Endogenous viral elements (EVEs) offer insight into the evolutionary histories and hosts of contemporary viruses. This study leveraged DNA metagenomics and genomics to detect and infer the host of a non-retroviral dinoflagellate-infecting +ssRNA virus (dinoRNAV) common in coral reefs. As part of the Tara Pacific Expedition, this study surveyed 269 newly sequenced cnidarians and their resident symbiotic dinoflagellates (Symbiodiniaceae), associated metabarcodes, and publicly available metagenomes, revealing 178 dinoRNAV EVEs, predominantly among hydrocoral-dinoflagellate metagenomes. Putative associations between Symbiodiniaceae and dinoRNAV EVEs were corroborated by the characterization of dinoRNAV-like sequences in 17 of 18 scaffold-scale and one chromosome-scale dinoflagellate genome assembly, flanked by characteristically cellular sequences and in proximity to retroelements, suggesting potential mechanisms of integration. EVEs were not detected in dinoflagellate-free (aposymbiotic) cnidarian genome assemblies, including stony corals, hydrocorals, jellyfish, or seawater. The pervasive nature of dinoRNAV EVEs within dinoflagellate genomes (especially Symbiodinium), as well as their inconsistent within-genome distribution and fragmented nature, suggest ancestral or recurrent integration of this virus with variable conservation. Broadly, these findings illustrate how +ssRNA viruses may obscure their genomes as members of nested symbioses, with implications for host evolution, exaptation, and immunity in the context of reef health and disease.

Aquatic invertebrates are common reservoirs of a rapidly expanding group of circular Rep-encoding ssDNA (CRESS-DNA) viruses. This study identified and explored the phylogenetic relationship between novel CRESS-DNA viral genotypes associated with Pacific intertidal isopods Idotea wosnesenskii, Idotea resecata, and Gnorimosphaeroma oregonensis. One genotype associated with I. wosnesenskii, IWaV278, shared sequence similarity and genomic features with Tombusviridae (ssRNA) and Circoviridae (ssDNA) genomes and was putatively assigned to the Cruciviridae clade comprising chimeric viruses. The complete genome of IWaV278 (3478 nt) was computationally completed, validated via Sanger sequencing, and exhibited sequence conservation and codon usage patterns analogous to other members of the Cruciviridae. Viral surveillance (qPCR) indicated that this virus was temporally transient (present in 2015, but not 2017), specific to I. wosnesenskii at a single collection site (Washington, DC, USA), more prevalent among male specimens, and frequently detected within exoskeletal structures. 18S rRNA sequences identified two alveolate protists associated with IWaV278-positive tissues and mechanical epibiont removal of ciliated exoskeletal structures eliminated viral detection, suggesting that the putative host of IWaV278 may be an epibiont of I. wosnesenskii. This investigation provides additional phylogenetic evidence to resolve Cruciviridae evolution and offers insight into the biogeography, specificity, and potential host of a crucivirus genotype.

Pelagic‐feeding seabirds deliver nutrient subsidies that enhance the productivity, biodiversity, and resilience of terrestrial and marine ecosystems, particularly in nutrient‐poor tropical environments. However, the biogeophysical variables governing the fluxes of these nutrients within and among interconnected ecosystems remain poorly understood. To address this, we examined the spatial distribution of seabird‐vectored nutrients in the seascape of Tetiaroa, a semi‐enclosed coral atoll in French Polynesia, where seabird populations and associated nutrient cycles are recovering after recent rat eradication. We focus on the nitrogen isotope (δ¹⁵N) signatures of a dominant marine alga as evidence of seabird‐vectored nutrient uptake. Integrating stable isotope analysis within a seascape ecology framework, we show that breeding seabird biomass, depth, distance to land, geographic location within the atoll, and seafloor curvature drive spatial patterns of nutrient enrichment. Specifically, our models account for up to 88% of the variation in algal δ¹⁵N signatures and reveal peak enrichment in shallow, nearshore areas where water flow slows and converges due to localised seafloor curvature. These results extend previous research by highlighting seafloor geomorphology, notably curvature, as a modulator of fine‐scale nutrient delivery patterns. Although a complex model incorporating 11 high‐resolution biogeophysical variables enhanced spatial predictions by revealing fine‐scale variations, a simpler model using only five of these variables was comparably effective in capturing overall spatial trends. This study identifies the key seascape configuration and complexity characteristics likely to affect the spatial patterns of recovery potential following the restoration of seabird‐driven nutrient cycles, offering valuable guidance for ongoing restoration efforts in this coupled island‐reef system. Future investigations could assess how the effects of biogeophysical variables on nutrient delivery vary in magnitude and direction across different geographic, geological, and anthropogenic contexts.

Circularrep-encodingssDNA (CRESS-DNA) viruses are common constituents of invertebrate viral consortia. Despite their ubiquity and sequence diversity, the effects of CRESS-DNA viruses on invertebrate biology and ecology remain largely unknown. This study assessed the relationship between the transcriptional profile of benthic amphipods of genusDiporeiaand the presence of the CRESS-DNA virus, LM29173, in the Laurentian Great Lakes to provide potential insight into the influence of these viruses on invertebrate gene expression. Twelve transcriptomes derived fromDiporeiawere compared, representing organisms from two amphipod haplotype clades (Great Lakes Michigan and Superior, defined by COI barcode sequencing) with varying viral loads (up to 3 × 10⁶genome copies organism⁻¹). Read recruitment to de novo assembled transcripts revealed 2,208 significantly over or underexpressed contigs in transcriptomes with above average LM29173 load. Of these contigs, 31.5% were assigned a putative function. The greatest proportion of annotated, differentially expressed transcripts were associated with functions including: (1) replication, recombination, and repair, (2) cell structure/biogenesis, and (3) post-translational modification, protein turnover, and chaperones. Contigs putatively associated with innate immunity displayed no consistent pattern of expression, though several transcripts were significantly overexpressed in amphipods with high viral load. Quantitation (RT-qPCR) of target transcripts, non-muscular myosin heavy chain, β-actin, and ubiquitin-conjugating enzyme E2, corroborated transcriptome analysis and indicated that Lake Michigan and Lake Superior amphipods with high LM29173 load exhibit lake-specific trends in gene expression. While this investigation provides the first comparative survey of the transcriptional profile of invertebrates of variable CRESS-DNA viral load, additional inquiry is required to define the scope of host-specific responses to potential infection.

Endogenous viral elements (EVEs) offer insight into the evolutionary histories and hosts of contemporary viruses. This study leveraged DNA metagenomics and genomics to detect and infer the host of a non-retroviral dinoflagellate-infecting +ssRNA virus (dinoRNAV) common in coral reefs. As part of the Tara Pacific Expedition, this study surveyed 269 newly sequenced cnidarians and their resident symbiotic dinoflagellates (Symbiodiniaceae), associated metabarcodes, and publicly available metagenomes, revealing 178 dinoRNAV EVEs, predominantly among hydrocoral-dinoflagellate metagenomes. Putative associations between Symbiodiniaceae and dinoRNAV EVEs were corroborated by the characterization of dinoRNAV-like sequences in 17 of 18 scaffold-scale and one chromosome-scale dinoflagellate genome assembly, flanked by characteristically cellular sequences and in proximity to retroelements, suggesting potential mechanisms of integration. EVEs were not detected in dinoflagellate-free (aposymbiotic) cnidarian genome assemblies, including stony corals, hydrocorals, jellyfish, or seawater. The pervasive nature of dinoRNAV EVEs within dinoflagellate genomes (especially Symbiodinium ), as well as their inconsistent within-genome distribution and fragmented nature, suggest ancestral or recurrent integration of this virus with variable conservation. Broadly, these findings illustrate how +ssRNA viruses may obscure their genomes as members of nested symbioses, with implications for host evolution, exaptation, and immunity in the context of reef health and disease.