Biology subjects

Fudyma, J. D.

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

4 recordsLinked to original sources

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↗

bioRxiv2023

Almond rhizosphere viral, prokaryotic, and fungal communities differed significantly among four California orchards and in comparison to bulk soil communities

Characterization of rhizosphere microbiomes and their interactions is essential to a holistic understanding of plant health in support of sustainable agriculture. Viruses are a key, understudied component of rhizosphere microbiomes, with potential impacts on both plant-beneficial and -pathogenic organisms through infection. In this study, we sampled rhizospheres and bulk soils associated with 15 almond trees in four California orchards and generated viromic, 16S rRNA gene, and ITS1 amplicon sequencing datasets to compare viral, prokaryotic, and fungal communities. In total, 10,440 viral operational taxonomic units (vOTUs), 16,146 bacterial and archaeal OTUs, and 6,684 fungal OTUs were recovered. All three community types differed most significantly among the four orchards and secondarily between bulk and rhizosphere soils. Despite compositional differences, no significant differences in richness were observed between bulk and rhizosphere soils for any of the studied biota. Overall, viruses, prokaryotes, and fungi shared similar beta-diversity patterns in almond rhizospheres and bulk soils on a regional scale, counter to recently observed decoupling between viral and prokaryotic community biogeographic patterns in a variety of bulk soils.

ecology↗

bioRxiv2023

Dispersal, habitat filtering, and eco-evolutionary dynamics as drivers of local and global wetland viral biogeography

Wetlands store 20-30% of the worlds soil carbon, and identifying the microbial controls on these carbon reserves is essential to predicting feedbacks to climate change. Although viral infections likely play important roles in wetland ecosystem dynamics, we lack a basic understanding of wetland viral ecology. Here 63 viral size-fraction metagenomes (viromes) and paired total metagenomes were generated from three time points in 2021 at seven fresh- and saltwater wetlands in the California Bodega Marine Reserve. We recovered 12,826 viral population genomic sequences (vOTUs), 4.4% of which were also detected at the same field site two years prior, indicating a small degree of population stability or recurrence. Viral communities differed most significantly across the seven wetland sites and were also structured by habitat (plant community composition and salinity). Read mapping to a new version of our reference database, PIGEONv2.0 (now with 515,763 vOTUs), revealed 196 vOTUs present over large geographic distances, often reflecting shared habitat characteristics. Wetland vOTU microdiversity was significantly lower locally than globally and lower within than between time points, indicating greater divergence with increasing spatiotemporal distance. Viruses tended to have broad predicted host ranges via CRISPR spacer linkages to metagenome-assembled genomes (whether this reflects true biology remains to be seen), and increased SNP frequencies in CRISPR-targeted major tail protein genes suggest viral eco-evolutionary dynamics, potentially in response to both immune targeting and to changes in host cell receptors involved in viral attachment. Together, these results highlight the importance of dispersal, environmental selection, and eco-evolutionary dynamics as drivers of local and global wetland viral biogeography.

ecology↗

bioRxiv2021

RNA viral communities are structured by host plant phylogeny in oak and conifer leaves

Wild plants can suffer devastating diseases, experience asymptomatic, persistent infections, and serve as reservoirs for viruses of agricultural crops, yet we have a limited understanding of the natural plant virosphere. To access representatives of locally and globally distinct wild plants and investigate their viral diversity, we extracted and sequenced dsRNA from leaves from 16 healthy oak and conifer trees in the UC Davis Arboretum (Davis, California). From de novo assemblies, we recovered 389 RNA-dependent RNA polymerase (RdRp) gene sequences from 384 putative viral species, and a further 580 putative viral contigs were identified with virus prediction software followed by manual confirmation of virus annotation. Based on similarity to known viruses, most recovered viruses were predicted to infect plants or fungi, with the highest diversity and abundance observed in the Totiviridae and Mitoviridae families. Phyllosphere viral community composition differed significantly by host plant phylogeny, suggesting the potential for host-specific viromes. The phyllosphere viral community of one oak tree differed substantially from other oak viral communities and contained a greater proportion of putative mycoviral sequences, potentially due to the trees more advanced senescence at the time of sampling. These results suggest that oaks and conifers harbor a vast diversity of viruses with as-yet unknown roles in plant health and phyllosphere microbial ecology.

ecology↗