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

被引：181

作者：

Bissett, Andrew ^{[1
]}

Fitzgerald, Anna ^{[2
]}

Meintjes, Thys ^{[3
]}

Mele, Pauline M. ^{[4
,5
]}

Reith, Frank ^{[6
,7
,8
]}

Dennis, Paul G. ^{[9
]}

Breed, Martin F. ^{[7
,8
]}

Brown, Belinda ^{[10
]}

Brown, Mark V. ^{[11
]}

Brugger, Joel ^{[12
]}

Byrne, Margaret ^{[13
]}

Caddy-Retalic, Stefan ^{[7
,8
]}

Carmody, Bernie ^{[14
]}

Coates, David J. ^{[13
]}

Correa, Carolina ^{[15
]}

Ferrari, Belinda C. ^{[16
]}

Gupta, Vadakattu V. S. R. ^{[17
]}

Hamonts, Kelly ^{[18
,19
]}

Haslem, Asha ^{[20
]}

Hugenholtz, Philip ^{[21
,22
]}

Karan, Mirko ^{[23
]}

Koval, Jason ^{[15
]}

Lowe, Andrew J. ^{[7
,8
]}

Macdonald, Stuart ^{[24
]}

McGrath, Leanne ^{[25
]}

Martin, David ^{[26
]}

Morgan, Matt ^{[27
]}

North, Kristin I. ^{[15
]}

Paungfoo-Lonhienne, Chanyarat ^{[9
]}

Pendall, Elise ^{[19
]}

Phillips, Lori ^{[14
,28
]}

Pirzl, Rebecca ^{[26
]}

Powell, Jeff R. ^{[19
]}

Ragan, Mark A. ^{[22
]}

Schmidt, Susanne ^{[9
]}

Seymour, Nicole ^{[29
]}

Snape, Ian ^{[30
]}

Stephen, John R. ^{[25
]}

Stevens, Matthew ^{[20
]}

Tinning, Matt ^{[20
]}

Williams, Kristen ^{[27
]}

Yeoh, Yun Kit ^{[21
,22
]}

Zammit, Carla M. ^{[31
]}

Young, Andrew ^{[18
]}

机构：

[1] CSIRO, Oceans & Atmosphere, Hobart, Tas, Australia

[2] Bioplatforms Australia, Sydney, NSW, Australia

[3] Murdoch Univ, Ctr Comparat Genom, Perth, WA, Australia

[4] Victorian Dept Econ Dev Jobs Transport & Resource, Bundoora, Vic 3083, Australia

[5] La Trobe Univ, Agribio Ctr, Bundoora, Vic 3083, Australia

[6] CSIRO Land & Water, Adelaide, SA, Australia

[7] Univ Adelaide, Sch Biol Sci, North Terrace, Adelaide, SA 5005, Australia

[8] Univ Adelaide, Inst Environm, North Terrace, Adelaide, SA 5005, Australia

[9] Univ Queensland, Sch Agr & Food Sci, St Lucia, Qld 4072, Australia

[10] Parks Australia, Dept Environm, Canberra, ACT 2601, Australia

[11] UNSW Australia, Sch Biotechnol & Biomol Sci, Sydney, NSW 2052, Australia

[12] Monash Univ, Sch Earth Atmosphere & Environm, Clayton, Vic 3800, Australia

[13] Dept Parks & Wildlife, Sci & Conservat Div, Perth, WA, Australia

[14] DEDJTR Rutherglen, Melbourne, Vic, Australia

[15] Univ New S Wales, Ramaciotti Ctr Genom, Sydney, NSW, Australia

[16] Univ New S Wales, Sch Biotechnol & Biomol Sci, Sydney, NSW 2052, Australia

[17] CSIRO Agr, Adelaide, SA 5064, Australia

[18] CSIRO, Natl Res Collect Australia, Canberra, ACT, Australia

[19] Univ Western Sydney, Hawkesbury Inst Environm, Penrith, NSW 1797, Australia

[20] Australian Genome Res Facil Ltd, Walter & Eliza Hall Inst, Parkville, Vic, Australia

[21] Univ Queensland, Sch Chem & Mol Biosci, Australian Ctr Ecogen, St Lucia, Qld 4072, Australia

[22] Univ Queensland, Inst Mol Biosci, St Lucia, Qld 4072, Australia

[23] James Cook Univ, Australian SuperSite Network, Townsville, Qld 4811, Australia

[24] Univ Tasmania, Hobart, Tas, Australia

[25] Australian Genome Res Facil Ltd, Adelaide, SA, Australia

[26] CSIRO, Atlas Living Australia, Canberra, ACT, Australia

[27] CSIRO Land & Water, Canberra, ACT, Australia

[28] Agr & Agri Food Canada, Sci & Technol Branch, 2585 Cty Rd 20, Harrow, ON N0R 1G0, Canada

[29] Dept Agr & Fisheries, Brisbane, Qld, Australia

[30] Australian Antarctic Div, Dept Sustainabil Environm Water Populat & Communi, 203 Channel Highway, Kingston, Tas 7050, Australia

[31] Univ Queensland, Earth Sci, Brisbane, Qld 4072, Australia

来源：

GIGASCIENCE | 2016年 / 5卷

关键词：

Microbiology; Microbial ecology; Soil biology; Australia; Database; Microbial diversity; Metagenomics; RIBOSOMAL-RNA SEQUENCES; BIODIVERSITY; PATTERNS; PRIMERS;

D O I：

10.1186/s13742-016-0126-5

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页数：11

共 52 条

[1] Foundations for the future: A long-term plan for Australian ecosystem science [J].