– ABOUT
Australian microbiome
Australia’s diverse terrestrial and coastal environments are home to essential microbial communities, playing crucial roles in ecosystem health and functioning. Despite their microscopic size, microbes drive various environmental processes and influence both the environment and living organisms. They are integral to global biogeochemical cycles and contribute to human and environmental well-being, including disease management.
From its outset in 2020, the mission of the Australian Microbiome (AM) project has been 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 delivers searchable information on the occurrence and distribution of potential microbiological resources, collated into a searchable public database that allows 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 enables large spatial and temporal- scale examinations of ecosystem function, biogeochemistry, bio-discovery, within natural Australian habitats.
OBJECTIVES
The initiative aims to develop an Australian microbial genomics resource for management, monitoring, and R&D purposes. The consortium efforts will:
- Sustain and strengthen the Australian environmental microbial genomic resource
- Engage a broad range of end users and improve collaboration between researchers in different research fields
- Enhance functionality to allow translation of the resource for applied outcomes (to broad range of end-users and uses) and foster innovative research.
DATA
For further information and to view and access initiative data, please go to the Bioplatforms Australia Data Portal.
PROJECTS
| Project name | Project Summary | Environment sampled | Data Strategy | Project Lead | Partners |
|---|---|---|---|---|---|
| IMOS NRS Marine microbial observatories | Provides continental-scale, phylogenetic sequencing data of microbial communities across multiple marine sites. Observations span a wide range of environmental zones and link physical, biological, and chemical data to microbial assemblages for enhanced monitoring of microbial biodiversity. | IMOS National Reference Station - pelagic | Genetic markers (bacterial 16S, archaeal 16S, eukaryotic 18S), Whole genome sequencing (Illumina) | Jodie Van de Kamp | Integrated Marine Observing System, CSIRO, University Technology Sydney, |
| BushBlitz and National-Marine Parks | Aims to document Australia’s flora and fauna, including microbial diversity in national and marine parks, complementing BushBlitz expeditions and supporting conservation efforts by understanding ecosystem diversity from macro to micro levels. | Australian soils (BushBlitz expeditions), marine seawater samples (marine research voyages) | Genetic markers (bacterial 16S, archaeal 16S, eukaryotic 18S, fungal ITS), Whole genome sequencing (Illumina) | Jo Harding, Andrew Bissett | CSIRO, Parks Australia |
| Australian Coastal Microbial Observatory Network | Establishes a network of microbial observatories along the Australian coastline to examine microbial dynamics in key coastal ecosystems and their role in environmental and human health, providing data to monitor and manage coastal microbiomes. | Coastal microbial observatory: Port Phillip Bay, Botany Bay, Great Barrier Reef | Genetic markers (bacterial 16S, archaeal 16S, eukaryotic 18S, fungal ITS) | Justin Seymour | IMOS, AIMS, UTS, UNSW, Deakin Uni |
| Recovery of soil microbial communities during post-agricultural land restoration | Investigates soil microbiota recovery in post-agricultural land, assessing how microbiome dynamics can inform ecosystem restoration efforts and contribute to biodiversity and soil health. | Australian post-agricultural soils in restoration | Genetic markers (bacterial 16S, archaeal 16S, eukaryotic 18S, fungal ITS) | Martin Breed | Flinders Uni, SA Water |
| Cotton soil microbiome | Builds a baseline of soil microbiomes in Australian cotton fields to support sustainable land management and understand microbial responses to agricultural practices. | Australian soils - cotton fields | Genetic markers (bacterial 16S, archaeal 16S, eukaryotic 18S, fungal ITS), Whole genome sequencing (Illumina) | Gupta Vadakattu | CSIRO, UNE |
| A coupled bio-physical, ecosystem-scale, examination of Australia’s International Indian Ocean Expedition line | Provides samples and data from the Indian Ocean to enhance species and functional modeling across marine ecosystems, contributing to a baseline for coastal and marine environmental management in the region. | Marine seawater samples (Indian Ocean research voyage) | Genetic markers (bacterial 16S, archaeal 16S, eukaryotic 18S), Whole genome sequencing (Illumina) | Martin Ostrowski | UTS, Macquarie Uni, Murdoch Uni |
| Brisbane River estuary | Assesses microbial and viral community changes along the Brisbane River estuary through metagenomics and single-cell genomics, contributing insights into ecological and human health impacts within the estuary. | Estuarine water samples | Genetic markers (bacterial 16S, archaeal 16S, eukaryotic 18S, fungal ITS), Whole genome sequencing (Illumina) | Chris Rinke | The University of Queensland |
| Crop-associated Soil Microbiome: Wheat and Barley | Focuses on soil and plant microbiome impacts on wheat and barley performance, with a view to informing biosecurity and management practices in Australian agriculture. | Australian soils - wheat and barley fields | Genetic markers (bacterial 16S, archaeal 16S, eukaryotic 18S, fungal ITS) | Andrew Bissett | CSIRO, IndigoAg |
| Australian MAG database | Establishes a metagenome-assembled genomes (MAG) database to augment functional microbiome studies within the Australian Microbiome Initiative, improving environmental data precision. | Coastal and pelagic marine seawater samples | Whole genome sequencing (Illumina) | Torsten Thomas | UNSW, AIMS, UTS |
| How does the soil microbiome vary within urban green spaces used by people and dogs | Studies soil microbiome variations in urban green spaces used by people and dogs, assessing potential impacts on human immunity and ecosystem health. | Australian soils - urban | Genetic markers (bacterial 16S, archaeal 16S, eukaryotic 18S, fungal ITS) | Amy Hahs | University of Melbourne |
| Can urban green spaces provide microbially biodiverse health refuges for city residents? A study of soil and aerial microbiomes across the greater Hobart region | Examines the microbial diversity of urban green spaces along a rural-to-urban gradient in Hobart, Tasmania, with the aim of understanding health benefits related to microbial exposure. | Australian soils - urban | Genetic markers (bacterial 16S, archaeal 16S, eukaryotic 18S, fungal ITS) | Penelope Jones | University of Tasmania |
| East coast of Australia - Mapping estuarine health from the sediment microbiome | Investigates microbial biodiversity in estuarine sediments along Australia's east coast, aiming to identify microbial indicators of estuarine health and environmental drivers. | Estuarine water and sediment samples | Genetic markers (bacterial 16S, archaeal 16S, eukaryotic 18S) | Katie Dafforn | MQ, UNSW, CSIRO |
| Indicators of water quality health in coastal lakes | Analyzes microbial diversity in coastal lakes to assess water quality, especially in response to urban pollution and environmental stressors, in collaboration with local councils and DPIE. | Coastal seawater samples | Genetic markers (bacterial 16S, archaeal 16S, eukaryotic 18S), Whole genome sequencing (Illumina) | Megan Huggett | University of Newcastle, UTS, MQ, DPIE |
| Derwent Estuary Program | Establishes a high-resolution microbial observatory in the Derwent Estuary, coupling genomics data with environmental models to monitor pollution impacts and ecosystem health. | Estuarine water samples | Genetic markers (bacterial 16S, archaeal 16S, eukaryotic 18S) | Jodie Van de Kamp | CSIRO |
| Post-mining restoration of soil microbiota | Studies soil microbial community restoration in post-mining landscapes, assessing if restored sites approach native conditions and informing ecological restoration practices. | Australian post-mining soils in restoration | Genetic markers (bacterial 16S, archaeal 16S, eukaryotic 18S, fungal ITS) | Siegy Krauss | DBCA, University of Reading (UK), Flinders University, South32, Iluka, Tronox |
| Some like it acidic: leveraging the unique acidic saline lakes of Western Australia to interrogate the origins of haloacidophily | Investigates microbial communities in the unique acidic, saline lakes of Western Australia to understand extremophile adaptations, with potential bioleaching applications. | Acidic saline lake water and sediment samples | Genetic markers (bacterial 16S, archaeal 16S, eukaryotic 18S, fungal ITS), Whole genome sequencing (Illumina) | Elizabeth Watkin | Curtin University, UWA |
| Pacific Ocean P15S – GO-Ships Line: A decadally repeated 7,000km transect from 66 °S to 0 ° along ~-170 Longitude | Samples microbial communities across a 7,000km Pacific transect, contributing to a global marine metagenomics database and monitoring environmental changes over time. | Marine seawater samples (Pacific Ocean research voyage) | Whole genome sequencing (Illumina) | Mark Brown | University of Newcastle, UTS, CSIRO, Dalhousie University (US) |
| Effect of fuel age and prescribed burns on soil microbial community | Examines the impact of fire intervals on soil microbiomes in Banksia Woodlands, providing data on microbial succession post-fire and implications for ecosystem stability. | Australian soils - Banksia woodlands | Genetic markers (bacterial 16S, archaeal 16S, eukaryotic 18S, fungal ITS) | Aaron Brace | Edith Cowan University |
| Evaluating green technologies for wide production of a sustainable eco-friendly biofertiliser | Tests sustainable fertiliser technologies for their impact on soil health, crop growth, and environmental parameters in sugarcane, macadamia, and avocado plantations. | Australian soils - sugarcane, macadamia, and avocado plantations | Genetic markers (bacterial 16S, archaeal 16S, eukaryotic 18S, fungal ITS), Whole genome sequencing (Illumina) | Chaniarat Paungfoo | University of Queensland, SOSBio |
| Antarctic spatio-temporal - response of Antarctic soil microbiomes to environmental change | Compares Antarctic soil microbiomes sampled in 2005 and 2019 to understand climate-related shifts in microbial communities, with a focus on novel carbon fixation pathways. | Australian soils - Antarctica | Genetic markers (bacterial 16S, archaeal 16S, eukaryotic 18S, fungal ITS) | Belinda Ferrari | UNSW, Australian Antarctic Division |
| Threatened ecological communities, soil indicators of ecosystem health | Studies microbial diversity in soils of threatened ecological communities, linking soil biodiversity to ecosystem health and conservation efforts. | Australian soils | Genetic markers (bacterial 16S, archaeal 16S, eukaryotic 18S, fungal ITS), Whole genome sequencing (Illumina) | Jeff Powell | Western Sydney University |
| Plant-microbial traits | Examines how microbial and plant traits vary across climate and soil gradients to inform ecosystem management, conservation, and restoration efforts. | Australian soils | Genetic markers (bacterial 16S, archaeal 16S, eukaryotic 18S, fungal ITS), Whole genome sequencing (Illumina) | Jeff Powell | Western Sydney University, Macquarie University |
| Sydney Harbour – water quality | Investigates water quality in Sydney Harbour, using DNA sequencing to monitor microbial indicators and support management of recreational waters. | Estuarine water samples - Sydney Harbour | Genetic markers (bacterial 16S, archaeal 16S, eukaryotic 18S) | Justin Seymour | UTS, DPEIE, BeachWatch and SIMS |
| Victorian soil atlas | Develops a state-wide inventory of soil microbiota in Victoria to inform soil management and conservation policies, based on standardized microbiome sampling methods. | Australian soils - Victoria | Genetic markers (bacterial 16S, archaeal 16S, eukaryotic 18S, fungal ITS) | Matt Bruce | Victorian Department of Environment, Land, Water and Planning (DELWP), Royal Botanic Gardens – Victoria |
| Pilot Oyster farms - Wallis lake, NSW | Collaborates with oyster farmers to understand how environmental factors impact oyster growth, health, and flavour, aiming to optimise farm management practices. | Coatal seawater samples - oyster farms | Genetic markers (bacterial 16S, archaeal 16S, eukaryotic 18S) | Penny Ajani | UTS, NSWFA, NSW DPI, NSW Farmers, WAAA, Food Agility CRC |
| Australian MAG database | Studies fungal diversity in areas affected by the 2020 East Gippsland fires, particularly examining species that support ecosystems dependent on fungal biodiversity. | Seawater samples - coastal, marine | Genetic markers (bacterial 16S, archaeal 16S, eukaryotic 18S, fungal ITS) | Naveed Davoodian | Royal Botanic Gardens – Victoria |
| Talaroo Hot Spring Ecosystem | Analyzes microbial diversity across thermal gradients in Talaroo Hot Springs, a unique ecological site managed by the Ewamian people, with potential for sustainable management applications. | Talaroo hot spring | Genetic markers (bacterial 16S, archaeal 16S, eukaryotic 18S), Whole genome sequencing (Illumina) | Chris Rinke | University of Queensland |
| Long term monitoring of the Towra point coastal site | Monitors microbial community changes at a coastal research site near oyster farms, linking microbial data with ecosystem health and oyster production. | Coasta seawater samples - Towra point | Genetic markers (bacterial 16S, archaeal 16S, eukaryotic 18S) | Penelope Ajani | UTS |
| Soil and root microbiomes of crop probiotic treated field grown sugar cane | Investigates effects of microbial probiotics on soil and root microbiomes in sugarcane, assessing whether probiotics enhance plant health and soil quality in agricultural systems. | Australian soils - sugarcane plantations | Genetic markers (bacterial 16S, archaeal 16S, eukaryotic 18S, fungal ITS) | S. Berg | University of Queensland |
| Biocontrol microbes for cucurbits crop disease | Identifies potential biocontrol microbes for cucurbit crop diseases like Gummy Stem Blight, aiming to enhance sustainable crop disease management. | Australian soils - cucurbits plantations | Genetic markers (bacterial 16S, archaeal 16S, eukaryotic 18S, fungal ITS) | Susanne Schmidt | University of Queensland |
| Metagenomic profiling of biocrusts in northern grazing lands | This project with MLA investigates biocrusts’ role in enhancing soil health and nitrogen regeneration in northern Australian pastures. By studying biocrust functions across fire intervals, grazing breaks, and cattle densities, the project aims to inform sustainable land management strategies. | Australian soils - grazing land biocrust | Genetic markers (bacterial 16S, archaeal 16S, eukaryotic 18S, fungal ITS), Whole genome sequencing (Illumina) | Susanne Schmidt | UQ, MLA, NT Gov, QLD DAF, U Seville IRNAS-CSIC – Spain |
PARTNERS
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advisory committee members
KEY INFORMATION
ACKNOWLEDGEMENT INFORMATION
Bioplatforms Initiative DOI: https://doi.org/10.25953/v12e-zq81
Umbrella Bioproject ID: PRJNA597010
Please use this ID when submitting any derived data to a database that is a member of the International Nucleotide Sequence Database Collaboration (INSDC), such as GenBank/NCBI, ENA or DDBJ.
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Citation Guidelines
To cite the general initiative:
Australian Microbiome Initiative, 2020, https://doi.org/10.25953/v12e-zq81
To cite a specific dataset:
Australian Microbiome Initiative, 2020, https://doi.org/10.25953/v12e-zq81, [year-of-data-download], [full dataset title], [dataset-access-URL], accessed [date-of-access].
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Acknowledgement Statement
We would like to acknowledge the contribution of the Australian Microbiome Initiative Consortium in the generation of data used in this publication. The Initiative is supported by funding from Bioplatforms Australia, enabled by the Commonwealth Government National Collaborative Research Infrastructure Strategy (NCRIS).
If relevant, also credit other organisations involved in the collection of the particular dataset you are using, as listed in the ‘project_lead’ and ‘project_collaborators’ in the metadata record.
CONTACT US
Project Manager
Sophie Mazard – Bioplatforms Australia
smazard@bioplatforms.com
Science Lead
Andrew Bissett – CSIRO
andrew.bissett@csiro.au
General Manager – Science Programs
Sarah Richmond – Bioplatforms Australia
srichmond@bioplatforms.com
DATA AND COLLABORATION POLICY
Data generated through this initiative is subject to the Data policy and Communications policy.