Abstract
Purpose
Studying the legume nodule microbiome is important for understanding the development and nutrition of the plants inhabited by the various microbes within and upon them. We analyzed the microbiomes of these underground organs from both an important crop plant (Medicago sativa) and a related legume (M. polymorpha) using metagenomic and culture-based techniques to identify the main cultivatable contributors to plant growth enhancement.
Methods
Using high-throughput sequencing, culturing, and in planta techniques, we identified and analyzed a broad population of the bacterial taxa within Medicago nodules and the surrounding soil.
Results
Fifty-one distinct bacterial strains were isolated and characterized from nodules of both Medicago species and their growth-promoting activities were studied. Sequencing of 16S rRNA gene amplicons showed that in addition to Ensifer, the dominant genus, a large number of Gram-positive bacteria belonging to the Firmicutes and Actinobacteria were also present. After performing ecological and plant growth-promoting trait analyses, selecting the most promising strains, and then performing in planta assays, we found that strains of Bacillus and Micromonospora among others could play important roles in supporting the growth, health, and productivity of the host plant.
Conclusion
To our knowledge, the comparison of the biodiversity of the microbiota of undomesticated vs. cultivated Medicago roots and nodules is novel and shows the range of potential Plant Growth-Promoting Bacteria that could be used for plants of agricultural interest. These and other nodule-isolated microbes could also serve as inoculants with rhizobia with the goal of replacing synthetic fertilizers and pesticides for sustainable agriculture.
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Acknowledgements
Research on alfalfa was supported in part by funds from a UCLA Faculty Award, the Shanbrom Foundation, and from the National Institutes of Health (C06RR015511) for studies on plants under controlled environmental conditions. The U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, supported this research under Contract No. DE-AC02-05CH11231. PMH was awarded a postdoctoral fellowship from the “Fundación Ramón Areces” (Spain). We thank Noor Khan for her comments on the manuscript and also thank Melissa Kosty, Bryce Foster, Simon Roux, Brian Foster and Alex Copeland for their help in the acquisition of sequencing data.
Funding
Support came in part from a UCLA Faculty Award, the Shanbrom Foundation, the National Institutes of Health (C06RR015511) for controlled environmental studies, the Mildred Mathias Botanical Garden (UCLA), and California State Polytechnic University (Pomona, CA). The U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, supported this research under Contract No. DE-AC02-05CH11231. PMH was awarded a postdoctoral fellowship from the “Fundación Ramón Areces” (Spain).
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Martínez-Hidalgo, P., Humm, E.A., Still, D.W. et al. Medicago root nodule microbiomes: insights into a complex ecosystem with potential candidates for plant growth promotion. Plant Soil 471, 507–526 (2022). https://doi.org/10.1007/s11104-021-05247-7
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DOI: https://doi.org/10.1007/s11104-021-05247-7