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Gigascience. 2016 May 18;5:21. doi: 10.1186/s13742-016-0126-5. eCollection 2016.

Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database.

Author information

1
CSIRO, Oceans and Atmosphere, Hobart, Tasmania Australia.
2
Bioplatforms Australia, Sydney, New South Wales Australia.
3
Centre for Comparative Genomics, Murdoch University, Perth, Western Australia Australia.
4
Victorian Department of Economic Development, Jobs, Transport and Resources and La Trobe University, Agribio Centre, Bundoora, Victoria 3083 Australia.
5
CSIRO Land and Water, Adelaide, South Australia Australia ; School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace Adelaide, South Australia 5005 Australia.
6
School of Agriculture and Food Science, The University of Queensland, St Lucia, Queensland 4072 Australia.
7
School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace Adelaide, South Australia 5005 Australia.
8
Parks Australia, Department of the Environment, Canberra, ACT 2601 Australia.
9
School of Biotechnology and Biomolecular Sciences, UNSW Australia, Sydney, New South Wales 2052 Australia.
10
School of Earth, Atmosphere and Environment, Monash University, Clayton, Victoria 3800 Australia.
11
Science and Conservation Division, Department of Parks and Wildlife, Perth, Western Australia Australia.
12
DEDJTR Rutherglen, Melbourne, Victoria Australia.
13
Ramaciotti Centre for Genomics, University of New South Wales, Sydney, New South Wales Australia.
14
School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052 Australia.
15
CSIRO Agriculture, Adelaide, South Australia 5064 Australia.
16
CSIRO, National Research Collections Australia, Canberra, Australian Capital Territory Australia ; Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales Australia.
17
Australian Genome Research Facility Ltd, Walter and Eliza Hall Institute, Parkville, Victoria Australia.
18
Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland 4072 Australia ; Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072 Australia.
19
Australian SuperSite Network, James Cook University, Townsville, Queensland Australia.
20
University of Tasmania, Hobart, Tasmania Australia.
21
Australian Genome Research Facility Ltd, Adelaide, South Australia Australia.
22
Atlas of Living Australia, CSIRO, Canberra, Australian Capital Territory Australia.
23
CSIRO Land and Water, Canberra, ACT Australia.
24
Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales Australia.
25
DEDJTR Rutherglen, Melbourne, Victoria Australia ; Agriculture and Agri-food Canada, Science and Technology branch, 2585 County Road 20, Harrow, ON N0R 1G0 Canada.
26
Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072 Australia.
27
Department of Agriculture and Fisheries, Brisbane, Queensland Australia.
28
Australian Antarctic Division, Department of Sustainability, Environment, Water, Population and Communities, 203 Channel Highway, Kingston, Tasmania 7050 Australia.
29
University of Queensland, Earth Sciences, St Lucia, Brisbane, Queensland 4072 Australia.
30
CSIRO, National Research Collections Australia, Canberra, Australian Capital Territory Australia.

Abstract

BACKGROUND:

Microbial inhabitants of soils are important to ecosystem and planetary functions, yet there are large gaps in our knowledge of their diversity and ecology. The 'Biomes of Australian Soil Environments' (BASE) project has generated a database of microbial diversity with associated metadata across extensive environmental gradients at continental scale. As the characterisation of microbes rapidly expands, the BASE database provides an evolving platform for interrogating and integrating microbial diversity and function.

FINDINGS:

BASE currently provides amplicon sequences and associated contextual data for over 900 sites encompassing all Australian states and territories, a wide variety of bioregions, vegetation and land-use types. Amplicons target bacteria, archaea and general and fungal-specific eukaryotes. The growing database will soon include metagenomics data. Data are provided in both raw sequence (FASTQ) and analysed OTU table formats and are accessed via the project's data portal, which provides a user-friendly search tool to quickly identify samples of interest. Processed data can be visually interrogated and intersected with other Australian diversity and environmental data using tools developed by the 'Atlas of Living Australia'.

CONCLUSIONS:

Developed within an open data framework, the BASE project is the first Australian soil microbial diversity database. The database will grow and link to other global efforts to explore microbial, plant, animal, and marine biodiversity. Its design and open access nature ensures that BASE will evolve as a valuable tool for documenting an often overlooked component of biodiversity and the many microbe-driven processes that are essential to sustain soil function and ecosystem services.

KEYWORDS:

Australia; Database; Metagenomics; Microbial diversity; Microbial ecology; Microbiology; Soil biology

PMID:
27195106
PMCID:
PMC4870752
DOI:
10.1186/s13742-016-0126-5
[Indexed for MEDLINE]
Free PMC Article

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