IMOS - Marine Microbiome Initiative Facility

Researchers: Van de Kamp, Jodie (Principal investigator) ,  Van de Kamp, Jodie (Principal investigator) ,  AODN Data Manager (Point of contact, Resource provider of) ,  Data Officer (Point of contact, Resource provider of) ,  Data Officer (Point of contact, Resource provider of)
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Brief description Marine microorganisms control the productivity and biogeochemistry of the global ocean. In light of this fundamental importance the Global Ocean Observing System (GOOS) has designated microbial biomass and diversity as emerging essential ocean variables (EOV) and a necessary component of an integrated and sustained ocean observing system. The IMOS Marine Microbiome Initiative Facility facilitates the delivery of DNA-based data on the distribution, diversity and function of marine microbes in Australian coastal waters and oceans through the collection and processing of water samples from the IMOS National Reference Stations (NRS) and a newly established network of coastal sites. IMOS NRS are a series of sites designed to monitor oceanographic parameters in Australian coastal ocean waters using moored sensors and water sampling field trips. These sites span ~30° of latitude and ~38° longitude, range from tropical to cold temperate zones, and are influenced by both local and globally significant oceanographic and climatic features. Water samples are collected monthly from several depths at the 7 current NRS, Maria Island (TAS), Kangaroo Island (SA), Rottnest Island (WA), Darwin (NT), Yongala (QLD), North Stradbroke Island (QLD) and Port Hacking (NSW), establishing a globally unique continental-scale time-series (since 2012 for some NRS) of the marine microbial communities in Australian coastal and shelf waters. The IMOS Coastal Sampling sub-Facility is a network of coastal microbial observatories designed to operationally mirror the NRS, but provide novel capacity to understand coastal microbial processes. Coastal environments are highly dynamic due to both natural perturbations and anthropogenic impacts and represent sites where environmental microbial assemblages can have substantial human health and economic impacts. Phase 1 of establishing this network designated three sites of significance based on stakeholder/end user feedback, economic importance, and/or human health and scientific relevance. Sampling sites include coastal waters of the Great Barrier Reef (QLD), Botany Bay (NSW), and Port Phillip Bay (VIC). Data is generated and made available through the Australian Microbiome Initiative, a national bio-resource, providing a searchable database of marine microbial occurrence data. This is an Australian wide collaboration founded on two established Bioplatforms Australia framework data initiatives: Marine Microbes and Biomes of Australian Soil Environments (BASE). The consortium involves researchers from more than 40 institutions supported by the following core partners: Bioplatforms Australia; Integrated Marine Observing System (IMOS); CSIRO and Parks Australia through the Bush Blitz program. The DNA-based data generated by this facility provide crucial spatial and temporal information that underpin the understanding of Australian marine microbiology. Coupled with the suite of biological, physical and chemical observations already established at IMOS National Reference Stations, the Marine Microbiome Initiative supports the understanding of status and trends of oceanic health, biogeochemistry and primary productivity. This data is freely available through the Bioplatforms Australia Data Portal (About - The Australian Microbiome Initiative - Organizations - data.bioplatforms.com) including the raw data files as well as processed data products in the form of microbial DNA-sequence based occurrence tables and metagenomics gene maps (gene maps currently in development). Registration is free and required to download data. Please acknowledge all relevant parties, as detailed in acknowledgement section.

Lineage Maintenance and Update Frequency: asNeeded

Lineage Statement: All workflows (from sampling through to data products) used to generate data for the Australian Microbiome Initiative are publicly available at Australian Microbiome (github.com). The Australian Microbiome Initiative Scientific Manual (AusMicrobiome/scientific_manual: Australian Microbiome Initiative Scientific Manual (github.com)) lists and describes the standard operating procedures used to generate data for the Australian Microbiome Initiative. Protocols have been contributed by consortium members and/or service providers, and should be cited from the primary literature, not by reference to this document.

Notes Credit
Australian Government’s National Collaborative Research Infrastructure Strategy (NCRIS)

Notes Credit
Integrated Marine Observing System (IMOS). IMOS is a national collaborative research infrastructure, supported by Australian Government.

Notes Credit
Bioplatforms Australia is a national collaborative research infrastructure, supported by Australian Government.

Notes Credit
Bush Blitz program funded by the Australian Government and BHP.

Notes Credit
CSIRO Oceans and Atmosphere

Notes Purpose
The initiative aims to develop an Australian microbial genomics resource for management, monitoring, and R&D purposes.

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