. 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

Andrew Bissett¹, Anna Fitzgerald², Leon Court, Thys Meintjes³, Pauline M Mele⁴, Frank Reith⁵, Paul G Dennis⁶, Martin F Breed⁷, Belinda Brown⁸, Mark V Brown⁹, Joel Brugger¹⁰, Margaret Byrne¹¹, Stefan Caddy-Retalic⁷, Bernie Carmody¹², David J Coates¹¹, Carolina Correa¹³, Belinda C Ferrari¹⁴, Vadakattu V S R Gupta¹⁵, Kelly Hamonts¹⁶, Asha Haslem¹⁷, Philip Hugenholtz¹⁸, Mirko Karan¹⁹, Jason Koval¹³, Andrew J Lowe⁷, Stuart Macdonald²⁰, Leanne McGrath²¹, David Martin²², Matt Morgan²³, Kristin I North¹³, Chanyarat Paungfoo-Lonhienne⁶, Elise Pendall²⁴, Lori Phillips²⁵, Rebecca Pirzl²², Jeff R Powell²⁴, Mark A Ragan²⁶, Susanne Schmidt⁶, Nicole Seymour²⁷, Ian Snape²⁸, John R Stephen²¹, Matthew Stevens¹⁷, Matt Tinning¹⁷, Kristen Williams²³, Yun Kit Yeoh¹⁸, Carla M Zammit²⁹, Andrew Young³⁰

Affiliations

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.

PMID: 27195106
PMCID: PMC4870752
DOI: 10.1186/s13742-016-0126-5

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

Andrew Bissett et al. Gigascience. 2016.

. 2016 May 18:5:21.

doi: 10.1186/s13742-016-0126-5. eCollection 2016.

Authors

Affiliations

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.

PMID: 27195106
PMCID: PMC4870752
DOI: 10.1186/s13742-016-0126-5

Erratum in

Erratum to: Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database.
Bissett A, Fitzgerald A, Court L, Meintjes T, Mele PM, Reith F, Dennis PG, Breed MF, Brown B, Brown MV, Brugger J, Byrne M, Caddy-Retalic S, Carmody B, Coates DJ, Correa C, Ferrari BC, Gupta VVSR, Hamonts K, Haslem A, Hugenholtz P, Karan M, Koval J, Lowe AJ, Macdonald S, McGrath L, Martin D, Morgan M, North KI, Paungfoo-Lonhienne C, Pendall E, Phillips L, Pirzl R, Powell JR, Ragan MA, Schmidt S, Seymour N, Snape I, Stephen JR, Stevens M, Tinning M, Williams K, Yeoh YK, Zammit CM, Young A. Bissett A, et al. Gigascience. 2017 May 1;6(5):1. doi: 10.1093/gigascience/gix021. Gigascience. 2017. PMID: 30137319 Free PMC article. No abstract available.

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.

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Figures

**Fig. 1**
Position of BASE sample sites (August 2015). a Australian mainland and Christmas Island samples; b location of Antarctic sampling locations (white), with Davis station indicated in red; and c finer detail of sampling position indicated by red arrow in (a)

**Fig. 2**
Sampling strategy. Approximately 1 kg of soil was taken, at two soil depths, by bulking 9 – 30 soil cores a 25 × 25 m quadrat. Each sample was assigned a unique identifier and subdivided for DNA extraction and sequencing, soil physico-chemical analyses and soil and DNA sample archiving for future use. A photograph of each site was also taken

**Fig. 3**
Microbial diversity under different land-use categories sampled in BASE. a Bacterial phyla comprising > 1 % of total bacterial 16S rRNA gene amplicons; b archaeal families comprising > 1 % of total archaeal 16S rRNA gene amplicons; c fungal phyla comprising > 1 % of total fungal ITS1 region amplicons; and d eukaryotic phyla comprising > 1 % of 18S rRNA gene amplicons. All abundances are expressed in % of the total read number for each group, and land-use categories refer to land-use categories as described in the Australian land use and management classification (http://www.agriculture.gov.au/abares/aclump/land-use/alum-classification-version-7-may-2010)

See this image and copyright information in PMC

References

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

Affiliations

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

Authors

Affiliations

Erratum in

Abstract

Figures

References

Publication types

MeSH terms

LinkOut - more resources

Full Text Sources

Other Literature Sources

Research Materials