Burkholderia sp. SSG is a potent biological control agent. Even though its survival on the leaf surface declined rapidly, SSG provided extended, moderate plant protection from a broad spectrum of pathogens. This study used Arabidopsis Col-0 and its mutants, eds16-1, npr1-1, and pad4-1 as model plants and compared treated plants with non-treated controls to elucidate whether SSG triggers plant defense priming. Only eds16-1 leaves with SSG became purplish, suggesting the involvement of salicylic acid (SA) in SSG-induced priming. cDNA sequencing of Col-0 plants and differential gene expression analysis identified 120 and 119 differentially expressed genes (DEGs) at 6- and 24-h post-treatment (hpt) with SSG, respectively. Most of these DEGs encoded responses to biotic and abiotic stimuli or stresses; four DEGs had more than two isoforms. A total of 23 DEGs were shared at 6 and 24 hpt, showing four regulation patterns. Functional categorization of these shared DEGs, and 44 very significantly upregulated DEGs revealed that SSG triggered various defense priming mechanisms, including responses to phosphate or iron deficiency, modulation of defense-linked SA, jasmonic acid, ethylene, and abscisic acid pathways, defense-related gene regulation, and chromatin modification. These data support that SSG is an induced systemic resistance (ISR) trigger conferring plant protection upon pathogen encounter.
Agrochemicals are important tools for safeguarding plants from invasive pathogens, insects, mites, and weeds. How they may affect the plant microbiome, a critical component of crop health and production, was poorly understood.
In a recent study, we observed a rapid decline of the boxwood blight pathogen Calonectria pseudonaviculata (Cps) soil population in all surveyed gardens across the United States, and we speculated that these garden soils might be suppressive to Cps. This study aimed to characterize the soil bacterial community in these boxwood gardens. Soil samples were taken from one garden in California, Illinois, South Carolina, and Virginia and two in New York in early summer and late fall of 2017 and 2018. Soil DNA was extracted and its 16S rRNA amplicons were sequenced using the Nanopore MinION® platform. These garden soils were consistently dominated by Rhizobiales and Burkholderiales, regardless of garden location and sampling time. These two orders contain many species or strains capable of pathogen suppression and plant fitness improvement. Overall, 66 bacterial taxa were identified in this study that are known to have strains with biological control activity (BCA) against plant pathogens. Among the most abundant were Pseudomonas spp. and Bacillus spp., which may have contributed to the Cps decline in these garden soils. This study highlights the importance of soil microorganisms in plant health and provides a new perspective on garden disease management using the soil microbiome.
DNA metabarcoding of pollen is a useful tool for studying bee foraging ecology. However, several questions about this method remain unresolved, including the extent to which sequence read data is quantitative, which type of sequence count removal threshold to use and how that choice affects our ability to detect rare flower visits, and how sequence artefacts may confound conclusions about bee foraging behavior. To address these questions, we isolated pollen from five plant species and created treatments comprised of pollen from each species alone and combinations of pollen from multiple species that varied in richness and evenness. We used ITS2 and rbcL metabarcoding to identify plant species in the samples, compared the proportion of pollen by mass to the proportion of sequencing reads for each plant species in each treatment, and analyzed the sequencing data using both liberal and conservative thresholds. We collected pollen from foraging bees, analyzed metabarcoding data from those samples using each threshold, and compared the differences in the pollinator networks constructed from the data. Regardless of the threshold used, the relationship between the proportion of pollen by mass and sequencing reads was inconsistent, suggesting that the number of sequence reads is a poor proxy for pollen abundance in mixed-species samples. Using a liberal threshold resulted in greater detection of original plant species in mixtures but also detected additional species in mixtures and single-species samples. The conservative threshold reduced the number of additional plant species detected, but several species in mixtures were not detected above the threshold, resulting in false negatives. Pollinator networks produced using the two thresholds differed and illustrated tradeoffs between detection of rare species and estimation of network complexity. Threshold selection can have a major effect on conclusions drawn from studies using metabarcoding of bee pollen to study plant-pollinator interactions.
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