Biology subjects

Epstein, B.

Publications and source records attributed to Epstein, B..

9 recordsLinked to original sources

bioRxiv2025

Rhizobia independently adapt to soil and legume host environments, but soil conditions influence the abundance of high-quality partners.

Rhizobia live as free-living microorganisms in the soil and in association with legume hosts. Both environments exert selective pressures on rhizobia, influencing the reproductive success of individual strains (e.g., fitness). The soil, a heterogeneous and fluctuating environment, is often overlooked, and little is known about whether selection in the soil influences the outcomes of the rhizobia-legume mutualism. We exposed a mixture of 68 Sinorhizobium meliloti strains to eight soil treatments (temperature, osmotic, and texture perturbations) and selection by two Medicago plant hosts. We found that cold (4{degrees}C) and warm (32{degrees}C) temperatures, as well as salt addition, had the strongest effects on diversity, community composition, or population size. Strain relative fitness was strongly positively correlated among soil treatments, except for cold. Genome-wide association analysis revealed a complex genetic architecture for soil fitness. In contrast, when comparing rhizobial fitness between soil and host environments, we found minimal strain fitness correlations, suggesting independent genetic bases and habitat-specific adaptations. Lastly, by examining the relationship between rhizobial fitness in the soil and their nitrogen-fixing plant benefits, we found that soil selection influenced the relative abundance of high- and low-quality strains; However, whether these effects were positive or negative for the plant was host dependent. Our results suggest that rhizobial evolution in soil and host are largely independent, but soil selection can alter mutualism benefits. IMPORTANCERhizobia-legume mutualism is crucial for introducing nitrogen into agricultural and natural ecosystems, and rhizobia persistence in the soil is an important component of agroecosystems. However, we know little about how individual strains of rhizobia persist and adapt to this environment, especially in the context of the soils spatial and temporal variations (temperature, moisture, and soil texture). We found that rhizobia similarly adapt to abiotic soil conditions but their reproductive success in the soil is independent from their reproductive success in the host. Intriguingly, we found that certain soil conditions increase (or decrease) the relative abundance of more effective nitrogen-fixing strains. Understanding how rhizobia adapt to diverse environments is crucial for developing effective bioinoculants that maintain high persistence in the soil while are also highly competitive to colonize the host and are beneficial to the plant.

ecology↗

bioRxiv2025

Genetic variation in host selectivity and adaptive strain enrichment within legume-rhizobia symbiosis: processes are host-dependent, far from perfect, and correlate with nodule morphology

Mutualism breakdown can be prevented if partner species preferentially select and reward partners that provide greater benefit. We examined these two components using the legume Medicago truncatula and its nitrogen-fixing symbiont Sinorhizobium meliloti. First, we reanalyzed data from 202 accessions to show significant genetic variation in the capacity of Medicago to restrict strain diversity, finding that hosts with shorter nodules were more selective. A genome-wide association study on host selectivity identified genes including the hormone leginsulin, pectin degradation, multidrug and toxic compound efflux, Zinc transport, and DNA methylation. Second, we used two well-studied Medicago genotypes with contrasting nodule morphologies to assess the effectiveness of adaptive enrichment mechanisms by sampling the relative frequencies of rhizobial strains in pools of small nodules (indicating a lack of host investment) compared to large nodules (indicating increased host investment) and pairing these results with previous single-strain assessments of strain benefits to hosts. While both hosts enriched beneficial strains in large nodules, the host that formed larger and more variably sized nodules and thus had greater potential to increase rhizobial populations was less effective. Our findings reveal that host genetic variation affects strain selectivity and suggest that nodule traits warrant attention when exploring mutualism evolution.

evolutionary biology↗

bioRxiv2024

In multi-strain inoculations, mutation of Medicago symbiosis genes creates a complex selective landscape for naturally-occurring genetic variation in rhizobia

In the mutualism between leguminous plants and rhizobia bacteria, rhizobia live inside root nodules, creating potential for host genes to shape the rhizobial selective environment. Many host genes that affect symbiosis have been identified; however, the extent to which these genes affect selection acting on rhizobia is unknown. In this study, we inoculated 18 Medicago truncatula symbiotic mutants (including mutants that alter Nodule Cysteine-Rich (NCR) peptide production, plant defense, and nodule number regulation) with a mixture of 86 Sinorhizobium meliloti strains. Most mutations resulted in reduced host benefits, but the effects on rhizobial benefit (i.e., relative strain fitness) varied widely, revealing widespread host-by-strain fitness interactions. Genome-wide association analyses identified variants on rhizobial replicons pSymA and pSymB as important in mediating strain fitness responses to host mutations. Whereas most top variants affected rhizobial fitness with one host mutant (limited effect variants), nine affected fitness across six or more host mutations. These pervasive variants occurred primarily on pSymA, the symbiotic replicon, and include fixL and some metabolic genes. In contrast to the limited effect variants, variants with pervasive positive effects on strain fitness when host genes were mutated tended to adversely affect fitness in wild-type hosts. Competition assays across Medicago genotypes confirmed a pervasive role for one candidate (malonyl-CoA synthase), and AlphaFold multimer modelling suggests that many rhizobial top candidates could interact with host NCR peptides. Our results reveal how host genetic variation affects rhizobial fitness, setting the stage for improving rhizobial inoculants and breeding legume hosts better adapted to multi-strain environments.

evolutionary biology↗

bioRxiv2023

Local adaptation to mercury contamination by nitrogen-fixing rhizobia is driven by horizontal gene transfer, copy number, and enhanced gene expression

Mercury (Hg) is highly toxic and has the potential to cause severe health problems for foraging animals and humans when transported into edible plant parts. Soil rhizobia that form symbiosis with legumes may possess mechanisms to prevent heavy metal translocation from roots to shoots in plants by exporting metals from nodules or compartmentalizing metal ions inside nodules. Using long-read sequencing, we assembled the genomes of Sinorhizobium medicae and Rhizobium leguminosarum from the Almaden mercury mine in Spain with high variation in Hg-tolerance to identify structural and transcriptomic differences between low and high Hg-tolerant strains. While independent mercury reductase A (merA) genes are prevalent in -proteobacteria, Mer operons are rare and often vary in their gene organization. Our analyses identified multiple structurally conserved merA homologs in the genomes of S. medicae, including a dihydrolipoamide 2-oxoglutarate dehydrogenase (D2OD), but only the strains that possessed a Mer operon exhibited hypertolerance to Hg. Using RNAseq reads mapped to the unique genome assemblies, we found the Hg-tolerant strains which possessed a Mer operon, that nearly all genes within the operon were significantly up-regulated in response to Hg stress in free-living conditions and in nodules. In both free-living and nodule environments, we found the Hg-tolerant strains with a Mer operon exhibited the fewest number of DEGs in the genome, indicating a rapid and efficient detoxification of Hg2+ from the cells that reduced general stress responses to the Hg-treatment. Expression changes in S. medicae while inside of nodules showed that both rhizobia strain and host-plant tolerance affected the number of DEGs. Aside from Mer operon genes, nif genes which are involved in nitrogenase activity in S. medicae showed significant up-regulation in the most Hg-tolerant strain while inside the most Hg-accumulating host-plant, indicating a genotype-by-genotype interaction that influences nitrogen-fixation under stress conditions. Transfer of the Mer operon to non-tolerant strains resulted in an immediate increase in Hg tolerance, indicating that the operon is solely necessary to confer hypertolerance to Hg, despite paralogous merA genes present elsewhere in the genome. This study demonstrated that the Mer operon can be exchanged via horizontal gene transfer into non-tolerant rhizobia strains naturally and experimentally.

microbiology↗

bioRxiv2021

Partners in space: Discordant population structure between legume hosts and rhizobium symbionts in their native range

Coevolution is predicted to depend on how the genetic diversity of interacting species is geographically structured. Plant-microbe symbioses such as the legume-rhizobium mutualism are ecologically and economically important, but distinct life history and dispersal mechanisms for these host and microbial partners, plus dynamic genome composition in bacteria, present challenges for understanding spatial genetic processes in these systems. Here we study the model rhizobium Ensifer meliloti using a hierarchically-structured sample of 191 strains from 21 sites in the native range and compare its population structure to that of its host plant Medicago truncatula. We find high local genomic variation and minimal isolation by distance across the rhizobium genome, particularly at the two symbiosis elements pSymA and pSymB, which have evolutionary histories and population structures that are similar to each other but distinct from both the chromosome and the host. While the chromosome displays weak isolation by distance, it is uncorrelated with hosts. Patterns of discordant population structure among elements with the bacterial genome has implications for bacterial adaptation to life in the soil versus symbiosis, while discordant population genetic structure of hosts and microbes might restrict local adaptation of species to each other and give rise to phenotypic mismatches in coevolutionary traits.

evolutionary biology↗

bioRxiv2020

Environment dependence of rhizobial relative fitness in the legume-rhizobia symbiosis

The environmental context of the nitrogen-fixing mutualism between leguminous plants and rhizobial bacteria varies over space and time. Variation in resource availability, population density, and composition likely affect the ecology and evolution of rhizobia and their symbiotic interactions with hosts. We examined how host genotype, nitrogen addition, rhizobial density, and community complexity affected selection on 68 rhizobia strains in the Ensifer meliloti - Medicago truncatula mutualism. As expected, the host genotype had the most substantial effect on the size, number, and strain composition of root nodules (the symbiotic organ). The understudied environmental variable of rhizobial density had a more significant effect on strain frequency in nodules than the addition of low nitrogen levels. Higher inoculum density resulted in a nodule community that was less diverse and more beneficial but only in the context of the more selective host genotype. Higher density resulted in more diverse and less beneficial nodule communities with the less selective host. Density effects on strain composition deserve additional scrutiny as they can create eco-evolutionary feedback. Lastly, we found that relative strain rankings were stable across increasing community complexity (community complexity (2, 3, 8, or 68 strains). This unexpected result suggests that higher-order interactions between strains are rare in the context of host nodule formation and development. Taken together, our empirical work highlights the importance of developing new theoretical predictions that incorporate density dependence. Further, it has translational relevance for overcoming establishment barriers in bio-inoculants and motivating host breeding programs that maintain beneficial plant-microbe interactions across diverse agro-ecological contexts. IMPORTANCELegume cash, forage, and cover crops establish beneficial associations with rhizobial bacteria who perform biological nitrogen fixation (BNF)--providing Nitrogen (N) fertilizer to plants without the economic and greenhouse gas emission costs of chemical N inputs. Here, for the first time, we examine the relative influence of three environmental factors that vary in agricultural fields on strain relative fitness in nodules when scores rhizobial strains compete. In addition to manipulating Nitrogen, we also use two biotic variables that have rarely been examined: the rhizobial communitys density and complexity. Taken together, our results suggest 1) breeding legume varieties that select beneficial strains despite environmental variation are possible, 2) changes in rhizobial population densities that occur routinely in agricultural fields could drive evolutionary changes in rhizobia populations, and 3) the lack of higher-order interactions between strains will allow the high-throughput assessments of rhizobia winners and losers during plant interactions.

ecology↗

bioRxiv2020

Historical and contemporary signatures of selection in response to transmissible cancer in the Tasmanian Devil (Sarcophilus harrisii)

Tasmanian devils (Sarcophilus harrisii) are evolving in response to a unique transmissible cancer, devil facial tumour disease (DFTD), first described in 1996. Persistence of wild populations and the recent emergence of a second independently evolved transmissible cancer suggest that transmissible cancers may be a recurrent feature in devils. Here we compared signatures of selection across temporal scales to determine whether genes or gene pathways under contemporary selection (6-8 generations) have also been subject to historical selection (65-85 million years), and test for recurrent selection in devils. First, we used a targeted sequencing approach, RAD-capture, to identify genomic regions subject to rapid evolution in approximately 2,500 devils in six populations as DFTD spread across the species range. We documented genome-wide contemporary evolution, including 186 candidate genes related to cell cycling and immune response. Then we used a molecular evolution approach to identify historical positive selection in devils compared to other marsupials and found evidence of selection in 1,773 genes. However, we found limited overlap across time scales, with historical selection detected in only 16 contemporary candidate genes, and no overlap in enriched functional gene sets. Our results are consistent with a novel, multi-locus evolutionary response of devils to DFTD. Our results can inform management actions to conserve adaptive potential of devils by identifying high priority targets for genetic monitoring and maintenance of functional diversity in managed populations.

evolutionary biology↗

bioRxiv2019

Disease swamps molecular signatures of genetic-environmental associations to abiotic factors in Tasmanian devil (Sarcophilus harrisii) populations

Landscape genomics studies focus on identifying candidate genes under selection via spatial variation in abiotic environmental variables, but rarely by biotic factors such as disease. The Tasmanian devil (Sarcophilus harrisii) is found only on the environmentally heterogeneous island of Tasmania and is threatened with extinction by a nearly 100% fatal, transmissible cancer, devil facial tumor disease (DFTD). Devils persist in regions of long-term infection despite epidemiological model predictions of species extinction, suggesting possible adaptation to DFTD. Here, we test the extent to which spatial variation and genetic diversity are associated with the abiotic environment and/or by DFTD. We employ genetic-environment association (GEAs) analyses using a RAD-capture panel consisting of 6,886 SNPs from 3,286 individuals sampled pre- and post-disease arrival. Pre-disease, we find significant correlations of allele frequencies with environmental variables, including 349 unique loci linked to 64 genes, suggesting local adaptation to abiotic environment. Following DFTD arrival, however, we detected few of the pre-disease candidate loci, but instead frequencies of candidate loci linked to 14 genes correlated with disease prevalence. Loss of apparent signal of abiotic local adaptation following disease arrival suggests swamping by the strong selection imposed by DFTD. Further support for this result comes from the fact that post-disease candidate loci are in linkage disequilibrium with genes putatively involved in immune response, tumor suppression and apoptosis. This suggests the strength GEA associations of loci with the abiotic environment are swamped resulting from the rapid onset of a biotic selective pressure.

evolutionary biology↗

bioRxiv2019

Hybridizing salamanders experience accelerated diversification

Whether hybridization generates or erodes species diversity has long been debated, but to date most studies have been conducted at small taxonomic scales. Salamanders (order Caudata) represent a taxonomic order in which hybridization plays a prevalent ecological and evolutionary role. We employed a recently developed model of trait-dependent diversification to test the hypothesis that hybridization impacts the diversification dynamics of species that are currently hybridizing. We find strong evidence supporting this hypothesis, showing that hybridizing salamander lineages have significantly greater net-diversification rates than non-hybridizing lineages. This pattern is driven by concurrently increased speciation rates and decreased extinction rates in hybridizing lineages. Our results support the hypothesis that hybridization can act as a generative force in macroevolutionary diversification.

evolutionary biology↗