Spatial patterns in phage-Rhizobium coevolutionary interactions across regions of common bean domestication

Abstract

Bacteriophages play significant roles in the composition, diversity, and evolution of bacterial communities. Despite their importance, it remains unclear how phage diversity and phage-host interactions are spatially structured. Local adaptation may play a key role. Nitrogen-fixing symbiotic bacteria, known as rhizobia, have been shown to locally adapt to domesticated common bean at its Mesoamerican and Andean sites of origin. This may affect phage-rhizobium interactions. However, knowledge about the diversity and coevolution of phages with their respective Rhizobium populations is lacking. Here, through the study of four phage-Rhizobium communities in Mexico and Argentina, we show that both phage and host diversity is spatially structured. Cross-infection experiments demonstrated that phage infection rates were higher overall in sympatric rhizobia than in allopatric rhizobia except for one Argentinean community, indicating phage local adaptation and host maladaptation. Phage-host interactions were shaped by the genetic identity and geographic origin of both the phage and the host. The phages ranged from specialists to generalists, revealing a nested network of interactions. Our results suggest a key role of local adaptation to resident host bacterial communities in shaping the phage genetic and phenotypic composition, following a similar spatial pattern of diversity and coevolution to that in the host.

Fig. 1. Phylogenetic tree of all rhizobia collected from Mexico and Argentina (LC, n = 229) and from the standard laboratory collection (SC, n = 94).

The tree was constructed using the maximum likelihood method and is based on the concatenated sequences of two chromosomal genes (dnaA-recA) (see Methods). The bar scale indicates the number of nucleotide substitutions per site. Insets on the left side explain the contents of the four concentric circles. From the inner to the outermost circles: taxonomic classification of rhizobia, Rhizobium chromosomal STs (sequence types; no STs were assigned to SC strains), field of origin of the strains, and squares indicating the origin of the phages isolated using the corresponding strain. Bootstrap values are shown with proportionally-sized gray circles on the tree branches; smallest circles equal 75% and the largest circles equal a value of 100%.

Fig. 2. Differentiation of Rhizobium and phage communities.

A and B PCoA plots illustrating the differences in chromosomal composition between Rhizobium communities across common bean populations based on Jaccard distances (presence-absence) and Bray–Curtis distances (relative abundance), respectively. D and E PCoA plots showing the differences in the phage genomic type composition between phage communities across common bean populations based on Jaccard distances and Bray–Curtis distances. Bean fields are indicated by different colors: Tepoztlán (T), light blue; Yautepec (Y), dark blue; Salta (S), orange; Chicoana (C), red. Phages isolated by inoculating pooled samples from a given location into rhizobia from the laboratory’s standard collection of rhizobia (SC) are indicated with a star symbol. C and F Venn diagrams of the distribution of Rhizobium chromosomal STs and phage genomic types (PGTs), respectively.

Fig. 3. Structure of phage-Rhizobium interactions.

Phage-bacterium infection network of interactions between 196 phages (columns) and 229 Rhizobium strains (rows) performed with BiMat [84]. Either full (red) or partial (blue) lytic interactions were recorded as positive interactions in at least 2/3 of independent tests; blank cells indicate the absence of interaction. In the bottom row, colored bars indicate the bean field of origin of the phages: Tepoztlán (T, Mexico) = light blue; Yautepec (Y, Mexico) = dark blue; Salta (S, Argentina) = orange; Chicoana (C, Argentina) = red. The first column on the right indicates the site of origin of rhizobia with the same colors of the bars used for the phages. A Modular sorting of the interaction data, visualizing the presence of three modules. B Nested sorting of the interaction data, visualizing the spectrum of generalists to specialist phages. The isocline (black line) represents the division line in a perfectly nested matrix between an area of interactions and an area of no interactions. Name labels can be identified in the pdf version of this document, and the dataset is available as supplementary data online.

Fig. 4. Rhizobium susceptibility range and phage host range similarity.

Principal coordinates analysis (PCoA) plot showing the Bray–Curtis dissimilarity in the Rhizobium susceptibility range among common bean fields and Rhizobium species in (A) and the Bray–Curtis dissimilarity in the phage host range among regions and phage taxonomic families in (B). Each axis explains a certain fraction of dissimilarity, given within parentheses. Different Rhizobium species and phage taxonomic families are represented by symbols. The bean fields of origin are indicated by different colors: Tepoztlán (T), light blue; Yautepec (Y), dark blue; Salta (S), orange; Chicoana (C), red.

Fig. 5. Box plots of phage infection rates and Rhizobium susceptibility rates indicating phage local adaptation and Rhizobium maladaptation.

Phage infection rates between sympatric versus allopatric combinations averaged across all locations (A), averaged across populations within regions (B), or among populations (E). Rhizobium susceptibility rates between sympatric versus allopatric combinations averaged across all locations (C), averaged across populations within regions (D), or among populations (F). The mean is given for each box plot (black diamond). Differences between the means of sympatric (“S”) versus allopatric (“A”) phage infection rates (G) and the rates of the susceptibility of Rhizobium (H) are also shown. The origins of the phage and Rhizobium samples are indicated by T = Tepoztlán (Mexico), Y = Yautepec (Mexico), S = Salta (Argentina), and C = Chicoana (Argentina).