Introduction
The Australian Microbiome (Australian Microbiome – Australian Microbiome) is a continental-scale, collaborative project aspiring to characterise the diversity and ecosystem service provision of the microorganisms inhabiting Australian managed and non-managed environments.
The mission of the Australian Microbiome (AM) project is to develop a comprehensive, publicly-accessible database of microbial diversity across a geographically expansive and diverse range of Australian terrestrial and aquatic ecosystems. The AM database will deliver searchable information on the occurrence and distribution of potential microbiological resources, collated into a searchable public database that will allow researchers and other end-users to address a broad variety of questions in microbial ecology. By providing unprecedented access to environmental microbiological information across the Australian land- and sea-scape, the AM project will enable large spatial and temporal- scale examinations of ecosystem function, biogeochemistry, bio-discovery, within natural Australian habitats.
The AM aims to develop an Australian microbial genomics resource for management, monitoring, and R&D purposes.
Australian Microbiome sample map (November 2021). Samples extend from Christmas Island to Antarctica.
Colour legend: red = soil (two depths per location), white = marine (1-10 depths per location), blue = plant, black = marine host (e.g., coral, seagrass, sponge), large green = long-term timeseries (~ monthly, 2-6 depths over 7+ years).
This manual lists and describes the Standard Operating Procedures used to generate data for the Australian Microbiome which should be cited from the primary literature, not by reference to this document. For example, the appropriate citation for method 1.1 Soil Sampling for Biomes of Australian Soil Environments (BASE) is Bissett et al., (2016), not this document. If there are errors or omissions please let us know.
Protocols have been contributed by consortium members and/or service providers and are organised in the stages of a standard OMICS workflow:
- Sample Collection,
- Contextual Metadata Analytical Procedures,
- OMICS Sample Extraction and Purification Protocols,
- OMICS Sequencing Procedures,
- Bioinformatics
- Data Analyses
Individual protocols are represented by a unique code (number) which is recorded in a database against a corresponding metadata field. A summary table of AM protocol codes and their corresponding method is provided in Table 1. Information relating to database field names, definitions and controlled vocabulary can be found here:
https://github.com/AusMicrobiome/contextualdb_doc/tree/main
All sampling methods, data generated and analytical workflows for the Australian Microbiome activities are publicly accessible (with free registration) on the Bioplatforms Data Portal (https://data.bioplatforms.com/organization/about/australian-microbiome). The requirements for access and use of the data, as well as appropriate acknowledgements in communications that arise from the AM consortium’s activities and data use, are defined in the Data policy and Communication policy.