Exploring the corn microbiome: a detailed review on current knowledge, techniques, and future direction

Authors: Singh, Raksha; Goodwin, Stephen - Steve

Submitted to: PhytoFrontiers
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/18/2022
Publication Date: 6/1/2022
Citation: Singh, R., Goodwin, S.B. 2022. Exploring the corn microbiome: A detailed review on current knowledge, techniques, and future direction. Phytofrontiers. 2:158-175. https://doi.org/10.1094/PHYTOFR-04-21-0026-RVW.
DOI: https://doi.org/10.1094/PHYTOFR-04-21-0026-RVW

Interpretive Summary: Bacteria and fungi living in, on, or near plant leaves, stems, seeds, roots and soil comprise the microbial microbiome. Although manipulating plant microbiomes has a great potential for improving plant health and productivity, studies on crop microbiomes, especially in corn, have lagged. New technologies allow such studies to be performed easily and in more detail than was previously possible. To identify gaps in knowledge and promising areas for future research, 106 previously published papers on corn microbiomes were analyzed for the organisms targeted, methods of analysis, and potential for crop improvement. The results identified next-generation sequencing technologies augmented with biochemical and culture techniques as the most thorough approach for comprehensive analyses. Several strains with potential for crop improvement were highlighted, and the leaf microbiome was identified as an understudied topic that is ripe for future research. These results will be useful in identifying the best environments for corn production and the development novel approaches for disease management. This summary of previous publications will be especially useful to future investigators in identifying the most promising areas for new investigations.

Technical Abstract: In their natural environment plants are colonized by a plethora of microorganisms. These diverse microorganisms interact among each other and the host to form a complex microbiome. There is a growing body of research indicating that the microbiome plays a crucial role in plant performance by promoting growth, stress tolerance and resistance to pathogens. Although plant microbiomes have a great potential for improving plant health and productivity, studies on crop microbiomes, especially in corn, have only recently started to be performed. During the last few years progress in next-generation sequencing (NGS) technologies has enabled systemic studies of corn-associated microbiomes and their dynamics with the plant. The composition and differentiation of microbial communities are not only affected by environmental factors and agricultural management, but also by host phenotype and genotype. Although several challenges remain in understanding the microbiome, the combination of beneficial plant microbes, microbial community interactions and the optimization of the taxonomic composition of microbiomes determine the overall health and fitness of the plant and thus, lead to more sustainable agriculture. In this review, we provide an overview of the current knowledge and research on corn microbiomes using traditional culture-based approaches and next-generation genomic profiling, discuss results from these approaches with emphasis on the influence of environmental and host genetic factors on corn-microbe interactions, and outline future directions and challenges in corn microbiome research. A better understanding of the corn microbiome diversity, function and microbiology will contribute to the improvement of crop health and productivity.