Biology subjects

Geonczy, S. E.

Publications and source records attributed to Geonczy, S. E..

3 recordsLinked to original sources

bioRxiv2024

Virome responses to heating of a forest soil suggest that most dsDNA viral particles do not persist at 90°C

Many fundamental characteristics of soil viruses remain underexplored, including the effects of high temperatures on viruses and their hosts, as would be encountered under disturbances like wildland fire, prescribed burning, and soil solarization. In this study, we leveraged three data types (DNase-treated viromes, non-DNase-treated viromes, and 16S rRNA gene amplicon sequencing) to measure the responses of soil viral and prokaryotic communities to heating to 30{degrees}C, 60{degrees}C, or 90{degrees}C, in comparison to field and control conditions. We investigated (1) the response of dsDNA viral communities to heating of soils from two horizons (O and A) from the same forest soil profile, (2) the extent to which specific viral taxa could be identified as heat-sensitive or heat-tolerant across replicates and soil horizons, and (3) prokaryotic and virus-host dynamics in response to heating. We found that both viral and prokaryotic communities responded similarly to the treatment variables. Community composition differed most significantly by soil source (O or A horizon). Within both soil horizons, viral and prokaryotic communities clustered into three groups, based on beta-diversity patterns: the ambient community (field, control, and 30{degrees}C samples) and the 60{degrees}C and 90{degrees}C communities. As DNase-treated viromic DNA yields were below detection limits at 90{degrees}C, we infer that most viral capsids were compromised after the 90{degrees}C treatment, indicating a maximum temperature threshold between 60{degrees}C and 90{degrees}C for most viral particles in these soils. We also identified groups of heat-tolerant and heat-sensitive vOTUs across both soil sources. Overall, we found that over 70% of viral populations, like their prokaryotic counterparts, could withstand temperatures as high as 60{degrees}C, with shifts in relative abundance explaining most community compositional differences across heating treatments.

genomics↗

bioRxiv2022

Substantial differences in soil viral community composition within and among four Northern California habitats

Viruses contribute to food web dynamics and nutrient cycles in diverse ecosystems, yet the biogeographical patterns that underlie these viral dynamics are poorly understood, particularly in soil. Here, we identified trends in soil viral community composition in relation to habitat, moisture content, and physical distance. We generated 30 soil viromes from four distinct habitats (wetlands, grasslands, woodlands, and chaparral) by selectively capturing virus-sized particles prior to DNA extraction, and we recovered 3,432 unique viral species (vOTUs). Viral communities differed significantly by soil moisture content, with viral richness generally higher in wet compared to dry soil habitats. However, vOTUs were rarely shared between samples, including replicates <10 m apart, suggesting that soil viruses may not disperse well and that future soil viral community sampling strategies may need to account for extreme community differences over small spatial scales. Of the 19% of vOTUs detected in more than one sample, 93% were from the same habitat and site, suggesting greater viral community similarity in closer proximity and under similar environmental conditions. Within-habitat differences indicate that extensive sampling would be required for rigorous cross-habitat comparisons, and results belie emerging paradigms of higher viral activity in wet soils and soil viral community spatial heterogeneity.

microbiology↗

bioRxiv2021

Playing with FiRE: A genome resolved view of the soil microbiome responses to high severity forest wildfire

Warming climate has increased the frequency and size of high severity wildfires in the western United States, with deleterious impacts on forest ecosystem resilience. Although forest soil microbiomes provide a myriad of ecosystem functions, little is known regarding the impact of high severity fire on microbially-mediated processes. Here, we characterized functional shifts in the soil microbiome (bacterial, fungal, and viral) across wildfire burn severity gradients one year post-fire in coniferous forests (Colorado and Wyoming, USA). We generated the Fire Responding Ecogenomic database (FiRE-db), consisting of 637 metagenome-assembled bacterial genomes, 2490 viral populations, and 2 fungal genomes complemented by 12 metatranscriptomes from soils affected by low and high-severity, and complementary marker gene sequencing and metabolomics data. Actinobacteria dominated the fraction of enriched and active taxa across burned soils. Taxa within surficial soils impacted by high severity wildfire exhibited traits including heat resistance, sporulation and fast growth that enhanced post-fire survival. Carbon cycling within this system was predicted to be influenced by microbial processing of pyrogenic compounds and turnover of dominant bacterial community members by abundant viruses. These genome-resolved analyses across trophic levels reveal the complexity of post-fire soil microbiome activity and offer opportunities for restoration strategies that specifically target these communities.

microbiology↗