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

Bissett, Andrew, Fitzgerald, Anna, Meintjes, Thys, Mele, Pauline M., Reith, Frank, Dennis, Paul G., Breed, Martin F., Brown, Belinda, Brown, Mark V., Brugger, Joel, Byrne, Margaret, Caddy-Retalic, Stefan, Carmody, Bernie, Coates, David J., Correa, Carolina, Ferrari, Belinda C., Gupta, Vadakattu V.S.R., Hamonts, Kelly, Haslem, Asha, Hugenholtz, Philip, Karan, Mirko, Koval, Jason, Lowe, Andrew J., McDonald, Stuart, McGrath, Leanne, Martin, David, Morgan, Matt, North, Kristin I., Paungfoo-Lonhienne, Chanyarat, Pendall, Elise, Phillips, Lori, Pirzl, Rebecca, Powell, Jeff R., Ragan, Mark A., Schmidt, Susanne, Seymour, Nicole, Snape, Ian, Stephen, John R., Stevens, Matthew, Tinning, Matt, Williams, Kristen, Yeoh, Yun Kit, Zammit, Carla M., and Young, Andrew (2016) Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database. GigaScience, 5 (1). pp. 1-11.

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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.

Item ID: 45519
Item Type: Article (Research - C1)
ISSN: 2047-217X
Keywords: microbiology, microbial ecology, soil biology, Australia, database, microbial diversity, metagenomics
Additional Information:

This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

Funders: Australian Government National Collaborative Research Infrastructure Strategy (NCRIS) and Education Investment Fund (EIF) Super Science Initiative, Cotton Research and Development Corporation, CSIRO, Department of the Environment, Department of Parks and Wildlife, WA, Grains RDC (Soil Biology Initiative-II), South Australian Grains Industry Trust, Science Industry Endowment Fund
Research Data: http://dx.doi.org/10.4227/71/ 561c9bc670099
Date Deposited: 22 Jun 2016 07:36
FoR Codes: 06 BIOLOGICAL SCIENCES > 0605 Microbiology > 060504 Microbial Ecology @ 100%
SEO Codes: 97 EXPANDING KNOWLEDGE > 970106 Expanding Knowledge in the Biological Sciences @ 100%
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