Quantitative metagenomics for marine prokaryotes and photosynthetic eukaryotes.

High-throughput sequencing has provided unprecedented insights into microbial biodiversity in marine and other ecosystems. However, most sequencing-based studies report only relative (compositional) rather than absolute abundance, limiting their application in ecological modeling and biogeochemical analyses. Here, we present a metagenomic protocol incorporating genomic internal standards to quantify the absolute abundances of prokaryotes and eukaryotic phytoplankton, which together form the base of the marine food web, in unfractionated seawater.

Characterizing organisms from three domains of life with universal primers from throughout the global ocean.

We introduce the Global rRNA Universal Metabarcoding Plankton database (GRUMP), which consists of 1194 samples that were collected from 2003-2020 and cover extensive latitudinal and longitudinal transects, as well as depth profiles in all major ocean basins. DNA from unfractionated (>0.2 µm) seawater samples was amplified using the 515Y/926 R universal three-domain rRNA gene primers, simultaneously quantifying the relative abundance of amplicon sequencing variants (ASVs) from bacteria, archaea, eukaryotic nuclear 18S, and eukaryotic plastid 16S.

Antibiotic resistance gene levels within a highly urbanised estuary.

Antibiotic resistant bacteria are increasingly being found in aquatic environments, representing a potential threat to public health. To examine the dynamics and potential sources of antibiotic-resistant genes (ARGs) in urbanised waterways, we performed a six-month temporal study at six locations within the Sydney Harbour estuary. These locations spanned a salinity gradient from seawater at the mouth of the harbour to freshwater at the more urbanised western sites.

Faecal contamination determines bacterial assemblages over natural environmental parameters within intermittently opened and closed lagoons (ICOLLs) during high rainfall.

Intermittently closed and opened lakes and lagoons (ICOLLs) provide important ecosystem services, including food provision and nutrient cycling. These ecosystems generally experience low watershed outflow, resulting in substantial fluctuations in physicochemical parameters that are often compounded by anthropogenic contamination, however, how this impacts the patterns in microbiology within these environments remains uncharacterised. Therefore, we aimed to determine how seasonal heterogeneity in the physicochemical parameters, in comparison to faecal contamination, alter the dynamics of bacterial communities inhabiting ICOLLs on the eastern Australian coast.

Identification and quantification of Acanthamoeba spp. within seawater at four coastal lagoons on the east coast of Australia.

Acanthamoeba is an opportunistic free-living heterotrophic protist that is the most predominant amoeba in diverse ecological habitats. Acanthamoeba causes amoebic keratitis (AK), a painful and potentially blinding corneal infection. Major risk factors for AK have been linked to non-optimal contact lens hygiene practices and Acanthamoeba contamination of domestic and recreational water.

Molecular microbiological approaches reduce ambiguity about the sources of faecal pollution and identify microbial hazards within an urbanised coastal environment.

Urbanised beaches are regularly impacted by faecal pollution, but management actions to resolve the causes of contamination are often obfuscated by the inability of standard Faecal Indicator Bacteria (FIB) analyses to discriminate sources of faecal material or detect other microbial hazards, including antibiotic resistance genes (ARGs). We aimed to determine the causes, spatial extent, and point sources of faecal contamination within Rose Bay, a highly urbanised beach within Sydney, Australia's largest city, using molecular microbiological approaches. Sampling was performed across a network of transects originating at 9 stormwater drains located on Rose Bay beach over the course of a significant (67.

Variability in the Composition of Pacific Oyster Microbiomes Across Oyster Families Exhibiting Different Levels of Susceptibility to OsHV-1 μvar Disease.

Oyster diseases are a major impediment to the profitability and growth of the oyster aquaculture industry. In recent years, geographically widespread outbreaks of disease caused by ostreid herpesvirus-1 microvariant (OsHV-1 μvar) have led to mass mortalities among , the Pacific Oyster. Attempts to minimize the impact of this disease have been largely focused on breeding programs, and although these have shown some success in producing oyster families with reduced mortality, the mechanism(s) behind this protection is poorly understood.