Metagenome-assembled genome of withering syndrome causative agent, "Candidatus Xenohaliotis californiensis," from endangered white abalone (Haliotis sorenseni).

The genome of "Candidatus Xenohaliotis californiensis" was assembled from shotgun metagenomic sequencing of experimentally infected white abalone. Ninety-one percent genome completeness was achieved with low contamination. Sequencing this genome provides the opportunity to track pathogen evolution over time, conduct gene expression experiments, and study dynamics between this pathogen and its phage.

A Draft Reference Genome Assembly of the Critically Endangered Black Abalone, Haliotis cracherodii.

The once abundant black abalone, Haliotis cracherodii, is a large, long-lived grazing marine mollusk that inhabits the rocky intertidal along the coast of California. The species has experienced dramatic declines since the mid-1980s largely due to the fatal bacterial disease called withering syndrome, leading to the collapse of an economically important fishery and to its inclusion into the IUCN listing as a critically endangered species. In some places impacted by the disease, populations of black abalone have declined by more than 90%, prompting population crashes associated with very little recruitment of new individuals and changes to intertidal communities. Habitats that were dominated by crustose coralline algae and bare rock have become dominated instead by fleshy algae and sessile invertebrates. Here, we present the first high-quality black abalone reference genome, assembled with PacBio HiFi long-reads and assembled with Dovetail Omni-C data to generate a scaffold-level assembly. The black abalone reference genome will be an essential resource in understanding the evolutionary history of this species as well as for exploring its current levels of genetic diversity and establishing future management and restoration plans.

Differing responses of red abalone (Haliotis rufescens) and white abalone (H. sorenseni) to infection with phage-associated Candidatus Xenohaliotis californiensis.

The Rickettsiales-like prokaryote and causative agent of Withering Syndrome (WS)-Candidatus Xenohaliotis californiensis (Ca. Xc)-decimated black abalone populations along the Pacific coast of North America. White abalone-Haliotis sorenseni-are also susceptible to WS and have become nearly extinct in the wild due to overfishing in the 1970s. Candidatus Xenohaliotis californiensis proliferates within epithelial cells of the abalone gastrointestinal tract and causes clinical signs of starvation. In 2012, evidence of a putative bacteriophage associated with Ca. Xc in red abalone-Haliotis rufescens-was described. Recently, histologic examination of animals with Ca. Xc infection in California abalone populations universally appear to have the phage-containing inclusions. In this study, we investigated the current virulence of Ca. Xc in red abalone and white abalone at different environmental temperatures. Using a comparative experimental design, we observed differences over time between the two abalone species in mortality, body condition, and bacterial load by quantitative real time PCR (qPCR). By day 251, all white abalone exposed to the current variant of Ca. Xc held in the warm water (18.5 °C) treatment died, while red abalone exposed to the same conditions had a mortality rate of only 10%, despite a relatively heavy bacterial burden as determined by qPCR of posterior esophagus tissue and histological assessment at the termination of the experiment. These data support the current status of Ca. Xc as less virulent in red abalone, and may provide correlative evidence of a protective phage interaction. However, white abalone appear to remain highly susceptible to this disease. These findings have important implications for implementation of a white abalone recovery program, particularly with respect to the thermal regimes of locations where captively-reared individuals will be outplanted.

Health and survival of red abalone Haliotis rufescens from San Miguel Island, California, USA, in a laboratory simulation of La Niña and El Niño conditions.

The variability in Southern California's marine climate is dominated by the El Niño-Southern Oscillation, with cycling between El Niño events (characterized by warm water, low productivity, and frequent storms) and La Niña events (which exhibit the opposite conditions). Relative to the mainland and other Channel Islands, San Miguel Island (SMI) consistently maintains cooler water temperatures and supports significant populations of red abalone Haliotis rufescens, presumably owing to increased food production and diminished expression of the bacterial disease known as withering syndrome. We conducted a laboratory experiment to examine the effects of La Niña and El Niño conditions on the health and survival of red abalone from SMI. Six replicate tanks per treatment, each containing six abalone, were subjected to one of the following three temperature regimes (treatments): Bodega Bay, California ambient (AMB; mean, 11.4 degrees C), SMI La Niña regime (LAN; mean, 13.8 degrees C), and SMI El Niño regime (ELN; mean, 16.5 degrees C). After 328 d, survival in the ELN treatment was significantly lower than in the AMB and LAN groups. A body condition index was significantly lower in the ELN group than in the AMB group, and the LAN group was in between. A visual score of body shrinkage was significantly higher in both the LAN and ELN groups than in the AMB group. Other clinical signs of withering syndrome and the prevalence and infection intensity of the causative agent, Candidatus Xenohaliotis californiensis, increased as temperature increased in the three treatment groups from AMB to LAN to ELN, although the differences were not statistically significant. Generally, we found that increased temperature resulted in elevated disease expression, although less than observed in previous studies that used farmed abalone and higher, less variable temperature regimes. Water temperature modulates the effect of withering syndrome in wild red abalone, and very strong El Niño events are predicted to result in significant mortality at San Miguel Island.