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

Abstract

Wetlands store 20-30% of the world's 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), only 4.4% of which were detected at the same field site two years prior, indicating a small degree of population stability or recurrence. Viral communities differed most significantly among 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 (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, and increased SNP frequencies in CRISPR-targeted major tail protein genes suggest potential viral eco-evolutionary dynamics in response to both immune targeting and 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.

Fig. 1. Sampling design and overarching compositional patterns for Bodega Bay viral and prokaryotic communities.

A Sampling locations for all Bodega Bay samples. Center: locations of the seven wetland sites within the Bodega Marine Reserve, Left and Right: locations of each of the nine samples per site (a zoomed in view of each site with individual sample labels is in Supplementary Fig. 1). Per the legend below the images, circles correspond to locations with halophyte vegetation and saline soils, triangles correspond to locations without halophytes and non-saline soil, and squares correspond to mismatched locations. The ‘culvert’ label indicates the location of a human-made pipe below the road that allows for water movement. B, C Principal coordinates analysis (PCoA), based on Bray-Curtis dissimilarities derived from the table of vOTU abundances (read mapping to vOTUs). Each point is one sample (one virome), with viral communities from (B) all 63 viromes, and (C) the 45 viromes indicated by the dashed rectangle in (B). Panel (C) is a new PCoA to better show separation among overlapping samples in (B). D Co-occurrence network of vOTUs detected in more than one Bodega Bay virome, colored by the site in which they were most abundant (had the highest average per-bp coverage depth). Nodes represent vOTUs, and edges represent a significant co-occurrence between the vOTUs, calculated using a probabilistic co-occurrence model with the R package cooccur. E PCoA based on Bray-Curtis dissimilarities of 16S rRNA gene OTU community composition, where 16S rRNA gene reads were bioinformatically mined from 63 total metagenomes. For all PCoA plots (B, C, E), the percent variance explained by each axis is indicated in parenthesis.

Fig. 2. Global distribution and habitat context of Bodega Bay vOTUs, leveraging the PIGEONv2.0 database.

A vOTUs (n = 196) from PIGEONv2.0 recovered at Bodega Bay by read mapping, according to the location where they were first recovered, colored by the environment in which they were originally recovered. Circle size indicates the number of vOTUs. B Composition of the PIGEONv2.0 database of 515,763 vOTU sequences, colored by environment. C Relative proportions of all vOTUs recovered from PIGEONv2.0 at Bodega Bay, colored by the original environment from which they were recovered. D Relative proportions of vOTUs recovered from PIGEONv2.0 at Bodega Bay, as in panel (C), but separated by the Bodega vegetation group in which they were recovered, colored by original source environment. If a vOTU was recovered in both vegetation groups, it appears twice in the chart.

Fig. 3. Comparisons of viral variant (sub-population) diversity in local and global contexts.

Pairwise average nucleotide identities (ANIs) between vOTU variants, calculated between each sample-specific vOTU consensus sequence and the originally assembled (reference) vOTU sequence, using inStrain. Each point is the ANI for one vOTU variant in one Bodega Bay virome compared to the reference sequence for that vOTU. A Variant ANIs for: (left) vOTUs both assembled and recovered through read mapping from the Bodega Bay dataset (Bodega Bay reference sequences), and (right) vOTUs recovered at Bodega Bay via read mapping but originally derived from PIGEONv2.0 (PIGEONv2.0 reference sequences). Stars above boxes correspond to significant differences between groups (Student’s T test, significant when p < 0.001). B Variant ANIs for vOTUs both assembled and recovered via read mapping from Bodega Bay, either: (left) assembled and recovered in the same year (2019-2019 or 2021-2021), or (right) in different years (2019-2021 or 2021-2019). C Variant ANIs for vOTUs assembled from Bodega Bay in 2021, either assembled and recovered through read mapping at the same sampling time point, or at different time points, where T ± 1 equals 2 months between samplings, and T ± 2 equals 4 months. Only pairs of samples from the same wetland site were considered in this analysis. Letters above boxes correspond to significant differences between groups (Student’s T test, significant when p < 0.001). In all three panels, boxes show the median and interquartile range (IQR), and whiskers extend to Q1-1.5*IQR and Q3 + 1.5*IQR.

Fig. 4. Bodega Bay virus-host linkages and putative interactions derived from CRISPR spacer-protospacer matches.

A Unrooted phylogenetic tree (concatenated predicted protein alignment of 43 marker genes defined by CheckM) of prokaryotic metagenome-assembled genomes (MAGs) with at least one vOTU linked by CRISPR sequence homology. The numbers for MAGs correspond to numbers in the network in panel (B). Tree was constructed using GTDB-Tk under the WAG model. B Virus-host linkage network for MAGs with at least one vOTU linked through CRISPR homology. Circle nodes represent MAGs and are colored by phylum, while triangles represent vOTUs.