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

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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.

Related collections

Most cited references 31

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Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample.

J. Gregory Caporaso, Christian L. Lauber, William A. Walters … (2011)

The ongoing revolution in high-throughput sequencing continues to democratize the ability of small groups of investigators to map the microbial component of the biosphere. In particular, the coevolution of new sequencing platforms and new software tools allows data acquisition and analysis on an unprecedented scale. Here we report the next stage in this coevolutionary arms race, using the Illumina GAIIx platform to sequence a diverse array of 25 environmental samples and three known "mock communities" at a depth averaging 3.1 million reads per sample. We demonstrate excellent consistency in taxonomic recovery and recapture diversity patterns that were previously reported on the basis of metaanalysis of many studies from the literature (notably, the saline/nonsaline split in environmental samples and the split between host-associated and free-living communities). We also demonstrate that 2,000 Illumina single-end reads are sufficient to recapture the same relationships among samples that we observe with the full dataset. The results thus open up the possibility of conducting large-scale studies analyzing thousands of samples simultaneously to survey microbial communities at an unprecedented spatial and temporal resolution.

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Community structure and metabolism through reconstruction of microbial genomes from the environment.

Gene W. Tyson, Jarrod Chapman, Philip Hugenholtz … (2004)

Microbial communities are vital in the functioning of all ecosystems; however, most microorganisms are uncultivated, and their roles in natural systems are unclear. Here, using random shotgun sequencing of DNA from a natural acidophilic biofilm, we report reconstruction of near-complete genomes of Leptospirillum group II and Ferroplasma type II, and partial recovery of three other genomes. This was possible because the biofilm was dominated by a small number of species populations and the frequency of genomic rearrangements and gene insertions or deletions was relatively low. Because each sequence read came from a different individual, we could determine that single-nucleotide polymorphisms are the predominant form of heterogeneity at the strain level. The Leptospirillum group II genome had remarkably few nucleotide polymorphisms, despite the existence of low-abundance variants. The Ferroplasma type II genome seems to be a composite from three ancestral strains that have undergone homologous recombination to form a large population of mosaic genomes. Analysis of the gene complement for each organism revealed the pathways for carbon and nitrogen fixation and energy generation, and provided insights into survival strategies in an extreme environment.

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Archaea in coastal marine environments.

E Delong (1992)

Archaea (archaebacteria) are a phenotypically diverse group of microorganisms that share a common evolutionary history. There are four general phenotypic groups of archaea: the methanogens, the extreme halophiles, the sulfate-reducing archaea, and the extreme thermophiles. In the marine environment, archaeal habitats are generally limited to shallow or deep-sea anaerobic sediments (free-living and endosymbiotic methanogens), hot springs or deep-sea hydrothermal vents (methanogens, sulfate reducers, and extreme thermophiles), and highly saline land-locked seas (halophiles). This report provides evidence for the widespread occurrence of unusual archaea in oxygenated coastal surface waters of North America. Quantitative estimates indicated that up to 2% of the total ribosomal RNA extracted from coastal bacterioplankton assemblages was archaeal. Archaeal small-subunit ribosomal RNA-encoding DNAs (rDNAs) were cloned from mixed bacterioplankton populations collected at geographically distant sampling sites. Phylogenetic and nucleotide signature analyses of these cloned rDNAs revealed the presence of two lineages of archaea, each sharing the diagnostic signatures and structural features previously established for the domain Archaea. Both of these lineages were found in bacterioplankton populations collected off the east and west coasts of North America. The abundance and distribution of these archaea in oxic coastal surface waters suggests that these microorganisms represent undescribed physiological types of archaea, which reside and compete with aerobic, mesophilic eubacteria in marine coastal environments.

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Author and article information

Contributors

Andrew Bissett: Andrew.bissett@csiro.au

Journal

Journal ID (nlm-ta): Gigascience

Journal ID (iso-abbrev): Gigascience

Title: GigaScience

Publisher: BioMed Central (London )

ISSN (Electronic): 2047-217X

Publication date (Electronic): 18 May 2016

Publication date PMC-release: 18 May 2016

Publication date Collection: 2016

Volume: 5

Electronic Location Identifier: 21

Affiliations

[ ]CSIRO, Oceans and Atmosphere, Hobart, Tasmania Australia

[ ]Bioplatforms Australia, Sydney, New South Wales Australia

[ ]Centre for Comparative Genomics, Murdoch University, Perth, Western Australia Australia

[ ]Victorian Department of Economic Development, Jobs, Transport and Resources and La Trobe University, Agribio Centre, Bundoora, Victoria 3083 Australia

[ ]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

[ ]School of Agriculture and Food Science, The University of Queensland, St Lucia, Queensland 4072 Australia

[ ]Parks Australia, Department of the Environment, Canberra, ACT 2601 Australia

[ ]School of Biotechnology and Biomolecular Sciences, UNSW Australia, Sydney, New South Wales 2052 Australia

[ ]School of Earth, Atmosphere and Environment, Monash University, Clayton, Victoria 3800 Australia

[ ]Science and Conservation Division, Department of Parks and Wildlife, Perth, Western Australia Australia

[ ]DEDJTR Rutherglen, Melbourne, Victoria Australia

[ ]Ramaciotti Centre for Genomics, University of New South Wales, Sydney, New South Wales Australia

[ ]School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052 Australia

[ ]CSIRO Agriculture, Adelaide, South Australia 5064 Australia

[ ]CSIRO, National Research Collections Australia, Canberra, Australian Capital Territory Australia

[ ]Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales Australia

[ ]Australian Genome Research Facility Ltd, Walter and Eliza Hall Institute, Parkville, Victoria Australia

[ ]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

[ ]Australian SuperSite Network, James Cook University, Townsville, Queensland Australia

[ ]University of Tasmania, Hobart, Tasmania Australia

[ ]Australian Genome Research Facility Ltd, Adelaide, South Australia Australia

[ ]Atlas of Living Australia, CSIRO, Canberra, Australian Capital Territory Australia

[ ]CSIRO Land and Water, Canberra, ACT Australia

[ ]Agriculture and Agri-food Canada, Science and Technology branch, 2585 County Road 20, Harrow, ON N0R 1G0 Canada

[ ]Department of Agriculture and Fisheries, Brisbane, Queensland Australia

[ ]Australian Antarctic Division, Department of Sustainability, Environment, Water, Population and Communities, 203 Channel Highway, Kingston, Tasmania 7050 Australia

[ ]University of Queensland, Earth Sciences, St Lucia, Brisbane, Queensland 4072 Australia

Article

Publisher ID: 126

DOI: 10.1186/s13742-016-0126-5

PMC ID: 4870752

PubMed ID: 27195106

SO-VID: 692e414c-6652-43b4-b484-047094bc1b1f

License:

Open AccessThis 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.

History

Date received : 15 October 2015

Date accepted : 2 May 2016

Custom metadata

Keywords: microbiology,microbial ecology,soil biology,australia,database,microbial diversity,metagenomics

Data availability:

Keywords: microbiology, microbial ecology, soil biology, australia, database, microbial diversity, metagenomics

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

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Abstract

Background

Findings

Conclusions

Related collections

Martian Soil

Most cited references 31

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample.

Community structure and metabolism through reconstruction of microbial genomes from the environment.

Archaea in coastal marine environments.

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