking the functional relationships between plants and their microbial partners is the next step to effectively using the microbiome to improve plant fitness. Holo-omics represents a useful tool to be used in our efforts to develop an improved understanding into the basic biology of plant-microbiome interactions. Adoption of this strategy will in turn necessitate and fuel the development of alternative sequencing-data integration analysis techniques that may have benefit outside the realm of plant biology. Finally, ARS believes pursuit of this path will encourage microbial and plant biologists, as well as ecologists, statisticians, and computer scientists, to work together to develop unified experimental frameworks that integrate diverse scientific perspectives. It is this process of technical and conceptual harmonization of methodologies across the scientific community that remains perhaps the greatest challenge to affording us a more holistic view of our natural world.

Technical Abstract: In this review, ARS propose that strategies that pair host and microbial datasets - referred to here as holo-omics - provide a powerful approach for hypothesis development and advancement in this area. ARS discuss several experimental design considerations and present a case study to highlight the potential for holo-omics to generate a more holistic perspective of molecular networks within the plant microbiome system. In addition, ARS discuss the biggest challenges for conducting holo-omics studies; specifically, the lack of vetted analytical frameworks, publicly available tools, and required technical expertise to process and integrate heterogeneous data. Finally, ARS conclude with a perspective on appropriate use-cases for holo-omics studies, the need for downstream validation, and new experimental techniques that hold promise for the plant microbiome research field. ARS argue that utilizing a holo-omics approach to characterize host-microbiome interactions can provide important opportunities for broadening system-level understandings and significantly inform microbial approaches to improving host health and fitness.