Soledad Juárez’s research while affiliated with National Autonomous University of Mexico and other places

A Correction to this paper has been published: https://doi.org/10.1038/s41396-021-00963-5

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.

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, called rhizobia, have been shown to locally adapt to domesticated common bean at its Mesoamerican and Andean origin sites. 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 are spatially structured. Our cross-infection experiments demonstrate that phage infection rates were overall higher on sympatric than on 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. Phages ranged from specialists to generalists, revealing a nested network of interactions. Our results suggest a key role of local adaptation to resident host bacteria communities in shaping phage genetic and phenotypic composition, following a similar spatial pattern of diversity and coevolution as the host.

Phylogenetic tree of ribosomal proteins of Rhizobium species. Ribosomal clades are indicated by Roman numerals (I to VI) enclosed in colored ellipses. Subclades appear with black ellipses within the clades. The tree was constructed using maximum likelihood in the MEGA software package, by using 58 concatenated ribosomal proteins (refer to section “Materials and Methods” for more details).

Distribution of ANI values between pairs of genomes belonging to (a) 102 genomes, (b) 88 genomes, (c) and (e) 35 genomes of rC-I clade, and (d) and (f) 38 genomes o rC-II clade. Histograms show the frequency of pairwise comparisons within clades (turquoise color), and inter clades (pale red), distributed by segments of ANI values. In figures (e) and (f), blue color histograms show comparisons within subclades (see Supplementary Figure S1) defined by ANIm > 95%, and the green color histograms indicate inter subclades comparisons.

Bray Curtis dissimilarity index for accessory genes distribution within and between ribosomal clusters.

Pairwise ANIm comparison between complete R. leguminosarum symbiotic plasmids. Only the genome sequences of R. leguminosarum listed in the GenBank up to 14-03-2019 were downloaded. The ANIm comparison were performed using JSspecies as described in the methods section. The heatmap show the values of the corrected Gcov% / ANIm%; the color scale key inset shows the ranges from 0 to 1.

Genomic clusters of 102 Rhizobium and Sinorhizobium pairs obtained by pairwise ANIm comparisons.

The bacterial genus Rhizobium comprises diverse symbiotic nitrogen-fixing species associated with the roots of plants in the Leguminosae family. Multiple genomic clusters defined by whole genome comparisons occur within Rhizobium, but their equivalence to species is controversial. In this study we investigated such genomic clusters to ascertain their significance in a species phylogeny context. Phylogenomic inferences based on complete sets of ribosomal proteins and stringent core genome markers revealed the main lineages of Rhizobium. The clades corresponding to R. etli and R. leguminosarum species show several genomic clusters with average genomic nucleotide identities (ANI > 95%), and a continuum of divergent strains, respectively. They were found to be inversely correlated with the genetic distance estimated from concatenated ribosomal proteins. We uncovered evidence of a Rhizobium pangenome that was greatly expanded, both in its chromosomes and plasmids. Despite the variability of extra-chromosomal elements, our genomic comparisons revealed only a few chromid and plasmid families. The presence/absence profile of genes in the complete Rhizobium genomes agreed with the phylogenomic pattern of species divergence. Symbiotic genes were distributed according to the principal phylogenomic Rhizobium clades but did not resolve genome clusters within the clades. We distinguished some types of symbiotic plasmids within Rhizobium that displayed different rates of synonymous nucleotide substitutions in comparison to chromosomal genes. Symbiotic plasmids may have been repeatedly transferred horizontally between strains and species, in the process displacing and substituting pre-existing symbiotic plasmids. In summary, the results indicate that Rhizobium genomic clusters, as defined by whole genomic identities, might be part of a continuous process of evolutionary divergence that includes the core and the extrachromosomal elements leading to species formation.

Correlation between ANIm and Gcov. (a) 102 Rhizobium and Sinorhizobium genomes, (b) 88 genomes, (c) 35 genomes of rC-I clade, and (d) 38 genomes o rC-II clade. Spearman r and p-values are indicated in the inset.