The capacity to respond to environmental challenges ultimately relies on phenotypic variation which manifests from complex interactions of genetic and nongenetic mechanisms through development. While we know something about genetic variation and structure of many species of conservation importance, we know very little about the nongenetic contributions to variation.Rhizophora mangleis a foundation species that occurs in coastal estuarine habitats throughout the neotropics where it provides critical ecosystem functions and is potentially threatened by anthropogenic environmental changes. Several studies have documented landscape‐level patterns of genetic variation in this species, but we know virtually nothing about the inheritance of nongenetic variation. To assess one type of nongenetic variation, we examined the patterns of DNA sequence and DNA methylation in maternal plants and offspring from natural populations ofR. manglefrom the Gulf Coast of Florida. We used a reduced representation bisulfite sequencing approach (epi‐genotyping by sequencing; epiGBS) to address the following questions: (a) What are the levels of genetic and epigenetic diversity in natural populations ofR. mangle? (b) How are genetic and epigenetic variation structured within and among populations? (c) How faithfully is epigenetic variation inherited? We found low genetic diversity but high epigenetic diversity from natural populations of maternal plants in the field. In addition, a large portion (up to ~25%) of epigenetic differences among offspring grown in common garden was explained by maternal family. Therefore, epigenetic variation could be an important source of response to challenging environments in the genetically depauperate populations of this foundation species.

Vital for many marine and terrestrial species, and several other environmental services, such as carbon sink areas, the mangrove ecosystem is highly threatened due to the proximity of large urban centers and climate change. The forced fragmentation of this ecosystem affects the genetic diversity distribution among natural populations. Moreover, while restoration efforts have increased, few studies have analyzed how recently-planted areas impact the original mangrove genetic diversity. We analyzed the genetic diversity of two mangroves species (Laguncularia racemosa and Avicennia schaueriana) in three areas in Brazil, using inter-simple sequence repeat (ISSR) markers. Using the local approach, we identified the genetic diversity pool of a restored area compared to nearby areas, including the remnant plants inside the restored area, one well-conserved population at the shore of Guanabara Bay, and one impacted population in Araçá Bay. The results for L. racemosa showed that the introduced population has lost genetic diversity by drift, but remnant plants with high genetic diversity or incoming propagules could help improve overall genetic diversity. Avicennia schaueriana showed similar genetic diversity, indicating an efficient gene flow. The principal component analysis showing different connections between both species indicate differences in gene flow and dispersal efficiencies, highlighting the needed for further studies. Our results emphasize that genetic diversity knowledge and monitoring associated with restoration actions can help avoid bottlenecks and other pitfalls, especially for the mangrove ecosystem.

The capacity to respond to environmental challenges ultimately relies on phenotypic variation which manifests from complex interactions of genetic and non-genetic mechanisms through development. While we know something about genetic variation and structure of many species of conservation importance, we know very little about the non-genetic contributions to variation. Rhizophora mangle is a foundation species that occurs in coastal estuarine habitats throughout the neotropics where it provides critical ecosystem functions, and is potentially threatened by climate change. Several studies have documented landscape level patterns of genetic variation in this species, but we know virtually nothing about the inheritance of non-genetic variation. To assess one type of non-genetic variation, we examined the patterns of DNA sequence and DNA methylation in maternal plants and offspring from natural populations of R. mangle from the Gulf Coast of Florida. We used a reduced representation bisulfite sequencing approach (epi-genotyping by sequencing or epiGBS) to address the following questions: a) What are the levels of genetic and epigenetic diversity in natural populations of R. mangle ? b) How are genetic and epigenetic variation structured within and among populations? c) How faithfully is epigenetic variation inherited? We found low genetic diversity but high epigenetic diversity from natural populations of maternal plants in the field and that a large portion (up to ~25%) of epigenetic differences among offspring grown in common garden was explained by maternal family. Therefore, epigenetic variation could be an important source of response to challenging environments in the genetically depauperate populations of this foundation species.

Beneficial root-associated microbes can enhance plant resilience by complementing aspects of host immunity. The fungal root endophyte Serendipita indica ( Si ) is known to promote plant growth and confer broad stress tolerance. To assess how natural host genetic variation influences Si -mediated protection, we screened 47 Arabidopsis thaliana accessions for susceptibility to the fungal pathogen Bipolaris sorokiniana ( Bs ) with and without Si colonization. All accessions benefited from Si , indicating that endophyte-mediated disease mitigation occurs broadly across diverse host genotypes. A focused comparison of two genetically and geographically proximate Swedish accessions, T510 and T530, which displayed the most divergent protection scores, revealed substantial differences in Bs susceptibility. Transcriptome profiling under bi- and tripartite colonization showed conserved defense responses in both accessions. Bs infection downregulated growth- and development-related genes, consistent with a growth–immunity trade-off, with T530 exhibiting higher Bs colonization and a stronger transcriptional response than T510. Co-colonization with Si effectively suppressed pathogen growth and disease symptoms in both accessions. Comparative genomic and transcriptomic analyses identified four immune receptor genes, including the TIR-NLR ISI , present in T510 but absent in T530. An isi T-DNA insertion mutant phenocopied the heightened Bs susceptibility of T530, confirming that ISI contributes to root immunity, while Si -mediated protection remained intact despite increased pathogen susceptibility. Together, these findings demonstrate that fungal endophytes can mitigate the functional consequences of natural immune variation and enhance the resilience of genetically diverse plant populations. Highlights: S. indica confers broad protection against B. sorokiniana largely independent of host genotype or pathogen susceptibility. The TIR-NLR immune receptor ISI contributes to root immunity but is not essential for S. indica -mediated protection. Beneficial endophytes can mitigate natural immune variation effects and support overall plant health.

Summary: Host genetic diversity shapes pathogen susceptibility within plant populations, raising the question of whether beneficial root microbes can buffer these differences. The fungal root endophyte Serendipita indica ( Si ) promotes plant growth and can mitigate disease caused by the pathogen Bipolaris sorokiniana ( Bs ). Here, we assessed how natural host genetic variation influences Si ‐mediated protection against Bs in Arabidopsis thaliana . We screened 47 A. thaliana accessions for susceptibility to Bs with and without Si colonization and performed phenotypic, transcriptomic, and comparative genomic analyses of two genetically and geographically proximate Swedish accessions, T510 and T530, that differed strongly in Bs colonization. Si conferred consistent protection against Bs across all accessions, despite variation in baseline susceptibility and immune‐gene content. T510 and T530 differed in Bs colonization, disease symptoms, transcriptional responses, and immune‐gene repertoires, including presence–absence variation of the TIR‐NLR gene ISI . T530 lacks ISI , and mutation of ISI in Col‐0 increased Bs susceptibility, demonstrating that ISI contributes to root immunity. However, Si ‐mediated protection was retained in the absence of ISI , demonstrating that ISI is not required for this protective effect. Beneficial fungal endophytes can thus buffer phenotypic consequences of natural variation in pathogen susceptibility, stabilizing disease outcomes across genetically diverse plant populations.