Biology subjects

ter Horst, A. M.

Publications and source records attributed to ter Horst, A. M..

12 recordsLinked to original sources

bioRxiv2026

Host community activity, but not always composition, explains viral biogeography in bulk and rhizosphere soils over a tomato growing season

The soil microbiome is key to plant health and nutrient acquisition, and viruses likely play important but largely unknown roles in these processes. To interrogate bulk and rhizosphere soil viral biogeography, we collected samples over a tomato growing season in California from an experiment testing arbuscular mycorrhizal fungi (AMF) treatment. We generated 78 viromes, 16S rRNA gene, and ITS1 amplicon datasets, and 33 rhizosphere metatranscriptomes. Of 67,038 DNA viral species genomes (vOTUs), 25% were previously identified, predominantely in agricultural systems, suggesting habitat filtering and greater viral homogeneity across agricultural compared to natural soils globally. Rhizospheres had significantly higher DNA viral richness than bulk soils, whereas no significant richness differences were observed for other biota. 60% of vOTUs were shared between compartments, compared to only 21-23% of bacterial and fungal taxa. Although bulk soil viral biogeography resembled that of prokaryotes, with significant structuring by moisture content, greater virome similarity between high-moisture bulk soils and rhizospheres suggests that conditions with high host activity selected for similar viral communities. In rhizospheres, while bacterial and fungal communities differed most over time, DNA and RNA viral communities differed most by sampling location, matching prokaryotic transcriptional patterns and further implicating host activity in viral biogeography. Similarly, AMF treatment induced changes in the prokaryotic transcriptome but, across biota, only significantly affected DNA viral communities. Overall, results indicate strong viral responses to spatiotemporally localized conditions, with viral biogeography reflecting both dispersal opportunities (high between neighboring bulk and rhizosphere soils, low across fields) and selection via local host activity.

genomics↗

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↗

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

Soil viral communities differed by management and over time in organic and conventional tomato fields

Viruses are known contributors to biogeochemical cycling in diverse habitats, but viral community studies in soil are relatively rare. Although prior work has suggested spatial structuring as a primary driver of local soil viral community ecological patterns, here we show that agricultural management can significantly impact soil viral community composition. We generated 18 soil viromes and 24 total metagenomes from six plots, three under organic and three under conventional management in Davis, CA, USA. Despite the significant impact of management on viral community structure and soil physicochemistry, approximately 44% of the detected viral species (vOTUs) were present in soils from both management practices. These common vOTUs regularly comprised >65% of the viral community by relative abundance. Many (56%) of the vOTUs were detected both during the tomato growing season and post-harvest, indicating persistence through time. Together, these results indicate habitat-specific differences in viral community composition, yet relative stability and persistence of viral communities within agricultural soils, in contrast to their recently observed dynamics in natural soils.

microbiology↗

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↗

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

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↗

bioRxiv2021

DNase treatment improves viral enrichment in agricultural soil viromes

The small genomes of most viruses make it difficult to fully capture viral diversity in metagenomes dominated by DNA from cellular organisms. Viral size-fraction metagenomics (viromics) protocols facilitate enrichment of viral DNA from environmental samples, and these protocols typically include a DNase treatment of the post-0.2 m viromic fraction to remove contaminating free DNA prior to virion lysis. However, DNase may also remove desirable viral genomic DNA (e.g., contained in virions compromised due to frozen storage or laboratory processing), suggesting that DNase-untreated viromes might be useful in some cases. In order to understand how virome preparation with and without DNase treatment influences the resultant data, here we compared 15 soil viromes (7 DNase-treated, 8 untreated) from 8 samples collected from agricultural fields prior to tomato planting. DNase-treated viromes yielded significantly more assembled viral contigs, contained significantly less non-viral microbial DNA, and recovered more viral populations (vOTUs) through read mapping. However, DNase-treated and untreated viromes were statistically indistinguishable, in terms of ecological patterns across viral communities. Although results suggest that DNase treatment is preferable where possible, in comparison to previously reported total metagenomes from the same samples, both DNase-treated and untreated viromes were significantly enriched in viral signatures by all metrics compared, including a ~225 times greater proportion of viral reads in untreated viromes compared to total metagenomes. Thus, even without DNase treatment, viromics was preferable to total metagenomics for capturing viral diversity in these soils, suggesting that preparation of DNase-untreated viromes can be worthwhile when DNase treatment is not possible. ImportanceViromics is becoming an increasingly popular method for characterizing soil viral communities. DNase treatment of the viral size fraction prior to DNA extraction is meant to reduce contaminating free DNA and is a common step within viromics protocols to ensure sequences are of viral origin. However, some samples may not be amendable to DNase treatment due to viral particles being compromised either in storage (i.e. frozen) or during other sample processing. To date, the effect of DNase treatment on the recovery of viruses and downstream ecological interpretations of soil viral communities is not thoroughly understood. This work sheds light on these questions and indicates that while DNase treatment of soil viromes improves recovery of viral populations, this improvement is modest in comparison to the gains made by viromics over total soil metagenomics. Further, DNase treatment may not be necessary to observe the ecological patterns structuring soil viral communities.

microbiology↗

bioRxiv2020

Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations

BackgroundPeatlands are expected to experience sustained yet fluctuating higher temperatures due to climate change, leading to increased microbial activity and greenhouse gas emissions. Despite mounting evidence for viral contributions to these processes in peatlands underlain with permafrost, little is known about viruses in other peatlands. More generally, soil viral biogeography and its potential drivers are poorly understood at both local and global scales. Here, 87 metagenomes and five viral size-fraction metagenomes (viromes) from a boreal peatland in northern Minnesota (the SPRUCE whole-ecosystem warming experiment and surrounding bog) were analyzed for dsDNA viral community ecological patterns, and the recovered viral populations (vOTUs) were compared to our curated PIGEON database of 266,805 vOTUs from diverse ecosystems. ResultsWithin the SPRUCE experiment, viral community composition was significantly correlated with peat depth, water content, and carbon chemistry, including CH4 and CO2 concentrations, but not with temperature during the first two years of warming treatments. Peat vOTUs with aquatic-like signatures (shared predicted protein content with marine and/or freshwater vOTUs) were significantly enriched in more waterlogged surface peat depths. Predicted host ranges for SPRUCE vOTUs were relatively narrow, generally within a single bacterial genus. Of the 4,326 SPRUCE vOTUs, 164 were previously detected in other soils, mostly peatlands. None of the previously identified 202,372 marine and freshwater vOTUs in our PIGEON database were detected in SPRUCE peat, but 1.9% of 78,203 genus-level viral clusters (VCs) were shared between soil and aquatic environments. On a per-sample basis, vOTU recovery was 32 times higher from viromes compared to total metagenomes. ConclusionsResults suggest strong viral "species" boundaries between terrestrial and aquatic ecosystems and to some extent between peat and other soils, with differences less pronounced at the "genus" level. The significant enrichment of aquatic-like vOTUs in more waterlogged peat suggests that viruses may also exhibit niche partitioning on more local scales. These patterns are presumably driven in part by host ecology, consistent with the predicted narrow host ranges. Although more samples and increased sequencing depth improved vOTU recovery from total metagenomes, the substantially higher per-sample vOTU recovery after viral particle enrichment highlights the utility of soil viromics.

microbiology↗

bioRxiv2020

Viromes outperform total metagenomes in revealing the spatiotemporal patterns of agricultural soil viral communities

Viruses are abundant yet understudied members of soil environments that influence terrestrial biogeochemical cycles. Here, we characterized the dsDNA viral diversity in biochar-amended agricultural soils at the pre-planting and harvesting stages of a tomato growing season via paired total metagenomes and viromes. Size fractionation prior to DNA extraction reduced sources of non-viral DNA in viromes, enabling the recovery of a vaster richness of viral populations (vOTUs), greater viral taxonomic diversity, broader range of predicted hosts, and better access to the rare virosphere, relative to total metagenomes, which tended to recover only the most persistent and abundant vOTUs. Of 2,961 detected vOTUs, 2,684 were recovered exclusively from viromes, while only three were recovered from total metagenomes alone. Both viral and microbial communities differed significantly over time, suggesting a coupled response to rhizosphere recruitment processes and nitrogen amendments. Viral communities alone were also structured along a spatial gradient. Overall, our results highlight the utility of soil viromics and reveal similarities between viral and microbial community dynamics throughout the tomato growing season yet suggest a partial decoupling of the processes driving their spatial distributions, potentially due to differences in dispersal, decay rates, and/or sensitivities to soil heterogeneity.

microbiology↗

bioRxiv2018

Endogenous viral elements are widespread in arthropod genomes and commonly give rise to piRNAs

Arthropod genomes contain sequences derived from integrations of DNA and non-retroviral RNA viruses. These sequences, known as endogenous viral elements (EVEs), have been acquired over the course of evolution and have been proposed to serve as a record of past viral infection. Recent evidence indicates that EVEs can function as templates for the biogenesis of PIWI-interacting RNAs (piRNAs) in some mosquito species and cell lines, raising the possibility that EVEs may function as a source of immunological memory in these organisms. However, whether EVEs are capable of acting as templates for piRNA production in other arthropod species is unknown. Here we used publically available genome assemblies and small RNA sequencing datasets to characterize the repertoire and function of EVEs across 48 arthropod genomes. We found that EVEs are widespread in arthropod genomes and primarily correspond to unclassified ssRNA viruses and viruses belonging to the Rhabdoviridae and Parvoviridae families. Additionally, EVEs were enriched in piRNA clusters in a majority of species and we found that production of primary piRNAs from EVEs is common, particularly for EVEs located within piRNA clusters. While we found evidence suggesting that piRNAs mapping to a number of EVEs are produced via the ping-pong cycle, potentially pointing towards a role for EVE-derived piRNAs during viral infection, limited nucleotide identity between currently described viruses and EVEs identified here likely limits the extent to which this process plays a role during infection with known viruses.

microbiology↗