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A global genomic analysis of the bacterial symbiont that fixes nitrogen for chickpeas reveals new information about the biogeography of microorganisms and the process of horizontal gene transfer in bacteria, and has further implications on agriculture and carbon emissions.
Biogeography, the study of the distributions of plants and animals across time and space, is a tool that biologists have used for centuries to develop many modern concepts of evolution and ecology. Despite its long history of use on plants and animals, only recently have similar methods been able to be used on microorganisms, the class of life that comprise the majority of the Earth’s biodiversity. Recent advances in sequencing technology, however, have allowed scientists to fill this gap in our understanding (Ladau et al. 2013).
An application of this advancement of biogeography has been applied to the study of the bacterial symbiont of the chickpea crop (Greenlon et al. 2019). This symbiont is specifically responsible for aiding the chickpea with nitrogen fixation in return for fixed carbon and shelter in the form of root nodules. Chickpea was first domesticated in the fertile crescent sometime around 11,000 years ago, and is a member of family Fabaceae (commonly legumes) (von Wettberg et al. 2018). After its domestication, it spread throughout the Middle East and Mediterranean. In the past century, it has also been cultivated in countries like Canada, the U.S., and Australia.
Legumes are an incredibly important crop as their nitrogen fixation (again, facilitated by bacterial symbionts) can be used as a replacement for the fossil fuel reliant Haber-Bosch process, which accounts for 1 to 2% of global CO2 emissions (Jensen and Hauggaard-Nielsen 2003). Thus, examining the distribution and genetic diversity of the bacterial symbiont of the chickpea is an issue of both scientific (broadening our understanding of the biogeography of microorganisms) and economic (optimizing nitrogen fixation rates) relevance.
Greenlon, et al. collected 1,027 samples of bacterial symbionts associated with either chickpea or its wild relatives from across the vast majority of its agricultural range (including North America, Australia, Morocco, Ethiopia, India, and Turkey). They discovered that their samples include 36 distinct species of the genus Mesorhizobium. They discovered that the diversity of symbionts was much lower in the U.S., Canada, and Australia (countries with a much more recent history of cultivation) than in Turkey, India, Ethiopia, or Morocco (countries with a much longer history of cultivation). In terms of biogeography, they found that the geographic diversity of the Mesorhizobium was explained significantly by soil type, latitude, precipitation, and temperature.
Greenlon, et al. went on to examine the horizontal gene transfer (the movement of genetic material between organisms other than by reproduction) of the Mesorhizobium bacteria and how it relates to the symbiotic relationship between it and chickpea. They found positive correlations between the amount of gene transfer between two organisms and both their geographic and genomic distance from each other. They also found that key genes involved in their symbiotic relationship with chickpea plants were often transferred between different strains of Mesorhizobium through one of two distinct mechanisms. The distribution of these mechanisms was found to be more related to the phylogenetic distance between individuals than by the geographic distance. Finally they discovered that the region containing the majority of the genes related to the symbiotic relationship with chickpea was highly conserved across genomes, but also exhibited a higher rate of recombination than other parts of the genome.
A common practice for chickpea cultivation is the inoculation of the soil with specific species of bacteria that have been identified in the lab to be especially effective nitrogen fixers in an agricultural context. This practice leads to higher rates of nitrogen fixation and thus significant economic benefits. However, the results of this study suggests that the species used for the inoculation will likely be ecologically unstable over time and eventually outcompeted by local species more adapted to the environment, due to horizontal gene transfer of the genes involved in the symbiotic relationship. This suggests that researchers hoping to optimize nitrogen fixation should also screen for adaptations to the local environment as well.
A major question in microbiology, since the first discovery of the importance and ubiquity of horizontal gene transfer, is how evolutionarily stable species of bacteria can form if they exchange genes so freely. The results of this paper suggest that bacteria are able to form species due in part to both the relationship between genetic relatedness between genomes and the rate of horizontal gene transfer and also due to at least some species (Mesorhizobium bacteria, in this case) possessing mechanisms that foster specific genes to be transferred across specific groups.
This study is impressive in both its globe-spanning scope and the depth of its analysis. The implications of its results are far-reaching and of great importance, being among the first studies to incorporate biographical techniques to a micro-organism, and specifically one with a significant impact on global agriculture and carbon emissions. In future, it may be interesting to apply similar techniques and analyses to other legume-bacteria pairings, or even to plant symbionts in general.
Anthony Eckdahl is a senior biology major at Davidson College. Contact him at: aneckdahl@davidson.edu
References
Greenlon A., P. L. Chang, Z. M. Damtew, A. Muleta, N. Carrasquilla-Garcia, et al., 2019 Global-level population genomics reveals differential effects of geography and phylogeny on horizontal gene transfer in soil bacteria. Proc Natl Acad Sci USA 116: 15200–15209. https://doi.org/10.1073/pnas.1900056116
Jensen E. S., and H. Hauggaard-Nielsen, 2003 How can increased use of biological N 2 fixation in agriculture benefit the environment? Plant and Soil 252: 177–186. https://doi.org/10.1023/A:1024189029226
Ladau J., T. J. Sharpton, M. M. Finucane, G. Jospin, S. W. Kembel, et al., 2013 Global marine bacterial diversity peaks at high latitudes in winter. The ISME Journal 7: 1669–1677. https://doi.org/10.1038/ismej.2013.37
Macey D., 2018 Yellow Corn on Glass Bowl. https://unsplash.com/photos/h83Rm3njjcg
Wettberg E. J. B. von, P. L. Chang, F. Başdemir, N. Carrasquila-Garcia, L. B. Korbu, et al., 2018 Ecology and genomics of an important crop wild relative as a prelude to agricultural innovation. Nat Commun 9: 649. https://doi.org/10.1038/s41467-018-02867-z
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