Epidemic Spread of Symbiotic and Non-Symbiotic Bradyrhizobium Genotypes Across California
- 610 Downloads
The patterns and drivers of bacterial strain dominance remain poorly understood in natural populations. Here, we cultured 1292 Bradyrhizobium isolates from symbiotic root nodules and the soil root interface of the host plant Acmispon strigosus across a >840-km transect in California. To investigate epidemiology and the potential role of accessory loci as epidemic drivers, isolates were genotyped at two chromosomal loci and were assayed for presence or absence of accessory “symbiosis island” loci that encode capacity to form nodules on hosts. We found that Bradyrhizobium populations were very diverse but dominated by few haplotypes—with a single “epidemic” haplotype constituting nearly 30 % of collected isolates and spreading nearly statewide. In many Bradyrhizobium lineages, we inferred presence and absence of the symbiosis island suggesting recurrent evolutionary gain and or loss of symbiotic capacity. We did not find statistical phylogenetic evidence that the symbiosis island acquisition promotes strain dominance and both symbiotic and non-symbiotic strains exhibited population dominance and spatial spread. Our dataset reveals that a strikingly few Bradyrhizobium genotypes can rapidly spread to dominate a landscape and suggests that these epidemics are not driven by the acquisition of accessory loci as occurs in key human pathogens.
KeywordsRhizobia Symbiosis Epidemic Population genetics Evolution
The following grants supported this study: to ACH a Herbert Kraft Scholarship and a UC Riverside Graduate Research Mentorship Fellowship and to JLS NSF DEB 0816663 and NSF DEB 1150278.
- 9.Sprent JI (2001) Nodulation in legumes. Royal Botanic Gardens, KewGoogle Scholar
- 27.Pongsilp N, Teaumroong N, Nuntagij A et al (2002) Genetic structure of indigenous non-nodulating and nodulating populations of Bradyrhizobium in soils from Thailand. Symbiosis 33:39–58Google Scholar
- 31.Costello EK, Carlisle EM, Bik EM, et al. (2013) Microbiome assembly across multiple body sites in low-birthweight infants. mBio 4:e00782–13–e00782–13. doi: 10.1128/mBio.00782-13Google Scholar
- 34.Vinuesa P, Silva C, Werner D, Martínez-Romero E (2005) Population genetics and phylogenetic inference in bacterial molecular systematics: the roles of migration and recombination in Bradyrhizobium species cohesion and delineation. Mol Phylogenet Evol 34:29–54. doi: 10.1016/j.ympev.2004.08.020 CrossRefPubMedGoogle Scholar
- 35.Vinuesa P, Rojas-Jimenez K, Contreras-Moreira B et al (2008) Multilocus sequence analysis for assessment of the biogeography and evolutionary genetics of four Bradyrhizobium species that nodulate soybeans on the Asiatic continent. Appl Environ Microbiol 74:6987–6996. doi: 10.1128/AEM.00875-08 CrossRefPubMedPubMedCentralGoogle Scholar
- 42.Maddison WP, Maddison DR (2005) MacClade: analysis of phylogeny and character evolutionGoogle Scholar
- 56.Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New YorkGoogle Scholar
- 58.Orme D (2012) The caper package: comparative analysis of phylogenetics and evolution in RGoogle Scholar
- 59.Maddison, W. P., Maddison, D. R. (2011) MesquiteGoogle Scholar
- 60.SAS Institute Inc (1989) JMP. SAS Institute Inc., Cary, NCGoogle Scholar
- 65.Baldwin BG, Goldman DH (2012) The Jepson manual: vascular plants of California, 2nd edn. University of California Press, Berkeley, CalifGoogle Scholar