Plant Microbiomes May Improve Crop Yields

A key question that needs to be addressed by a variety of disciplines in the near future is how to feed the world’s rapidly growing population. In many parts of the world, agriculture is struggling to keep pace with an increasing population that is consistently devoting a smaller fraction of its time to food production. A promising area of research is attempting to help solve this problem: plant microbiomes. Just as humans have communities of microbes in our mouths, intestines, and many other parts of our bodies that perform essential functions on our behalf, so too do plants have an intricate community of fungi and bacteria that live in, on, and around their root system in an area called the rhizosphere. Much like the biosphere is the area around the surface of the Earth on which life can persist, the rhizosphere is the area on and around a plant’s root that hosts an especially diverse community of microbes.

Understanding how soil microbiomes take shape will be invaluable to future crop breeders. Manipulating the rhizosphere by crop scientists has the potential to improve plant health, increase yields, decrease needs for additional fertilizers, reduce diseases, and improve the overall health of the soil. A team of researchers recently explored this topic [1]. HilleRisLambers et al. put forward different theories for community assembly, and in addition to helping us understand plant microbiomes this research has the potential to benefit the entire discipline of ecology by helping determine what factors affect assembly of new communities. Veresoglou et al. conducted an exploration of microbial roles in, and fungal influences on, nitrogen fixation. They showed how much there is still to learn about what exact roles soil organisms play in the nitrogen cycle, and how different groups usually benefit associated plants nearby by competing with, limiting, or enhancing each other [2]. In addition, Bakker et al. synthesized information such as that presented above and explained how such knowledge will benefit crop breeders. They noted that crops may be improved by taking advantage of the many services provided by microbes, which include hormone production, improved nutrient uptake, enhanced stress tolerance, facilitation of plant immunity, and alteration of plant functional traits and tissue chemistry. [3]

An important question is how rhizospheres of different field crops across the country are related to each other, and upon what those relationships are based [4]. Is soil type the main factor, or does taxonomy play a larger role? What about geographic location? To determine the answer, researchers led by Jason Peiffer conducted a study in which they grew 26 different maize (corn) genotypes in 5 separate fields: one in Illinois, one in Missouri, and three in towns on the shore of Cayuga Lake, including Ithaca. They compared the bacterial composition of the rhizosphere to that of the nearby bulk soil for each of the plots, and, using sequencing of specific genes, they also examined the taxonomic composition of each of the different maize cultivars’ rhizospheres.

Peiffer et al. found that soils from the three New York plots had the most groups of related microbial taxa, despite the fact that the soils each had very different physical and chemical characteristics, leading the researchers to speculate that climate has a strong influence on the assembly of microbes present in the soil. They also noted that the microbes of the rhizosphere exhibited a great deal more taxonomic variety than those in the nearby bulk soil. Finally, they concluded that the particular cultivar of corn being grown had a small, but significant, effect on the microbial community around each type of plant. The researchers admitted that associations between cultivar and microbiome had been found to be stronger during an earlier greenhouse experiment, and that naturally occurring variation in field experiments, including soil type and preexisting communities, may dull the observed effects of relationships between crop and microbial genotypes. [4] The fact that there is an association between rhizosphere microbiota and cultivar type will have important implications for future work in the field, if crop managers can take a cultivar’s ideal microbiome into account and seek to promote the best mix of microbes in and around the plant and its soil.

Future research will likely continue to explore the relationship between different genotypic varieties of plants and the microbiomes that grow along with them. The interactions between different microbes in the soil, and especially the influences that myccorhizal fungi and nearby bacteria have on each other, should be explored more in depth to determine if nutrients, such as nitrogen, can be incorporated into the soil more quickly through natural means, hopefully reducing our strong dependence on artificial fertilizers. The assembly of microbial communities, their effects on their plant hosts, and our ability to influence them, should all be studied in further depth as well.

The ecological implications of these studies are quite significant. Our supplies of artificially fixed fertilizers, fossil fuels, arable land, and healthy soil are all limited. As our population continues to grow and a large percentage of it remains food insecure, it is vital that we develop sustainable agriculture solutions to make the most efficient use of our diminishing resources. Just as human microbiomes have been found to have many far-reaching affects on our health in the last few years, so too have plant microbiomes been found to provide a great many services to their hosts, from nutrient fixation and absorption to disease resistance. These studies and others like them seek to better understand the plant microbiome so that we can foster the development of healthier, more productive, and more sustainable crops in the future.

Works Cited:

[1] HilleRisLambers, J., Adler, P., Harpole, W., Levine, J., & Mayfield, M. (2012). Rethinking Community Assembly through the Lens of Coexistence Theory. Annual Review of Ecology, Evolution, and Systematics, 43, 227-248. doi:10.1146/annurev-ecolsys-110411-160411

[2] Veresoglou, S., Chen, B., & Rillig, M. (2011). Arbuscular mycorrhiza and soil nitrogen cycling. Soil Biology and Biochemistry, 46, 53-62. Retrieved October 19, 2015, from www.elsevier.com/locate/soilbio

[3] Bakker, M., Manter, D., Sheflin, A., Weir, T., & Vivanco, J. (2012). Harnessing the rhizosphere microbiome through plant breeding and agricultural management. Plant and Soil, 360(1), 1-13. doi:10.1007/s11104-012-1361-x

[4] Peiffer, J., Spor, A., Koren, O., Jin, Z., Tringe, S., Dangl, J., . . . Ley, R. (2013). Diversity and heritability of the maize rhizosphere microbiome under field conditions. PNAS, 110(16), 6548–6553-6548–6553. doi:10.1073/pnas.1302837110