Plant genetic effects on microbial hubs impact host fitness in repeated field trials.

Although complex interactions between hosts and microbial associates are increasingly well documented, we still know little about how and why hosts shape microbial communities in nature. In addition, host genetic effects on microbial communities vary widely depending on the environment, obscuring conclusions about which microbes are impacted and which plant functions are important. We characterized the leaf microbiota of 200 Arabidopsis thaliana genotypes in eight field experiments and detected consistent host effects on specific, broadly distributed microbial species (operational taxonomic unit [OTUs]). Host genetic effects disproportionately influenced central ecological hubs, with heritability of particular OTUs declining with their distance from the nearest hub within the microbial network. These host effects could reflect either OTUs preferentially associating with specific genotypes or differential microbial success within them. Host genetics associated with microbial hubs explained over 10% of the variation in lifetime seed production among host genotypes across sites and years. We successfully cultured one of these microbial hubs and demonstrated its growth-promoting effects on plants in sterile conditions. Finally, genome-wide association mapping identified many putatively causal genes with small effects on the relative abundance of microbial hubs across sites and years, and these genes were enriched for those involved in the synthesis of specialized metabolites, auxins, and the immune system. Using untargeted metabolomics, we corroborate the consistent association between variation in specialized metabolites and microbial hubs across field sites. Together, our results reveal that host genetic variation impacts the microbial communities in consistent ways across environments and that these effects contribute to fitness variation among host genotypes.

Early succession on slag compared to urban soil: A slower recovery.

Slag, waste from the steel-making process, contains large amounts of calcium, magnesium, iron and other heavy metals. Because of its composition, high pH and low water retention ability, slag is considered inhospitable to plants. Nevertheless, the spontaneously generated plant communities on slag are surprisingly diverse, but the assembly and structure of such communities are poorly studied. Previous studies suggest reduced rates of succession due to low growth rate and slow accumulation of topsoil. To investigate whether slag communities display similar patterns, we used two former industrial sites on the South Side of Chicago, IL, both with high pH (8-9.2) sand content (80%) and calcium concentration (> 9000 ppm). We removed all vegetation from both slag and non-slag plots to test whether recovery differed over one growing season (4 months). To directly assess plant growth, selected focal species were planted on both sites and harvested. We show that recovery from removal differed at slag and non-slag sites: the recruitment process on slag, measured by percent vegetative cover and number of species in plots, was significantly slower at 6-8 weeks of the manipulation and beyond, suggesting a potential stage-dependent effect of slag on plant growth. Certain slag plots recorded less cover than non-slag plots by >30% at maximum difference. Functional trait analysis found that graminoid and early successional species preferentially colonized slag. Overall, slag plots recovered more slowly from disturbance, suggesting a slow succession process that would hinder natural recovery. However, slag also has the potential to serve as plant refugia, hosting flora of analogous habitats native to the area: one of our industrial sites hosts nearly 80% native species with two species of highest Floristic Quality Index (10). Restoration efforts should be informed by the slow process of natural recovery, while post-industrial sites in urban areas serve as potential native plant refugia.

Source verification of mis-identified Arabidopsis thaliana accessions.

A major strength of Arabidopsis thaliana as a model lies in the availability of a large number of naturally occurring inbred lines. Recent studies of A. thaliana population structure, using thousands of accessions from stock center and natural collections, have revealed a robust pattern of isolation by distance at several spatial scales, such that genetically identical individuals are generally found close to each other. However, some individual accessions deviate from this pattern. While some of these may be the products of rare long-distance dispersal events, many deviations may be the result of mis-identification, in the sense that the data regarding location of origin data are incorrect. Here, we aim to identify such discrepancies. Of the 5965 accessions examined, we conclude that 286 deserve special attention as being potentially mis-identified. We describe these suspicious accessions and their possible origins, and advise caution with regard to their use in experiments in which accurate information on geographic origin is important. Finally, we discuss possibilities for maintaining the integrity of stock lines.

The scale of population structure in Arabidopsis thaliana.

The population structure of an organism reflects its evolutionary history and influences its evolutionary trajectory. It constrains the combination of genetic diversity and reveals patterns of past gene flow. Understanding it is a prerequisite for detecting genomic regions under selection, predicting the effect of population disturbances, or modeling gene flow. This paper examines the detailed global population structure of Arabidopsis thaliana. Using a set of 5,707 plants collected from around the globe and genotyped at 149 SNPs, we show that while A. thaliana as a species self-fertilizes 97% of the time, there is considerable variation among local groups. This level of outcrossing greatly limits observed heterozygosity but is sufficient to generate considerable local haplotypic diversity. We also find that in its native Eurasian range A. thaliana exhibits continuous isolation by distance at every geographic scale without natural breaks corresponding to classical notions of populations. By contrast, in North America, where it exists as an exotic species, A. thaliana exhibits little or no population structure at a continental scale but local isolation by distance that extends hundreds of km. This suggests a pattern for the development of isolation by distance that can establish itself shortly after an organism fills a new habitat range. It also raises questions about the general applicability of many standard population genetics models. Any model based on discrete clusters of interchangeable individuals will be an uneasy fit to organisms like A. thaliana which exhibit continuous isolation by distance on many scales.