Biology subjects

Koch, P. L.

Publications and source records attributed to Koch, P. L..

4 recordsLinked to original sources

bioRxiv2026

Time, Not fungicide treatment, influences the resistome of the turf phyllosphere

Antibiotic resistance genes (ARGs) are an emerging class of environmental contaminants with significant implications for public health. Previous studies have linked fungicide exposure to elevated levels of ARGs in soil microbiomes, but research investigating the impacts of fungicide on ARGs within phyllosphere bacterial communities is limited. To address this, creeping bentgrass was treated with the fungicide active ingredients chlorothalonil, fluxapyroxad, and propiconazole and sampled at 4 hours, 96 hours, and one week post-application. Quantitative PCR (qPCR) was performed to quantify the abundance of ARGs and a metal resistance genes (MRG) abundance relative to 16s. Additionally, 16S rRNA gene sequencing was performed to characterize bacterial community composition. Results indicated that fungicide treatments did not significantly alter the relative abundance of ARGs or an MRG within bent grass bacterial communities. However, significant changes were observed over time, with changes in ARG and MRG abundance mirroring temporal shifts in bacterial beta diversity. ARGs and the MRG relative abundance had significant correlations with Proteobacteria, Actinobacteria, Bacteriadota, and Firmicutes, including with genera Pseudoxanthomas, and Dyandobacter, which contain opportunistic human pathogens. This study demonstrates that fungicides have limited influence on the abundance of ARGs and MRGs in the phyllosphere and helps guide further investigations aiming to mitigate the spread of antibiotic resistance. ImportanceAntibiotic resistance makes it harder to treat bacterial infections. Recent evidence suggests that fungicides may increase the abundance of antibiotic resistance genes (ARGs) in soil. Leaves are also treated with fungicides, but it is unclear if there will be increases of antibiotic resistance in this environment because bacteria on leaves face different physiological stresses. Additionally, plants may serve as a route of infection to humans or animals with antibiotic resistant bacteria making it a critical micro-environment to investigate. The purpose of this study was to determine whether the prevalence of antibiotic resistance on plant surfaces changes after short-term exposure to fungicides. This study shows that over short-term application periods, time has a greater effect on the abundance of genes that cause antibiotic resistance than treatment with the fungicides chlorothalonil, fluxapyroxad, and propiconazole on plants. This work helps inform future efforts to mitigate the spread of antibiotic resistance.

microbiology↗

bioRxiv2024

Postglacial recolonization of the Southern Ocean by elephant seals occurred from multiple glacial refugia

The Southern Ocean is warming more rapidly than other parts of our planet. How this regions endemic biodiversity will respond to such changes can be illuminated by studying past events, through genetic analyses of time-series data sets including historic and fossil remains. Archaeological and subfossil remains show that the southern elephant seal (Mirounga leonina) was common along the coasts of Australia and New Zealand in the recent past. This species is now mostly confined to sub-Antarctic islands and the southern tip of South America. We analysed ancient seal samples from Australia (Tasmania), New Zealand, and the Antarctic mainland to examine how southern elephant seals have responded to a changing climate and anthropogenic pressures during the Holocene. Our analyses show that these seals formed part of a broader Australasian lineage, comprising seals from all sampled locations from the south Pacific sector of the Southern Ocean. Our study demonstrates that southern elephant seal populations have dynamically altered both range and population sizes under climatic and human pressures, over surprisingly short evolutionary timeframes for such a large, long-lived mammal. Significance StatementGenetic data, alongside historic, archaeological, and subfossil remains show that Australasian populations of the southern elephant seal have been shaped by range expansions and contractions following the Last Glacial Maximum, with subsequent contractions during the late Holocene. These expansion and contraction events are likely to have been a direct result of climate change-induced habitat expansion and contraction, along with Indigenous and European sealing. Prehistoric climate change and more recent human pressures have substantially altered the geographic distribution and population size of southern elephant seals over short evolutionary timescales.

ecology↗

bioRxiv2022

Expanded diversity of tfdA harboring bacteria across the natural and built environment

2,4-Dichlorophenoxyacetic acid (2,4-D) is an herbicide commonly used in aquatic and terrestrial environments that is degraded by bacteria through the TFD pathway. Previous work has relied on culture-based methods to develop primers for qPCR analysis of the gene cassette in environmental samples. In this study, we combined molecular and genomic approaches to examine the accuracy of established tfdA qPCR primers on environmental samples and update the phylogeny of tfdA genes detected in bacterial genomes. We found most putative 2,4-D degraders are within the Proteobacteria but also found several novel degraders including members of the phyla Candidatus Rokubacteria and Candidatus Eremiobacteraeota. In silico analysis of established primers showed potential amplification of < 5% of putative degrader sequences but 52-100% of experimentally verified degraders when allowing for three and one mismatches between template and primer sequences, respectively. Overall, our work expands the diversity of putative 2,4-D degraders and demonstrates the limitations of culture-based tools for investigating functional diversity of microorganisms in the environment. ImportanceCultivation-based methods can misrepresent the diversity of environmental microorganisms. Our work showcases one example of how culture-based development of molecular tools underestimates the full spectrum of 2,4-D degrading microorganisms. Accurately identifying microorganisms with 2,4-D degradation potential is crucial for understanding the biodegradation potential of a commonly used herbicide across terrestrial, aquatic, and subsurface environments. Additionally, this work reinforces well-documented pitfalls associated with relying on cultured representatives when constructing primers and the challenges of translating findings from a few cultured representatives to understudied or unknown microorganisms in complex environments.

microbiology↗

bioRxiv2020

Hyperlocal variation in soil iron and rhizosphere microbiome determines disease development in amenity turfgrass

Dollar spot, caused by the fungal pathogen Clarireedia spp., is an economically important disease of amenity turfgrass in temperate climates worldwide. This disease often occurs in a highly variable manner, even on a local scale with relatively uniform environmental conditions. The objective of this study was to investigate mechanisms behind this local variation, focusing on contributions of the soil and rhizosphere microbiome. Turfgrass, rhizosphere, and bulk soil samples were taken from within a 256 m2 area of healthy turfgrass, transported to a controlled environment chamber, and inoculated with C. jacksonii. Bacterial communities were profiled targeting the 16s rRNA gene, and 16 different soil chemical properties were assessed. Despite their initial uniform appearance, the samples differentiated into highly susceptible and moderately susceptible groups following inoculation in the controlled environment chamber. The highly susceptible samples harbored a unique rhizosphere microbiome with lower relative abundance of antibiotic-producing bacterial taxa and higher predicted abundance of genes associated with xenobiotic biodegradation pathways. In addition, stepwise regression revealed that bulk soil iron content was the only significant soil characteristic that positively regressed with decreased dollar spot susceptibility during the peak disease development stage. These findings suggest that localized variation in soil iron induces the plant to select for a particular rhizosphere microbiome that alters the disease outcome. More broadly, further research in this area may indicate how plot-scale variability in soil properties can drive variable plant disease development through alterations in the rhizosphere microbiome. IMPORTANCEDollar spot is the most economically important disease of amenity turfgrass, and more fungicides are applied targeting dollar spot than any other turfgrass disease. Dollar spot symptoms are small (3-5 cm), circular patches that develop in a highly variable manner within plot-scale even under seemingly uniform conditions. The mechanism behind this variable development is unknown. This study observed that differences in dollar spot development over a 256 m2 area were associated with differences in bulk soil iron concentration and correlated with a particular rhizosphere microbiome. These findings provide important clues for understanding the mechanisms behind the highly variable development of dollar spot, which may offer important clues for innovative control strategies. Additionally, these results also suggest that small changes in soil properties can alter plant activity and hence the plant-associated microbial community which has important implications for a broad array of important agricultural and horticultural plant pathosystems.

microbiology↗