Dataset Information

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

ABSTRACT: 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.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'.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.

SUBMITTER: Bissett A

PROVIDER: S-EPMC4870752 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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

Bissett Andrew A Fitzgerald Anna A Court Leon Meintjes Thys T Mele Pauline M PM Reith Frank F Dennis Paul G PG Breed Martin F MF Brown Belinda B Brown Mark V MV Brugger Joel J Byrne Margaret M Caddy-Retalic Stefan S Carmody Bernie B Coates David J DJ Correa Carolina C Ferrari Belinda C BC Gupta Vadakattu V S R VV Hamonts Kelly K Haslem Asha A Hugenholtz Philip P Karan Mirko M Koval Jason J Lowe Andrew J AJ Macdonald Stuart S McGrath Leanne L Martin David D Morgan Matt M North Kristin I KI Paungfoo-Lonhienne Chanyarat C Pendall Elise E Phillips Lori L Pirzl Rebecca R Pirzl Rebecca R Powell Jeff R JR Ragan Mark A MA Schmidt Susanne S Seymour Nicole N Snape Ian I Stephen John R JR Stevens Matthew M Tinning Matt M Williams Kristen K Yeoh Yun Kit YK Zammit Carla M CM Young Andrew A

GigaScience 20160518

<h4>Background</h4>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 integ ...[more]

PMID: 27195106

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Project description:Soil microbial communities play a critical role in nutrient transformation and storage in all ecosystems. Quantifying the seasonal and long-term temporal extent of genetic and functional variation of soil microorganisms in response to biotic and abiotic changes within and across ecosystems will inform our understanding of the effect of climate change on these processes. We examined spatial and seasonal variation in microbial communities based on 16S rRNA gene sequencing and phospholipid fatty acid (PLFA) composition across four biomes: a tropical broadleaf forest (Hawaii), taiga (Alaska), semiarid grassland-shrubland (Utah), and a subtropical coniferous forest (Florida). In this study, we used a team-based instructional approach leveraging the iPlant Collaborative to examine publicly available National Ecological Observatory Network (NEON) 16S gene and PLFA measurements that quantify microbial diversity, composition, and growth. Both profiling techniques revealed that microbial communities grouped strongly by ecosystem and were predominately influenced by three edaphic factors: pH, soil water content, and cation exchange capacity. Temporal variability of microbial communities differed by profiling technique; 16S-based community measurements showed significant temporal variability only in the subtropical coniferous forest communities, specifically through changes within subgroups of Acidobacteria. Conversely, PLFA-based community measurements showed seasonal shifts in taiga and tropical broadleaf forest systems. These differences may be due to the premise that 16S-based measurements are predominantly influenced by large shifts in the abiotic soil environment, while PLFA-based analyses reflect the metabolically active fraction of the microbial community, which is more sensitive to local disturbances and biotic interactions. To address the technical issue of the response of soil microbial communities to sample storage temperature, we compared 16S-based community structure in soils stored at -80°C and -20°C and found no significant differences in community composition based on storage temperature. Free, open access datasets and data sharing platforms are powerful tools for integrating research and teaching in undergraduate and graduate student classrooms. They are a valuable resource for fostering interdisciplinary collaborations, testing ecological theory, model development and validation, and generating novel hypotheses. Training in data analysis and interpretation of large datasets in university classrooms through project-based learning improves the learning experience for students and enables their use of these significant resources throughout their careers.

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Dataset Information

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

Publications

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

Similar Datasets

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