Biology subjects

Geonczy, S.

Publications and source records attributed to Geonczy, S..

3 recordsLinked to original sources

bioRxiv2024

Soil viral and prokaryotic communities shifted significantly after wildfire in chaparral and woodland habitats

Increased wildfire activity warrants more research into fire-driven biotic changes in soil, given that soil microbes contribute to biogeochemical processes by way of organic matter decomposition, nutrient cycling, and promoting plant growth. Viruses of prokaryotes apply pressure to microbial communities, making their responses to fire also important for understanding post-fire ecology. Leveraging viromes and 16S rRNA gene amplicon sequencing, here we studied viral and prokaryotic community responses to wildfire in woodland and chaparral soils at five timepoints over one year following the California LNU Complex wildfire. We also compared post-fire samples to unburned controls at the final three timepoints, beginning five months after the fire. Viromic DNA yields were low-to-undetectable (indicative of low viral particle abundances), particularly for the first post-fire timepoint, and comparisons to controls suggest a return to baseline viral particle abundances within five months of the wildfire. Viral and prokaryotic community composition and soil chemistry differed significantly in burned samples compared to controls from both habitats. Compared to controls, a greater proportion of viral species (vOTUs) from a burned conifer forest were detected in both burned habitats here, suggesting fire-associated habitat filtering. Published viromes collected from the same sites nine months pre-fire were more similar to controls than to post-fire viromes. Together, these results indicate significant changes in soil viral and prokaryotic communities due to wildfire.

microbiology↗

bioRxiv2024

Locally heterogeneous soil viral and prokaryotic responses to prescribed burn correspond with patchy burn severity in a mixed conifer forest

Prescribed burning, a strategy to mitigate wildfires, imparts physicochemical and biological changes to soil. The effects of burns on soil viruses and virus-host dynamics are largely unexplored, despite known viral and prokaryotic contributions to biogeochemical processes. Using a viromic (<0.2 {micro}m size fraction metagenomic) approach, we assessed how viral communities responded to a spring prescribed burn in a mixed conifer forest and whether soil chemical properties and/or prokaryotic host communities could explain the observed patterns. From 120 soil samples (two per depth at 0-3 and 3-6 cm from four burned and two control plots at five timepoints, two before and three after the burn), 91 viromes and 115 16S rRNA gene amplicon libraries were sequenced. Plot location had the greatest effect on explaining variance in viral communities, over treatment (burned or not), depth, and timepoint. Viral and prokaryotic communities exhibited locally heterogenous responses to the fire, with some burned communities resembling unburned controls. This was attributed to patchy burn severity (defined by soil chemistry). Low viromic DNA yields indicated substantial loss of viral biomass in high-severity locations. The relative abundances of Firmicutes, Actinobacteria, and the viruses predicted to infect them significantly increased along the burn severity gradient, suggesting survival of spore formers and viral infection of these abundant, fire-responsive taxa. Our analyses highlight the importance of a nuanced view of soil community responses to fire, not just to burn overall, but to the specific degree of burn severity experienced by each patch of soil, which differed for nearby soils in the same fire.

ecology↗

bioRxiv2023

Exploring viral particle, soil, and extraction buffer physicochemical characteristics and their impacts on extractable viral communities

Soil viruses are expected to be pivotal members of soil ecosystems, and recent advances in viral size fraction metagenomic (viromic) approaches have substantially improved our ability to interrogate soil viral ecology. However, the first step of viromics relies on extraction buffers to effectively remove viral particles from the soil matrix for downstream analysis, and viral extraction efficiency at this stage could be affected by the interplay between viral particles, soils, and extraction buffer chemistry. Here, we investigated whether extraction buffer chemistry affected extractable viral community composition measured by viromics from different soil types, for both biological (samples collected 1 meter apart) and technical (subsamples from the same soil homogenate) replicates. We first investigated protein-supplemented phosphate-buffered saline pH (PPBS, pHs 4.5, 5.5, 6.5, and 7.5) on a forest, grassland and wetland soil that exhibited different soil edaphic properties, and then we tested different buffer chemistries (PPBS, Carbonated Buffer, Glycine, and Saline Magnesium) on just the wetland soil. Spatial distance, or where the sample was taken in the field (i.e., biological replicate), was the primary driver of extractable viral community composition across all buffers and soils tested. Differences in viral community composition according to extraction buffer properties were only observed in the grassland technical replicates at PPBS buffer pH 4.5, as well as in both the wetland technical and biological replicates treated with different buffer chemistries, but the effects of buffer chemistry were secondary to spatial distance in all cases where spatial distance was a factor. The lack of buffering capacity in the grassland soil technical replicates likely increased sorption of some viral particles at pH 4.5, but neither protein composition nor isoelectric point (both calculated bioinformatically) explained this phenomenon. Given that most soil viral ecological studies to date include sample collection schemes over distances much farther apart than the 1-meter distances considered here, results suggest that extraction buffer chemistry is likely of much lower importance than ecological considerations, such as spatial distance, in the design of future soil viral ecological investigations. HIGHLIGHTSO_LISpatial distance was the main driver of extractable viral community composition. C_LIO_LIExtraction buffer chemistry secondarily structured wetland viral communities. C_LIO_LIAt pH 4.5, PPBS buffer likely increased viral sorption in homogenized grassland soil. C_LIO_LIIncreased sorption was not explained by estimated viral protein isoelectric points. C_LI

microbiology↗