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  1. Heck, Michelle (Ed.)

    Plant-associated microbial assemblages are known to shift at time scales aligned with plant phenology, as influenced by the changes in plant-derived nutrient concentrations and abiotic conditions observed over a growing season. But these same factors can change dramatically in a sub-24-hour period, and it is poorly understood how such diel cycling may influence plant-associated microbiomes. Plants respond to the change from day to night via mechanisms collectively referred to as the internal “clock,” and clock phenotypes are associated with shifts in rhizosphere exudates and other changes that we hypothesize could affect rhizosphere microbes. The mustardBoechera strictahas wild populations that contain multiple clock phenotypes of either a 21- or a 24-hour cycle. We grew plants of both phenotypes (two genotypes per phenotype) in incubators that simulated natural diel cycling or that maintained constant light and temperature. Under both cycling and constant conditions, the extracted DNA concentration and the composition of rhizosphere microbial assemblages differed between time points, with daytime DNA concentrations often triple what were observed at night and microbial community composition differing by, for instance, up to 17%. While we found that plants of different genotypes were associated with variation in rhizosphere assemblages, we did not see an effect on soil conditioned by a particular host plant circadian phenotype on subsequent generations of plants. Our results suggest that rhizosphere microbiomes are dynamic at sub-24-hour periods, and those dynamics are shaped by diel cycling in host plant phenotype.


    We find that the rhizosphere microbiome shifts in composition and extractable DNA concentration in sub-24-hour periods as influenced by the plant host’s internal clock. These results suggest that host plant clock phenotypes could be an important determinant of variation in rhizosphere microbiomes.

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    Free, publicly-accessible full text available June 29, 2024
  2. Abstract

    Circadian clocks confer adaptation to predictable 24‐h fluctuations in the exogenous environment, but it has yet to be determined what ecological factors maintain natural genetic variation in endogenous circadian period outside of the hypothesized optimum of 24 h. We estimated quantitative genetic variation in circadian period in leaf movement in 30 natural populations of theArabidopsisrelativeBoechera strictasampled within only 1° of latitude but across an elevation gradient spanning 2460–3300 m in the Rocky Mountains. Measuring ~3800 plants from 473 maternal families (7–20 per population), we found that genetic variation was of similar magnitude among versus within populations, with population means varying between 21.9 and 24.9 h and maternal family means within populations varying by up to ~6 h. After statistically accounting for spatial autocorrelation at a habitat extreme, we found that elevation explained a significant proportion of genetic variation in the circadian period, such that higher‐elevation populations had shorter mean period lengths and reduced intrapopulation ranges. Environmental data indicate that these spatial trends could be related to steep regional climatic gradients in temperature, precipitation, and their intra‐annual variability. Our findings suggest that spatially fine‐grained environmental heterogeneity contributes to naturally occurring genetic variation in circadian traits in wild populations.

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  3. Abstract

    The rhizosphere microbiome influences many aspects of plant fitness, including production of secondary compounds and defence against insect herbivores. Plants also modulate the composition of the microbial community in the rhizosphere via secretion of root exudates. We tested both the effect of the rhizosphere microbiome on plant traits, and host plant effects on rhizosphere microbes using recombinant inbred lines (RILs) ofBrassica rapathat differ in production of glucosinolates (GLS), secondary metabolites that contribute to defence against insect herbivores. First, we investigated the effect of genetic variation in GLS production on the composition of the rhizosphere microbiome. Using a Bayesian Dirichlet‐multinomial regression model (DMBVS), we identified both negative and positive associations between bacteria from six genera and the concentration of five GLS compounds produced in plant roots. Additionally, we tested the effects of microbial inoculation (an intact vs. disrupted soil microbiome) on GLS production and insect damage in these RILs. We found a significant microbial treatment × genotype interaction, in which total GLS was higher in the intact relative to the disrupted microbiome treatment in some RILs. However, despite differences in GLS production between microbial treatments, we observed no difference in insect damage between treatments. Together, these results provide evidence for a full feedback cycle of plant–microbe interactions mediated by GLS; that is, GLS compounds produced by the host plant “feed‐down” to influence rhizosphere microbial community and rhizosphere microbes “feed‐up” to influence GLS production.

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  4. Anderton, Christopher R. (Ed.)

    The rhizosphere, the zone of soil surrounding plant roots, is a hot spot for microbial activity, hosting bacteria capable of promoting plant growth in ways like increasing nutrient availability or fighting plant pathogens. This microbial system is highly diverse and most bacteria are unculturable, so to identify specific bacteria associated with plant growth, we used culture-independent community DNA sequencing combined with machine learning techniques.

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  5. Bulgarelli, Davide (Ed.)
    ABSTRACT The composition of microbial communities found in association with plants is influenced by host phenotype and genotype. However, the ways in which specific genetic architectures of host plants shape microbiomes are unknown. Genome duplication events are common in the evolutionary history of plants and influence many important plant traits, and thus, they may affect associated microbial communities. Using experimentally induced whole-genome duplication (WGD), we tested the effect of WGD on rhizosphere bacterial communities in Arabidopsis thaliana . We performed 16S rRNA amplicon sequencing to characterize differences between microbiomes associated with specific host genetic backgrounds (Columbia versus Landsberg) and ploidy levels (diploid versus tetraploid). We modeled relative abundances of bacterial taxa using a hierarchical Bayesian approach. We found that host genetic background and ploidy level affected rhizosphere community composition. We then tested to what extent microbiomes derived from a specific genetic background or ploidy level affected plant performance by inoculating sterile seedlings with microbial communities harvested from a prior generation. We found a negative effect of the tetraploid Columbia microbiome on growth of all four plant genetic backgrounds. These findings suggest an interplay between host genetic background and ploidy level and bacterial community assembly with potential ramifications for host fitness. Given the prevalence of ploidy-level variation in both wild and managed plant populations, the effects on microbiomes of this aspect of host genetic architecture could be a widespread driver of differences in plant microbiomes. IMPORTANCE Plants influence the composition of their associated microbial communities, yet the underlying host-associated genetic determinants are typically unknown. Genome duplication events are common in the evolutionary history of plants and affect many plant traits. Using Arabidopsis thaliana , we characterized how whole-genome duplication affected the composition of rhizosphere bacterial communities and how bacterial communities associated with two host plant genetic backgrounds and ploidy levels affected subsequent plant growth. We observed an interaction between ploidy level and genetic background that affected both bacterial community composition and function. This research reveals how genome duplication, a widespread genetic feature of both wild and crop plant species, influences bacterial assemblages and affects plant growth. 
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  6. In aquatic systems, microbes likely play critical roles in biogeochemical cycling and ecosystem processes, but much remains to be learned regarding microbial biogeography and ecology. The microbial ecology of mountain lakes is particularly understudied. We hypothesized that microbial distribution among lakes is shaped, in part, by aquatic plant communities and the biogeochemistry of the lake. Specifically, we investigated the associations of yellow water lilies ( Nuphar polysepala) with the biogeochemistry and microbial assemblages within mountain lakes at two scales: within a single lake and among lakes within a mountain range. We first compared the biogeochemistry of lakes without water lilies to those colonized to varying degrees by water lilies. Lakes with >10% of the surface occupied by water lilies had lower pH and higher dissolved organic carbon than those without water lilies and had a different microbial composition. Notably, cyanobacteria were negatively associated with water lily presence, a result consistent with the past observation that macrophytes outcompete phytoplankton and can suppress cyanobacterial and algal blooms. To examine the influence of macrophytes on microbial distribution within a lake, we characterized microbial assemblages present on abaxial and adaxial water lily leaf surfaces and in the water column. Microbial diversity and composition varied among all three habitats, with the highest diversity of microbes observed on the adaxial side of leaves. Overall, this study suggests that water lilies influence the biogeochemistry and microbiology of mountains lakes. 
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