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Estuaries are the important interface between the land and sea, providing significant environmental, economic, cultural and social values. However, they face unprecedented pressures including eutrophication, harmful algal blooms, habitat loss, and extreme weather due to climate change. Here we present an open access, quality-controlled water quality dataset collected from twelve diverse estuaries spanning 1000 km along the southeastern Australian coastline. Water depth, temperature and salinity data were collected across two years (2018-2021) capturing drought, wildfire and flood periods, using high accuracy Seabird MicroCAT field sensors located within oyster leases. These fully autonomous instruments collected and transmitted data every 10 minutes before downstream quality checking and uploading onto a public website. Simultaneous, high-resolution, longitudinal environmental data collected across multiple estuaries throughout a range of extreme weather events are exceptionally rare in the Southern Hemisphere, yet provide an invaluable resource for the aquaculture industry, researchers and environmental regulators alike.

Abstract Background The term holobiont is widely accepted to describe animal hosts and their associated microorganisms. The genomes of all that the holobiont encompasses, are termed the hologenome and it has been proposed as a unit of selection in evolution. To demonstrate that natural selection acts on the hologenome, a significant portion of the associated microbial genomes should be transferred between generations. Using the Sydney Rock Oyster (Saccostrea glomerata) as a model, we tested if the microbes of this broadcast spawning species could be passed down to the next generation by conducting single parent crosses and tracking the microbiome from parent to offspring and throughout early larval stages using 16S rRNA gene amplicon sequencing. From each cross, we sampled adult tissues (mantle, gill, stomach, gonad, eggs or sperm), larvae (D-veliger, umbo, eyed pediveliger, and spat), and the surrounding environment (water and algae feed) for microbial community analysis. Results We found that each larval stage has a distinct microbiome that is partially influenced by their parental microbiome, particularly the maternal egg microbiome. We also demonstrate the presence of core microbes that are consistent across all families, persist throughout early life stages (from eggs to spat), and are not detected in the microbiomes of the surrounding environment. In addition to the core microbiomes that span all life cycle stages, there is also evidence of environmentally acquired microbial communities, with earlier larval stages (D-veliger and umbo), more influenced by seawater microbiomes, and later larval stages (eyed pediveliger and spat) dominated by microbial members that are specific to oysters and not detected in the surrounding environment. Conclusion

The Sydney rock oyster (SRO; Saccostrea glomerata) is the most intensively farmed oyster species in Australia however, Queensland unknown (QX) disease has resulted in substantial losses and impeded productivity. QX disease is caused by infection with the parasite Marteilia sydneyi, and like other diseases, outbreaks are driven by a series of complex environmental and host factors such as seasonality, seawater salinity and oyster genetics. A potential but understudied factor in QX disease is the SRO microbiota, which we sought to examine before and during a QX disease outbreak. Using 16S rRNA (V1 – V3 region) amplicon sequencing, we examined the microbiota of SROs deployed in an estuary where QX disease occurs, with sampling conducted fortnightly over 22 weeks. Marteilia sydneyi was detected in the SROs by PCR (QX-positive), 16 weeks after the first sampling event and sporonts were observed in the digestive gland two weeks later on. There were no apparent patterns observed between the microbiota of QX-positive SROs with and without digestive gland sporonts however, the microbiota of QX-positive SROs was significantly different from those sampled prior to detection of M. sydneyi and from those negative for M. sydneyi post detection. As a result, shifts in microbiota structure occurred before sporulation in the digestive gland and either before or shortly after pathogen colonisation. The microbiota shifts associated with QX-positive oysters were principally driven by a relative abundance increase of operational taxonomic units (OTUs) assigned to unclassified species of the Borrelia and Candidatus Hepatoplasma genera and a relative abundance decrease in an OTU assigned to an unclassified species of the Mycoplasma genus. Since Mycoplasma species are common microbiota features of SROs and other oysters, we propose that there may be an important ecological link between Mycoplasma species and the health state of SROs.