Impacts of global change on the phyllosphere microbiome

Meng

et al. 2022

New Phytologist

Mountains are pivotal to maintaining habitat heterogeneity, global biodiversity, ecosystem functions and services to humans. They have provided classic model natural systems for plant and animal diversity gradient studies for over 250 years. In the recent decade, the exploration of microorganisms on mountainsides has also achieved substantial progress. Here, we review the literature on microbial diversity across taxonomic groups and ecosystem types on global mountains. Microbial community shows climatic zonation with orderly successions along elevational gradients, which are largely consistent with traditional climatic hypotheses. However, elevational patterns are complicated for species richness without general rules in terrestrial and aquatic environments and are driven mainly by deterministic processes caused by abiotic and biotic factors. We see a major shift from documenting patterns of biodiversity towards identifying the mechanisms that shape microbial biogeographical patterns and how these patterns vary under global change by the inclusion of novel ecological theories, frameworks and approaches. We thus propose key questions and cutting-edge perspectives to advance future research in mountain microbial biogeography by focusing on biodiversity hypotheses, incorporating meta-ecosystem framework and novel key drivers, adapting recently developed approaches in trait-based ecology and manipulative field experiments, disentangling biodiversity-ecosystem functioning relationships and finally modelling and predicting their global change responses.

Section: Introductionmentioning

confidence: 99%

Embracing mountain microbiome and ecosystem functions under global change

Meng

et al. 2022

New Phytologist

“…Experimental studies have demonstrated that the phyllosphere harbors diverse microbial communities that in uenced ecosystem functioning [14][15][16][17][18][19]. Recent studies stress the importance of understanding the mechanisms underlying how plant-microbe interactions in the phyllosphere could in uence host survival and tness in the context of global change [20,21]. Several studies have illustrated that host genotypes can in uence the composition of the leaf microbiome [22][23][24], but little is clear how the plant shapes its leaf microbiota and how the leaf microbiome contributes to plant phenotypic traits [25][26][27].…”

Section: Introductionmentioning

confidence: 99%

Disentangling leaf-microbiome interactions in Arabidopsis thaliana by network mapping

Cheng

et al. 2022

Preprint

Background The leaf microbiota plays a key role in plant development, but a detailed mechanism of microbe-plant relationships remains elusive. Many genome-wide association studies (GWAS) have begun to map leaf microbes, but few has systematically characterized the genetics of how microbes act and interact. Previously, we integrated behavioral ecology and game theory to define four types of microbial interactions – mutualism, antagonism, aggression, and altruism, in a microbial community assembly. Results Here, we apply network mapping to identify specific plant genes that mediate the topological architecture of microbial networks. Analyzing leaf microbiome data from an Arabidopsis GWAS, we identify several heritable hub microbes for leaf microbial communities and detect 140–728 SNPs responsible for emergent properties of microbial network. We reconstruct Bayesian genetic networks from which to identify 22–43 hub genes found to code molecular pathways related to leaf growth, abiotic stress responses, disease resistance and nutrition uptake. A further path analysis visualizes how genetic variants of Arabidopsis affect its fecundity through the internal workings of the leaf microbiome. We find that microbial networks and their genetic control vary along spatiotemporal gradients. Our study provides a new avenue to reveal the “endophenotype” role of microbial networks in linking genotype to end-point phenotypes in plants. Conclusions Our integrative theory model provides a powerful tool to understand the mechanistic basis of structural-functional relationships within the leaf microbiome and supports the need for future research on plant breeding and synthetic microbial consortia with a specific function.

“…Experimental studies have demonstrated that the phyllosphere harbors diverse microbial communities that influenced ecosystem functioning (14)(15)(16)(17)(18)(19). Recent studies stress the importance of understanding the mechanisms underlying how plant-microbe interactions in the phyllosphere could influence host survival and fitness in the context of global change (20,21). Several studies have illustrated that host genotypes can influence the composition of the leaf microbiome (22)(23)(24), but little is clear how the plant shapes its leaf microbiota and how the leaf microbiome contributes to plant phenotypic traits (25)(26)(27).…”

Section: Introductionmentioning

confidence: 99%

Disentangling leaf-microbiome interactions inArabidopsis thalianaby network mapping

Cheng

et al. 2022

Preprint

The leaf microbiota plays a key role in plant development, but a detailed mechanism of microbe-plant relationships remains elusive. Many genome-wide association studies (GWAS) have begun to map leaf microbes, but few has systematically characterized the genetics of how microbes act and interact. Previously, we integrated behavioral ecology and game theory to define four types of microbial interactions – mutualism, antagonism, aggression, and altruism, in a microbial community assembly. Here, we apply network mapping to identify specific plant genes that mediate the topological architecture of microbial networks. Analyzing leaf microbiome data from an Arabidopsis GWAS, we identify several heritable hub microbes for leaf microbial communities and detect 140-728 SNPs responsible for emergent properties of microbial network. We reconstruct Bayesian genetic networks from which to identify 22-43 hub genes found to code molecular pathways related to leaf growth, abiotic stress responses, disease resistance and nutrition uptake. A further path analysis visualizes how genetic variants of Arabidopsis affect its fecundity through the internal workings of the leaf microbiome. We find that microbial networks and their genetic control vary along spatiotemporal gradients. Our study provides a new avenue to reveal the “endophenotype” role of microbial networks in linking genotype to end-point phenotypes in plants. Our integrative theory model provides a powerful tool to understand the mechanistic basis of structural-functional relationships within the leaf microbiome and supports the need for future research on plant breeding and synthetic microbial consortia with a specific function.IMPORTANCEIt is found that plant genes act as microbiome gatekeepers to select which microbes get to live inside the leaves for health. Many genome-wide association studies (GWAS) have begun to map leaf microbes, but few has systematically characterized the genetics of how microbes act and interact. This work illustrates a more comprehensive picture of the genetic architecture underlying the leaf microbiome by network mapping. This study also dissects how genetic variants affect its fecundity by direct path and indirect path through microbial network, revealing the “endophenotype” role of microbial networks in linking genotype to end-point phenotypes. Future studies could benefit from this work to improve understanding the underlying genetic mechanisms that govern the relationships between plants and their microbiomes, and to manipulate plant genetic system to reconfigure microbiome. Plants could become more efficient at selecting their microbial partners to improve their health, resilience, and productivity.