Viruses of Atlantic Bonefish (Albula vulpes) in Florida and the Caribbean show geographic patterns consistent with population declines

Abstract

Atlantic Bonefish ( Albula vulpes ) are economically important due to their popularity with recreational anglers. In the State of Florida, USA, bonefish population numbers declined by approximately 60% between the 1990s and 2015. Habitat loss, water quality impairment, chemical inputs, and other anthropogenic factors have been implicated as causes, but the role of pathogens has been largely overlooked, especially with respect to viruses. We used a metagenomic approach to identify and quantify viruses in the blood of 103 A. vulpes sampled throughout their Western Atlantic range, including populations in Florida that have experienced population declines and populations in Belize, Mexico, Puerto Rico, and The Bahamas that have remained apparently stable. We identified four viruses, all of which are members of families known to infect marine fishes ( Flaviviridae , Iflaviridae , Narnaviridae , and Nodaviridae ), but all of which were previously undescribed. Bonefish from Florida and Mexico had higher viral richness (numbers of distinct viruses per individual fish) than fish sampled from other areas, and bonefish from the Upper Florida Keys had the highest prevalence of viral infection (proportion of positive fish) than fish sampled from any other location. Bonefish from Florida also had markedly higher viral loads than fish sampled from any other area, both for a novel narnavirus and for all viruses combined. Bonefish viruses may be indicators of environmentally driven physiological and immunological compromise, causes of ill health, or both. Supplementary information The online version contains supplementary material available at 10.1007/s10641-022-01306-9.

Cascading effects of climate change on recreational marine flats fishes and fisheries

“…Flats fishes such as bonefish can therefore be colonized by environmental bacteria, although with unknown health consequences. Furthermore, Campbell et al ( 2022 ) demonstrate infection of bonefish across their western Atlantic range with four previously unknown viruses, with patterns of viral load mirroring patterns of anthropogenic degradation, but again with unknown health consequences.…”

Viromics Reveals the High Diversity of Viruses from Fishes of the Tibet Highland

“…According to the phylogenetic tree, the calicivirus is a brand-new member of a taxon that has previously been found in marine fishes. The family Iflaviridae is thought to infect marine fish and was first described in Belize's bonefish ( 36 ). The new iflavirus clustered with the invertebrate soybean thrips, according to the phylogenetic tree, nevertheless the RdRp gene shared only a 38.91% similarity with it.…”

Five Species of Wild Freshwater Sport Fish in Wisconsin, USA, Reveal Highly Diverse Viromes

“…Metagenomic next-generation sequencing was performed as previously described [ 6 , 18 , 25 , 26 ]. In brief, samples were centrifuged at 10,000× g (4 °C) for 10 min to remove debris, then supernatants were transferred to a new tube and centrifuged further at 25,000× g (4 °C) for 3 h to pellet viruses.…”

“…A virus was considered present if a fish had ≥2 overlapping viral reads of 50 bp or more. Reads that mapped to each virus, or any of the viruses examined (total viral load), were then normalized for sequencing depth and viral sequence length and log-transformed to become log10 viral reads per million per kilobase of target sequence (Log10vRPM/kb) [ 6 , 25 , 26 ].…”

“…Much of our current understanding of viruses infecting fish is based on the study of pathogenic viruses in symptomatic hosts. However, the recent rise of metagenomic sequencing has led to the discovery that fish harbor a greater number of viruses than any other class of vertebrates [ 1 , 2 , 3 , 4 , 5 , 6 , 7 ]. Most families of RNA viruses once thought to infect mammals have been described in bony fishes [ 1 ].…”