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The Spread of Bradyrhizobium Lineages Across Host Legume Clades: from Abarema to Zygia

  • Plant Microbe Interactions
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Abstract

To analyze macroevolutionary patterns in host use by Bradyrhizobium root-nodule bacteria, 420 strains from 75 legume host genera (sampled in 25 countries) were characterized for portions of six housekeeping genes and the nifD locus in the symbiosis island chromosomal region. Most Bradyrhizobium clades utilized very divergent sets of legume hosts. This suggests that Bradyrhizobium spread across the major legume lineages early in its evolution, with only a few derived clades subsequently developing a narrower pattern of host use. Significant modularity existed in the network structure of recent host jumps (inferred from cases where closely related strain pairs were found on different legume taxa). This implies that recent host switching has occurred most often within particular subgroups of legumes. Nevertheless, the observed link structure would allow a bacterial lineage to reach almost any of the 75 legume host genera in a relatively small number of steps. However, permutation tests also showed that symbionts from certain host plant clades were significantly more similar than would be the case if bacteria were distributed at random on the trees. Related legumes thus harbored related sets of symbionts in some cases, indicating some degree of phylogenetic conservatism in partner selection.

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Acknowledgments

For providing strains, I am very grateful to Alexis Andrus, Julie Ardley, Craig Barrett, John Bishop, Dulal Borthakur, Jeremy Burdon, Euan James, Christine Le Roux, Kristina Lindström, Wanda Malek, Stephen Mondo, Ingrid Parker, Alvaro Peix, Riley Pratt, Raul Rivas, Susana Rodríguez-Echeverría, Encarna Velazquez, Pablo Vinuesa, and Anne Willems. Financial support was provided by US National Science Foundation grant MCB-0640246.

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  1. Department of Biological Sciences, State University of New York, Binghamton, NY, 13902, USA

    Matthew A. Parker

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Correspondence to Matthew A. Parker.

Electronic Supplementary Material

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Table S1

Source information for 113 Bradyrhizobium strains. (DOCX 118 kb)

Table S2

GenBank accession numbers for 420 Bradyrhizobium strains. (DOCX 131 kb)

Table S3

Geographic distribution for 20 Bradyrhizobium clades in the housekeeping gene tree. (DOCX 70 kb)

Fig. S1

Bayesian tree for six concatenated housekeeping loci (with clade posterior probability values) in 420 Bradyrhizobium strains. (PDF 46 kb)

Fig. S2

Phylogenetic network for recA sequences from type strains of 21 Bradyrhizobium species and 1–2 representative strains for each of the 20 clades in the concatenated housekeeping tree (Fig. 2; clades are designated by a letter after the strain name). Network was inferred by the NeighborNet algorithm (Huson DH, Bryant D [2006], Application of phylogenetic networks in evolutionary studies, Mol Biol Evol 23: 254–267). (PDF 7 kb)

Fig. S3

Bayesian tree for nifD sequences from 420 Bradyrhizobium strains. Stains whose host belonged to one of the nine major legume clades (Fig. 1) are marked with different color highlights. (PDF 771 kb)

Fig. S4

Relative nucleotide divergence in nifD vs. six concatenated housekeeping loci, plotted for Bradyrhizobium strains from two different legume host genera (n = 85,878 strain pairs), and strain pairs associated with the same legume host genus (n = 2112). In 10,000 bootstrap samples of linear regression coefficients, there was zero overlap of slope or intercept estimates for the two data sets. (PDF 587 kb)

Fig. S5

Network of Bradyrhizobium host shifts across 75 legume genera in the nifD tree (Fig. S3). Each edge linking two legume genera represents a single bacterial strain from one host whose closest relative in the nifD tree came from the other legume genus. Modules in the network are indicated by different colors. (PDF 39 kb)

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Parker, M.A. The Spread of Bradyrhizobium Lineages Across Host Legume Clades: from Abarema to Zygia . Microb Ecol 69, 630–640 (2015). https://doi.org/10.1007/s00248-014-0503-5

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