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

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.Fil: Van Cauwenberghe, Jannick. University of California at Berkeley; Estados Unidos. Universidad Nacional Autónoma de México; MéxicoFil: Santamaría, Rosa I.. Universidad Nacional Autónoma de México; MéxicoFil: Bustos, Patricia. Universidad Nacional Autónoma de México; MéxicoFil: Juárez, Soledad. Universidad Nacional Autónoma de México; MéxicoFil: Ducci, Maria Antonella. Universidad Nacional de Salta; Argentina. Instituto Nacional de Tecnología Agropecuaria; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Salta; ArgentinaFil: Figueroa Fleming, Trinidad. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Salta; Argentina. Universidad Nacional de Salta; ArgentinaFil: Etcheverry, Angela Virginia. Universidad Nacional de Salta; ArgentinaFil: González, Víctor. Universidad Nacional Autónoma de México; Méxic

Selection mosaics in a plant bacteria mutualism: The genetic structure of Rhizobium leguminosarum nodulating Vicia cracca in different nitrogen environments

Leguminose plant species are able to acquire nitrogen (N) through the interaction with N fixing bacteria of the genus Rhizobium, offering a clear fitness advantage over plant competitors, particularly under N limiting conditions. In the last 50 years anthropogenic eutrophication has strongly increased available soil N through atmospheric deposition and fertilizer runoff. Because eutrophication shows spatial variation, geographical selection mosaics in Rhizobium – host interactions are expected to occur because selection on the traits mediating co-evolution varies. This results in spatial variation in co-evolutionary interactions (i.e. “The geographical mosaic of co-evolution” sensu Thompson (2005)). These co-evolutionairy interactions may have an ecological impact on the plant community, the ecosystem or even on higher trophic levels. This study will be conducted on the mutualistic association between the clonal leguminose Vicia cracca (bird vetch) and the N-fixing bacteria Rhizobium leguminosarum biovar viciae. There will be close cooperation withthe Rhizobium experts from the Centre of Microbial and PlantGenetics at KULeuven. Our main objectives are to: characterizethe genotypic variation of V. cracca and Rhizobium across a gradient of eutrophication, test the local adaptation of the V. cracca – Rhizobium mutualism through a cross-infection experiment, investigate the degree in which specific Rhizobium populations impacts host genotype sorting, determine the impact of the Rhizobium strain composition on the plant community and test the effect of the V. cracca – Rhizobium mutualism on aphid genotype sorting.nrpages: 177status: publishe

How might bacteriophages shape biological invasions?

ABSTRACT Invasions by eukaryotes dependent on environmentally acquired bacterial mutualists are often limited by the ability of bacterial partners to survive and establish free-living populations. Focusing on the model legume-rhizobium mutualism, we apply invasion biology hypotheses to explain how bacteriophages can impact the competitiveness of introduced bacterial mutualists. Predicting how phage-bacteria interactions affect invading eukaryotic hosts requires knowing the eco-evolutionary constraints of introduced and native microbial communities, as well as their differences in abundance and diversity. By synthesizing research from invasion biology, as well as bacterial, viral, and community ecology, we create a conceptual framework for understanding and predicting how phages can affect biological invasions through their effects on bacterial mutualists

Effects of local environmental variables and geographical location on the genetic diversity and composition of Rhizobium leguminosarum nodulating Vicia cracca populations

Different legume populations are known to accommodate different genotypes of Rhizobium leguminosarum. However, in contrast to interspecific diversity and composition, very little is known regarding which environmental factors drive the genetic diversity and genetic composition of a single Rhizobium species. Based on chromosomal and plasmid genes, we quantified the genetic diversity and compositional differences of R. leguminosarum biovar viciae genotypes associated with twenty-four different Vicia cracca populations across a wide environmental and geographical range. Long-term soil nitrogen availability had a positive effect on chromosomal and plasmid diversity, whereas salinity had a negative effect on chromosomal diversity. Soil pH and geographic distance were the main factors driving compositional differences among populations. In contrast to differences in chromosomal composition, differences in the symbiotic plasmid composition were primarily related to geographic distance or unmeasured related environmental factors (e.g. host plant genetic differentiation). We propose different hypotheses to explain how long-term soil nitrogen availability affects rhizobial genetic diversity. Furthermore, our findings demonstrate that ecological processes that are known to operate at the interspecific level do not necessarily result in the same patterns at the intraspecific level.publisher: Elsevier articletitle: Effects of local environmental variables and geographical location on the genetic diversity and composition of Rhizobium leguminosarum nodulating Vicia cracca populations journaltitle: Soil Biology and Biochemistry articlelink: http://dx.doi.org/10.1016/j.soilbio.2015.08.001 content_type: article copyright: Copyright © 2015 Elsevier Ltd. All rights reserved.status: publishe

Data from: Selection mosaics differentiate Rhizobium–host plant interactions across different nitrogen environments

The nature and direction of coevolutionary interactions between species is expected to differentiate among distinct environments. Consequently, locally coevolved symbiotic traits would be well matched in similar environments, but mismatched elsewhere. In a classic mutualistic tradeoff, rhizobia provide nitrogen (N) to legume host plants in return for photosynthates. Despite earlier predictions, there is little evidence so far that spatial differences in soil N content mediate the coevolutionary outcome of the legume–Rhizobium mutualism. To test the existence of such selection mosaics, different genotypes of Vicia cracca and Rhizobium leguminosarum originating from spatially and environmentally highly differentiated sites were cross inoculated across different soil N regimes. In accordance with theoretical predictions, we found highly significant effects of genotype by genotype by environment (G× G × E) interactions, on both nodulation and plant growth, even when R. leguminosarum genotypes showed high genetic similarity. Our results show that the trajectory of the coevolutionary interactions between rhizobia and legumes is differentiated across different environments, and that selection mosaics may play an important role in shaping differences in the genetic composition of rhizobial populations

Population structure of root nodulating Rhizobium leguminosarum in Vicia cracca populations at local to regional geographic scales

The genetic diversity and population structure of about 350 Rhizobium leguminosarum biovar viciae isolates from Vicia cracca were analysed. A hierarchical sampling design was used covering three regions, one region in Belgium and two in France, in which multiple local V. cracca populations were sampled. Rhizobium isolates were genotyped using RAPD and by sequencing two chromosomal housekeeping genes (glnII and recA) and one plasmid-borne gene (nodC). Twenty-six nodC types and sixty-seven chromosomal types were identified, many of which appeared to be regional or local endemics. We found strong genetic differentiation both among V. cracca populations that are separated by only a few kilometres, and among regions that are 50 to 350km apart. Despite significant plasmid exchange, chromosomal and nod types were similarly structured among host populations and regions. We found two lineages of which one prevailed in the Belgian region while the other dominated the French regions. Although a significant correlation between genetic differentiation and geographic distance was found, it is deemed more likely that the observed biogeographic patterns are rather due to coevolutionary interactions and environmental pressures. Furthermore, the impact of recombination on the chromosomal differentiation was found to be considerable.publisher: Elsevier articletitle: Population structure of root nodulating Rhizobium leguminosarum in Vicia cracca populations at local to regional geographic scales journaltitle: Systematic and Applied Microbiology articlelink: http://dx.doi.org/10.1016/j.syapm.2014.08.002 content_type: article copyright: Copyright © 2014 Elsevier GmbH. All rights reserved.status: publishe

Symbiont abundance is more important than pre-infection partner choice in a Rhizobium – legume mutualism

It is known that the genetic diversity of conspecific rhizobia present in root nodules differs greatly among populations of a legume species, which has led to the suggestion that both dispersal limitation and the local environment affect rhizobial genotypic composition. However, it remains unclear whether rhizobial genotypes residing in root nodules are representative of the entire population of compatible symbiotic rhizobia. Since symbiotic preferences differ among legume populations, the genetic composition of rhizobia found within nodules may reflect the preferences of the local hosts, rather than the full diversity of potential nodulating rhizobia present in the soil. Here, we assessed whether Vicia cracca legume hosts of different provenances select different Rhizobium leguminosarum genotypes than sympatric V. cracca hosts, when presented a natural soil rhizobial population. Through combining V. cracca plants and rhizobia from adjacent and more distant populations, we found that V. cracca hosts are relatively randomly associated with rhizobial genotypes. This indicates that pre-infection partner choice is relatively weak in certain legume hosts when faced with a natural population of rhizobia.publisher: Elsevier articletitle: Symbiont abundance is more important than pre-infection partner choice in a Rhizobium – legume mutualism journaltitle: Systematic and Applied Microbiology articlelink: http://dx.doi.org/10.1016/j.syapm.2016.05.007 content_type: article copyright: © 2016 Elsevier GmbH. All rights reserved.status: publishe

Response variables per treatment -Van Cauwenberghe et al. 2016 Oikos

Response variables per treatment -Van Cauwenberghe et al. 2016 Oiko

Recombination and horizontal transfer of nodulation and ACC deaminase (acdS) genes within Alpha- and Betaproteobacteria nodulating legumes of the Cape Fynbos biome

The goal of this work is to study the evolution and the degree of horizontal gene transfer (HGT) within rhizobial genera of both Alphaproteobacteria (Mesorhizobium, Rhizobium) and Betaproteobacteria (Burkholderia), originating from South African Fynbos legumes. By using a phylogenetic approach and comparing multiple chromosomal and symbiosis genes, we revealed conclusive evidence of high degrees of horizontal transfer of nodulation genes among closely related species of both groups of rhizobia, but also among species with distant genetic backgrounds (Rhizobium and Mesorhizobium), underscoring the importance of lateral transfer of symbiosis traits as an important evolutionary force among rhizobia of the Cape Fynbos biome. The extensive exchange of symbiosis genes in the Fynbos is in contrast with a lack of significant events of HGT among Burkholderia symbionts from the South American Cerrado and Caatinga biome. Furthermore, homologous recombination among selected housekeeping genes had a substantial impact on sequence evolution within Burkholderia and Mesorhizobium. Finally, phylogenetic analyses of the non-symbiosis acdS gene in Mesorhizobium, a gene often located on symbiosis islands, revealed distinct relationships compared to the chromosomal and symbiosis genes, suggesting a different evolutionary history and independent events of gene transfer. The observed events of HGT and incongruence between different genes necessitate caution in interpreting topologies from individual data types.status: publishe

Characterization of the papilionoid-<i>Burkholderia</i> interaction in the Fynbos biome:The diversity and distribution of beta-rhizobia nodulating <i>Podalyria calyptrata </i>(Fabaceae, Podalyrieae)

status: publishe