Biology subjects

Edwards, J. D.

Publications and source records attributed to Edwards, J. D..

3 recordsLinked to original sources

bioRxiv2024

Functional traits of ectomycorrhizal trees influence their effects on surrounding soil organic matter properties

Ectomycorrhizal (EM) effects on forest ecosystem carbon (C) and nitrogen (N) cycling are highly variable, which may be due to underappreciated functional differences among EM-associating trees. We hypothesize that differences in functional traits among EM tree genera will correspond to differences in soil organic matter (SOM) dynamics. We explored how differences among three genera of angiosperm EM trees (Quercus, Carya, and Tilia) in functional traits associated with leaf litter quality, resource use and allocation patterns, and microbiome assembly related to overall soil biogeochemical properties. In support of our hypothesis, we found consistent differences among EM tree genera in function traits. Quercus trees had lower litter quality, lower {delta}13C in SOM, higher {delta}15N in leaf tissues, greater oxidative extracellular enzyme activities, and higher EM fungal diversity than Tilia trees, while Carya trees were often intermediary. These functional traits corresponded to overall SOM C and N dynamics and soil fungal and bacterial community composition. Our findings suggest that trait variation among EM-associating tree species should be an important consideration in assessing plant-soil relationships such that EM trees cannot be categorized as a unified functional guild.

ecology↗

bioRxiv2020

Invasive garlic mustard demonstrates stronger relationships with pathotrophic than mycorrhizal fungi

The invasive forest plant garlic mustard (Alliaria petiolata) has been shown to alter soil microbial communities in the northeastern part of its invaded range in the United States, and this disruption of soil communities may contribute to its invasion success. However, garlic mustard allelochemistry can vary with invasion age, and it is not clear whether garlic mustards impacts on soil microbes are consistent over its invaded range. Here, we compare the composition and diversity of soil fungal, bacterial, and archaeal communities among garlic mustard present, absent, and removed treatments in replicated blocks across five forests in the midwestern United States with relatively young garlic mustard invasions (approximately 17-26 years old, with consistent management). We collected samples in May and August, corresponding to garlic mustard active and senescent life history stages. While soil fungal and bacterial/ archaeal communities (based on ITS2 region and 16S rRNA gene DNA sequencing, respectively) differed significantly between different blocks/ forests and over time, we found no significant effect of garlic mustard treatment on soil microbial community composition or the relative abundance of mycorrhizal, saprotrophic, or pathogenic fungal guilds. The lack of garlic mustard impacts on the soil microbial community in recently invaded central Illinois forests suggests that these well-documented impacts in the northeastern United States and in older invasions cannot necessarily be generalized across all environmental contexts.

ecology↗

bioRxiv2020

Gene disruption by structural mutations drives selection in US rice breeding over the last century

The genetic basis of general plant vigor is of major interest to food producers, yet the trait is recalcitrant to genetic mapping because of the number of loci involved, their small effects, and linkage. Observations of heterosis in many crops suggests that recessive, malfunctioning versions of genes are a major cause of poor performance, yet we have little information on the mutational spectrum underlying these disruptions. To address this question, we generated a long-read assembly of a tropical japonica rice (Oryza sativa) variety, Carolina Gold, which allowed us to identify structural mutations (>50 bp) and orient them with respect to their ancestral state using the outgroup, Oryza glaberrima. Supporting prior work, we find substantial genome expansion is the sativa branch. While transposable elements (TEs) account for the largest share of size variation, the majority of events are not directly TE-mediated. Tandem duplications are the most common source of insertions and are highly enriched among 50-200bp mutations. To explore the relative impact of various mutational classes on crop fitness, we then track these structural events over the last century of US rice improvement using 101 resequenced varieties. Within this material, a pattern of temporary hybridization between medium and long-grain varieties was followed by recent divergence. During this long-term selection, structural mutations that impact gene exons have been removed at a greater rate than intronic indels and single-nucleotide mutations. These results support the use of ab initio estimates of mutational burden, based on structural data, as an orthogonal predictor in genomic selection. Significance StatementSome crop varieties have superior performance across years and environments. In hybrids, harmful mutations in one parent are masked by the ancestral alleles in the other parent, resulting in increased vigor. Unfortunately, these mutations are very difficult to identify precisely because, individually, they only have a small effect. In this study, we use long-read sequencing to characterize the entire mutational spectrum between two rice varieties. We then track these mutations through the last century of rice breeding. We show that large structural mutations in exons are selected against at a greater rate than any other mutational class. These findings illuminate the nature of deleterious alleles and will guide attempts to predict variety vigor based solely on genomic information.

genetics↗