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BASE – Biomes of Australian Soil Environments
Andrew Bissett, Andrew Young, Kelly Hamonts & Kristen Williams
Presentation Outline
 Introduction to BASE

 Methodology
 Progress to date
–
–
–
–

Environmental sampling
Amplicon se...
INTRODUCTION TO BASE

3 | BASE: Biomes of Australian Soil Environments | Andrew Young
What is BASE?
 BASE: Biomes of Australian Soil
Environments

 Aim of BASE is to develop a National
Framework Data set of...
Why BASE?
Very little is known about the identity,
abundance or distribution of soil
microbial communities. Yet they are
e...
What will BASE do?
 Measure and map microbial community diversity and
composition, edaphic and other site specific variab...
What will BASE do?
 Test biogeographical and evolutionary hypotheses
regarding microbial ecology and plant-microbe coevol...
Who is involved in BASE?
 BioPlatforms Australia
 CSIRO
 VicDPI
 DOTE and DECWA
•

Atlas of Living Australia

•

Austr...
METHODOLOGY

9 | BASE: Biomes of Australian Soil Environments | Andrew Young
Environmental sampling
 600+ sampling points in intact natural biomes
across the continent
⁻ Stratified by soil type, veg...
Amplicon sequencing
 Amplicon sequencing (Illumina)
-

Bacteria –16S
Fungi –ITS
Archaea – 16S
Euk – 18S

 Bioinformatics...
Metagenome sequencing
 Use amplicon sequencing data to:
 Identify “interesting” samples for metagenomic
sequencing
 Ind...
Sampling – data –sampling workflow
 Quantify diversity and abundance of microbial
communities
 Model abundance and compo...
PROGRESS TO DATE

14 | BASE: Biomes of Australian Soil Environments | Andrew Young
Soil chemistry and vegetation data
 Edaphic variables
– all samples have data for: Soil moisture, Texture, Ammonium, Nitr...
Amplicon sequencing
 Sequenced 100 samples using 454 pyrosequencing with
bacterial and fungal tags
 Data available onlin...
Metagenome sequencing
 HiSeq data generated for 6 sites (12 samples)
 Test whether amplicon data can inform suitability ...
BASE database
 Developed an offline (access) relational database that allows
searching of sequence and contextual data
 ...
SOME RESULTS

19 | BASE: Biomes of Australian Soil Environments | Andrew Young
Model – using site contextual data
Exploratory models compared OTU presence/absence and abundance
using soil chemistry dat...
Xmas Island

Minerology sites
NRS
TERN supersites
Trend transect

Antarctica

22 | Presentation title | Presenter name
Bacteria

•

Fungi

Edaphic and spatial components were significant in explaining community structure for
both bacterial a...
24 | Presentation title | Presenter name
25 | Presentation title | Presenter name
26 | Presentation title | Presenter name
27 | Presentation title | Presenter name
NEXT STEPS…

28 | BASE: Biomes of Australian Soil Environments | Andrew Young
Extended environmental sampling
 Add Temporal component to sampling
 Long term monitoring sites
 Sites with biogeochemi...
Agricultural sampling
 Cropping, grazing, horticulture
⁻ Stratified soil type and by production
system

 Measure same pa...
Modeling
 Extend Generalised Dissimilarity modelling to include Phlogenetic
Distance metrics
 Create species distributio...
Database availability development

32 | BASE: Biomes of Australian Soil Environments | Andrew Young
The BASE Team:
CSIRO: Andrew Bissett, Leon Court, Kelly Hamonts,
Shamsul Hoque, Kristen Williams, Andrew Young
Bioplatform...
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BASE (Biomes of Australian Soil Environments) - Andrew Bissett

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BASE is a large scale collaborative effort to build a publically available, national database of soil microbial boiodiversity. The collaboration includes involvement of BioPlatforms Australia, CSIRO, Victorian Department of Primary Industry and many other parties interested in soil biodiversity. The BASE project is collecting soil biodiversity, physicochemical and climatic data from across the Australian continent and using this data to develop models of microbial distributions in relation to soil edaphic and climatic data, land-use, vegetation type etc. Biodiversity data being generated is in the form of amplicon sequences targeting Bacteria, Archaea and Eukaryotes and amplicon free metagenomic data. So far BASE has collected samples from approximately 300 sites. I will provide a description of the BASE project and its progress thus far, including sample collection, amplicon sequencing, metagenomic sequencing and database implementation.

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  • Can we make it explicit here that BASE, as funded by SIEF, is a pilot?
  • The top figure is the observed versus predicted dissimilarity ; the lower figure is scaled by the ecological distance (after the link function has been applied)
  • Transcript of "BASE (Biomes of Australian Soil Environments) - Andrew Bissett"

    1. 1. BASE – Biomes of Australian Soil Environments Andrew Bissett, Andrew Young, Kelly Hamonts & Kristen Williams
    2. 2. Presentation Outline  Introduction to BASE   Methodology  Progress to date – – – – Environmental sampling Amplicon sequencing Metagenome sequencing Modeling 2 | BASE: Biomes of Australian Soil Environments | Andrew Young  Future steps  Sampling  Sequence Analysis  Modeling  Data Management
    3. 3. INTRODUCTION TO BASE 3 | BASE: Biomes of Australian Soil Environments | Andrew Young
    4. 4. What is BASE?  BASE: Biomes of Australian Soil Environments  Aim of BASE is to develop a National Framework Data set of Australian soil microbial diversity  Combines metagenomics of environmental samples with soil“contextual” data and modelling at continental scale  TO present a publically available database of soil related diversity information 4 | BASE: Biomes of Australian Soil Environments | Andrew Young
    5. 5. Why BASE? Very little is known about the identity, abundance or distribution of soil microbial communities. Yet they are ecologically very important. They:  Mediate key ecological processes e.g. nutrient cycling, carbon cycling, water purification  Form crucial symbiotic associations with plants e.g. nitrogen fixation  Play roles in bioregulation e.g. disease suppressive soils  Etc. 5 | BASE: Biomes of Australian Soil Environments | Andrew Young Soil bacteria Soil fungi
    6. 6. What will BASE do?  Measure and map microbial community diversity and composition, edaphic and other site specific variables across Australia  Model relationships between microbial community structure and soil environment, vegetation composition and climate  Provide a publically available research database (a National Framework Dataset) for exploration of soil biological diversity and function 6 | BASE: Biomes of Australian Soil Environments | Andrew Young
    7. 7. What will BASE do?  Test biogeographical and evolutionary hypotheses regarding microbial ecology and plant-microbe coevolution  Explore relationships between Australia’s microbial diversity and that of the rest of the world  Examine effects of land management  Inform restoration and management of soil diversity and ecosystem services 7 | BASE: Biomes of Australian Soil Environments | Andrew Young
    8. 8. Who is involved in BASE?  BioPlatforms Australia  CSIRO  VicDPI  DOTE and DECWA • Atlas of Living Australia • Australian Antarctic Division • Australian National Data Service (ANDS) • Department of Agriculture, Forestry and Fisheries • Department of Sustainability Environment Water Population and Communities (SEWPAC) • Grains Research and Development Corporation • La Trobe University • Science and Industry Endowment Fund (SIEF) • South Australian Research and Development Institute (SARDI) • Tasmanian Land Conservancy • Terrestrial Ecosytem Research Network (TERN) • Monash University • University of Adelaide • University of New South Wales • University of Queensland • University of Western Australia • University of Western Sydney 8 | BASE: Biomes of Australian Soil Environments | Andrew Young
    9. 9. METHODOLOGY 9 | BASE: Biomes of Australian Soil Environments | Andrew Young
    10. 10. Environmental sampling  600+ sampling points in intact natural biomes across the continent ⁻ Stratified by soil type, vegetation composition and climate ⁻ Mainly National reserve system thus far  25mx25m quadrats ⁻ 9 soil cores split into 0-10cm and >20cm depth ⁻ Cores bulked, mixed and stored for soil chemistry and DNA analysis ⁻ Site specific data recorded (Vegetation, slope, aspect, etc.) 10 | BASE: Biomes of Australian Soil Environments | Andrew Young
    11. 11. Amplicon sequencing  Amplicon sequencing (Illumina) - Bacteria –16S Fungi –ITS Archaea – 16S Euk – 18S  Bioinformatics pipeline: - BASE database - EMP protocol of closed reference OTU picking - Specifc analysis pathways for specifc projects/questions 11 | BASE: Biomes of Australian Soil Environments | Andrew Young
    12. 12. Metagenome sequencing  Use amplicon sequencing data to:  Identify “interesting” samples for metagenomic sequencing  Indentify likely samples for differential binning matches  Similar compositions, different abundances  HiSeq  Incorporate metagenomic information into models  Metabolic diversity turnover  Functional distribution models 12 | BASE: Biomes of Australian Soil Environments | Andrew Young
    13. 13. Sampling – data –sampling workflow  Quantify diversity and abundance of microbial communities  Model abundance and composition in relation to environmental parameters measured at each site  Model against continental environmental data “surfaces”  Extrapolate to continental scale  Undertake environmental gap analysis  Add new samples and refine model 13 | BASE: Biomes of Australian Soil Environments | Andrew Young
    14. 14. PROGRESS TO DATE 14 | BASE: Biomes of Australian Soil Environments | Andrew Young
    15. 15. Soil chemistry and vegetation data  Edaphic variables – all samples have data for: Soil moisture, Texture, Ammonium, Nitrate, Nitrogen, Phosphorus, Potassium, Sulphur, Total Carbon, Organic Carbon, Conductivity, pH, Copper, Iron, Manganese, Zinc, Exc. Aluminium, Exc. Calcium, Exc. Magnesium, Exc. Potassium, Exc. Sodium, Boron, Grain Size (% gravel, sand, silt, clay), project specific data (minerology, MIR, biogeochemical rates,……..).  Non-edaphic/climate/site – all samples have data for: Overlying plant cover (% and identity), slope, aspect, location, elevation, land-use history, land-management history.  Data for first 400 samples are available online (BPA website), ALA 15 | BASE: Biomes of Australian Soil Environments | Andrew Young
    16. 16. Amplicon sequencing  Sequenced 100 samples using 454 pyrosequencing with bacterial and fungal tags  Data available online via BPA (although not in such a useful format)  Illumina reads for first 600 samples due next week 16 | BASE: Biomes of Australian Soil Environments | Andrew Young
    17. 17. Metagenome sequencing  HiSeq data generated for 6 sites (12 samples)  Test whether amplicon data can inform suitability for sample analysis, binning etc.  Sequences generated from both 350bp and 550bp fragments to assess efficacy of both  Data being analysed now 17 | BASE: Biomes of Australian Soil Environments | Andrew Young
    18. 18. BASE database  Developed an offline (access) relational database that allows searching of sequence and contextual data  Currently migrating this to online tool, with AAD, ALA and Centre for Comparative Genomics (BPA)  Raw Sequence data available via BPA data store 18 | BASE: Biomes of Australian Soil Environments | Andrew Young
    19. 19. SOME RESULTS 19 | BASE: Biomes of Australian Soil Environments | Andrew Young
    20. 20. Model – using site contextual data Exploratory models compared OTU presence/absence and abundance using soil chemistry data (common between sites) using data from first 98 sites for which all data were available Model (3 & 9) 5778 site pairs Presence/ Absence Abundance % Deviance Explained # predictors 73.0 13 Conductivity 74.1 14 Conductivity 20 | BASE: Biomes of Australian Soil Environments | Andrew Young Main predictor
    21. 21. Xmas Island Minerology sites NRS TERN supersites Trend transect Antarctica 22 | Presentation title | Presenter name
    22. 22. Bacteria • Fungi Edaphic and spatial components were significant in explaining community structure for both bacterial and fungal communities • pH and conductivity most important • Communities at different soils depths were significantly different only for bacteria 23 | Presentation title | Presenter name
    23. 23. 24 | Presentation title | Presenter name
    24. 24. 25 | Presentation title | Presenter name
    25. 25. 26 | Presentation title | Presenter name
    26. 26. 27 | Presentation title | Presenter name
    27. 27. NEXT STEPS… 28 | BASE: Biomes of Australian Soil Environments | Andrew Young
    28. 28. Extended environmental sampling  Add Temporal component to sampling  Long term monitoring sites  Sites with biogeochemical rate data  Sites identified as containing residual information  Sites with NO residual information (to test model)  More metagenomic samples (as guided by amplicon data) 29 | BASE: Biomes of Australian Soil Environments | Andrew Young
    29. 29. Agricultural sampling  Cropping, grazing, horticulture ⁻ Stratified soil type and by production system  Measure same parameters as environmental sites 30 | BASE: Biomes of Australian Soil Environments | Andrew Young
    30. 30. Modeling  Extend Generalised Dissimilarity modelling to include Phlogenetic Distance metrics  Create species distribution models  Incorporate temporal aspect into models  Test models 31 | BASE: Biomes of Australian Soil Environments | Andrew Young
    31. 31. Database availability development 32 | BASE: Biomes of Australian Soil Environments | Andrew Young
    32. 32. The BASE Team: CSIRO: Andrew Bissett, Leon Court, Kelly Hamonts, Shamsul Hoque, Kristen Williams, Andrew Young Bioplatforms Australia: Anna Fitzgerald, John Stephens and Catherine Zhang University of Adelaide: Frank Reith DEC WA: Margaret Byrne and David Coates DSEWPaC: Belinda Brown and Parks field staff at: Kakadu, Christmas Is, Booderee, Uluru TERN: Supersites SIEF: Strategic resourcing Others: Vic DPI, Gondwana Link, Bushblitz, Antarctic Division 33 | BASE: Biomes of Australian Soil Environments | Andrew Young
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