Top-heavy trophic structure within benthic viral dark matter

Abstract

Viruses exert considerable influence on microbial population dynamics and community structure, with cascading effects on ecosystem-scale biogeochemical cycling and functional trajectories. Creating broadly generalizable theory on viral trophic ecology requires further inquiry into historically unexplored microbial systems that currently lack empirically demonstrated patterns in viral infectivity, such as structurally complex benthic communities. This becomes increasingly relevant considering recently proposed revisions to the fundamental mechanisms that modulate the strength and direction viral trophic linkages. Here, we employed deep longitudinal multiomic sequencing to characterize the viral assemblage (including ssDNA, dsDNA, and dsRNA viruses) and profile lineage-specific host-virus interactions within benthic cyanobacterial mats sampled from Bonaire, Caribbean Netherlands, over a complete diel time-series, and reconstruct patterns in intra-mat trophic structure. We recovered 11,020 unique viral populations spanning at least 10 viral families across the orders Caudovirales, Petitvirales, and Mindivirales, with evidence for extensive genomic novelty from reference and environmental viral sequences. Analysis of coverage ratios of viral sequences and computationally predicted hosts spanning 15 phyla and 21 classes revealed virus:host abundance and activity ratios consistently exceeding 1:1, with overall power-law scaling indicating an increasingly top-heavy intra-mat trophic structure with significant top-down pressure. Diel activity of cyanophages showed clear temporal patterns that seem to follow host physiological condition. These data generate important hypotheses concerning taxon-dependent variation in the relative contribution of top-down vs. bottom-up forcing in driving mat community dynamics, and establish a useful database of viral sequences from this previously unexplored system toward the generation of generalizable trans-system theory on viral trophic ecology.

Predation, community asynchrony, and metacommunity stability in cyanobacterial mats

“…Samples were collected from a single macroscopically decaying cyanobacterial mat individual found on sediment at 12.6m depth for molecular inference of viral infection dynamics (micropredation) associated with visible mat decay (Appendix S1: Figure S3). Meta’omic sequencing-based approaches provide robust indirect quantification of trophic interaction direction and strength for viruses of cellular microorganisms (Coutinho et al 2017, Cissell and McCoy 2022a). Samples were collected on 04 June 2019 at 09:58 Atlantic Standard Time from 3 points across an imaginary transect spanning the senescing mat individual, including samples from the following mat areas: the visibly healthy portion of the mat (hereafter ‘ Living ’), the mat area at the immediate edge between healthy and senescent mat biomass (hereafter ‘ Border ’), and the visibly senescent portion of the mat (hereafter ‘ Decay ’).…”

“…TPM normalization utilized the summed length of predicted ORFs on each feature (from Prodigal ), rather than total genomic length for sequence length standardization. Virus-Microbe Activity Ratios (VMARs) were calculated like VMR as described above (Cissell and McCoy 2022a). Abundance-normalized TPM estimates were created by dividing TPM normalized expression data by CPM normalized abundance data obtained from metagenomes (normalization procedure described above).…”

“…population-specific interactions from viral specialist predators [Fig. 5; Cissell and McCoy 2022a]), to whole community scales (i.e. generalist grazing from reef fishes [Fig.…”

“…Mat community patches on the reefs surrounding the Caribbean island of Bonaire form spatially distinct mats with discrete patch boundaries, which may be longitudinally tracked macroscopically for evidence of predation and for broad community dynamics while efficiently solving the classic issue of community delineation and circumscription (Crowley 1978). Additionally, these distinct mat communities can be probed using molecular tools to probe relevant population scale functional dynamics and demography (Cissell & McCoy in review), and interactions with viral predators (Cissell and McCoy 2022a). Furthermore, recent molecular evidence from the comparison of average total nucleotide identity of Metagenome Assembled Genomes (MAGs) reconstructed among multiple spatially distinct benthic cyanobacterial mats on the fringing reefs of Bonaire revealed strong genomic conservation among mat communities, and suggests that cyanobacterial mats form true, dispersal-linked metacommunities on reefs (Cissell & McCoy in review).…”

“…As inCissell & McCoy (2022a), HMM searches and BLASTp with non-reference based HMM searches were implemented to extract viral signatures from individually assembled metagenomic scaffolds. A total of 811 shared nonredundant 95% vOTUs were recovered and manually curated, with a mean sequence length of 6,647bp.…”