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Introducing BASE:Biome of Australian Soil Environments.<br />John R Stephen PhD, AGRF Ltd<br />
A collaborative project to build knowledge for diverse needs <br />
The scale of the question<br />Australia; 5% of the Earth’s landmass; rainforest, desert, sub-Antarctic…<br />
Sample selection for BASE - Positives<br />Australian soils have been physically well characterised<br />Characterisation ...
No EMP-high context data <br />
BPA, BASE and EMP<br />Bioplatforms Australia provides services and scientific infrastructure in the specialist fields of ...
BPA, BASE and EMP<br />Bioplatforms Australia provides services and scientific infrastructure in the specialist fields of ...
EMP association<br />Sample selection for BASE is focussed on Australia’s national interests<br />Here: To understand and ...
Australian Soil Classification<br />
There are 85 defined Biogeographic Regions in Australia<br />
National Reserve System<br />Atlas of Australian Soils(and/or geology)<br />Landscapes<br />Define few or many categories ...
How well does the NRS represent Australian soils?<br />
Major farming systems<br />Soils (Australian Soil Classification)<br />
Coastal dairy<br />Inland dairy<br />Southern dairy<br />Southern sheep & beef<br />Inland sheep & beef<br />High rainfall...
Inland dairy<br />Southern dairy<br />Southern sheep & beef<br />Inland sheep & beef<br />High rainfall sheep & beef<br />...
Why build a Soil Biodiversity Map for Australia?<br />The Australian economy maintains a large dependence on the primary i...
Soil microbial diversity<br /><ul><li>Microbial communities are primary drivers of soil ecological processes
These processes are equally vital for broad ecosystem functions and for sustainable primary production (e.g. nutrient cycl...
Involved in symbiotic and pathogenic co-evolutionary relationships with plant hosts e.g legume-rhizobia
Likely to play role in determining broad scale patterns of plant species abundance and community resilience
Few data on species diversity, composition and abundance of soil microbial communities
Metagenomics now provides an opportunity to investigate and quantify soil communities at large scales</li></li></ul><li>Wh...
Primary Deliverable<br />Assessment of Rehabilitation <br />Create a framework for objective & quantitative data to inform...
What will the data look like?<br />It will be layered over existing national and state environmental and vegetation data<b...
Metadata<br />Indicative Soil Samples<br />+<br />Environment <br />(including microbial environment)<br />Vegetation Type...
Collaboration model<br />Land-managers<br />Research bodies<br />samples<br />Dept. National Parks<br />CSIRO<br />BPAsequ...
Carbon Sequestration<br />Biochar can sequester carbon in the soil for hundreds to thousands of years, provide nutrients f...
Data accrual and conservation planning – a continuous improvement cycle to guide sampling<br />Looking to a future that in...
BPA proposed support<br />Australian Antarctic Division<br />Farming Industry R&D<br />National Parks<br />Terrestrial Eco...
Wheat crop (MCM)<br />Example: Land-use comparison 1: Remnant vs managed)<br />Calcarosol<br />Ferrosol<br />Remnant veget...
Approaches<br />6 x 1 m2<br />50m2<br />Soil samples<br />x 6 & composited<br />Shotgun & Titanium 454 pyrosequencer<br />...
MCM<br />MCR<br />Summary of assembly(Titanium 454 Pyrosequencing- Celera assembler)<br />Mele et al (in preparation)<br />
Example: Land-use comparison 2<br />Restorating& rehabilitating native ecosystems<br />Major focus on revegetation activit...
riverbank stabilization
rehabilitating after mining
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John Stephen: Introducing BASE: Biome of Australian Soil Environments. A collaborative Project to Build Knowledge for Diverse Needs

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John Stephen's talk at the 1st Earth Microbiome Project meeting in Shenzhen

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  • As expected, this data set presented problems for assembly. It is a metagenomics sample of a diverse community. The input reads are 90% unpaired Titanium (majority are not paired end, only did 2 plates). There are about 10M reads from each community: Managed (ag) and Remnant (park land). Most of the assembly is small. We see ~70% of reads in small contigs and ~27% left as singletons. This is probably due to diversity in the sample and low coverage provided by the input data.
  • Transcript of "John Stephen: Introducing BASE: Biome of Australian Soil Environments. A collaborative Project to Build Knowledge for Diverse Needs"

    1. 1. Introducing BASE:Biome of Australian Soil Environments.<br />John R Stephen PhD, AGRF Ltd<br />
    2. 2. A collaborative project to build knowledge for diverse needs <br />
    3. 3. The scale of the question<br />Australia; 5% of the Earth’s landmass; rainforest, desert, sub-Antarctic…<br />
    4. 4. Sample selection for BASE - Positives<br />Australian soils have been physically well characterised<br />Characterisation assists sample selection<br />Sample sites (often remote) can be accessed by<br /> National Parks <br /> Farming R&D bodies<br /> Mining R&D<br /> University Ecologists<br />
    5. 5. No EMP-high context data <br />
    6. 6. BPA, BASE and EMP<br />Bioplatforms Australia provides services and scientific infrastructure in the specialist fields of genomics, proteomics, metabolomics and bioinformatics.<br />Pacific Biosciences as EMP sponsor<br /> – RS instrument budgeted <br />
    7. 7. BPA, BASE and EMP<br />Bioplatforms Australia provides services and scientific infrastructure in the specialist fields of genomics, proteomics, metabolomicsand bioinformatics.<br />Coordinating implementation of Systems Biology approaches in Australia.<br />Wine-making fermentations at Australian Wine Research Institute.<br />
    8. 8. EMP association<br />Sample selection for BASE is focussed on Australia’s national interests<br />Here: To understand and ensure compatibility with EMP requirements (MIxS) to maximise the value of the study globally<br />(Information gathering mission)<br />
    9. 9. Australian Soil Classification<br />
    10. 10. There are 85 defined Biogeographic Regions in Australia<br />
    11. 11. National Reserve System<br />Atlas of Australian Soils(and/or geology)<br />Landscapes<br />Define few or many categories to sample the environmental continuum<br />Bioregions (climatic variation)<br />Primary Stratification<br />
    12. 12. How well does the NRS represent Australian soils?<br />
    13. 13. Major farming systems<br />Soils (Australian Soil Classification)<br />
    14. 14. Coastal dairy<br />Inland dairy<br />Southern dairy<br />Southern sheep & beef<br />Inland sheep & beef<br />High rainfall sheep & beef<br />Low rainfall cropping<br />Medium rainfall cropping<br />Mixed farming<br />Major farming systems<br />
    15. 15. Inland dairy<br />Southern dairy<br />Southern sheep & beef<br />Inland sheep & beef<br />High rainfall sheep & beef<br />Low rainfall cropping<br />Grain sites<br />Livestock sites<br />Medium rainfall cropping<br />Mixed farming<br />Coastal dairy<br />Sites of interest to rural industries<br />Crop rotations<br />Hermitage site (>45yrs)<br />Crop (tillage/stubble) <br />(Harden site) >20yrs<br />Crop lime trials >10 yrs<br />Crop rotation/stubble retention (Avon site) >30yrs <br />Crop rotations <br />(SCRIME site) >10 yrs<br />P fertiliser/grazing trials<br />(Hamilton site) >20 yrs<br />Grazing trials (Ellinbank) >10 yrs<br />Urea fertiliser/grazing trials<br />(DemoDairy Terang) >15 yrs<br />“Enhanced metadata”<br />
    16. 16. Why build a Soil Biodiversity Map for Australia?<br />The Australian economy maintains a large dependence on the primary industries of mining and farming<br />Generate comprehensive survey / audit of Australian soil biodiversity <br />Biodiscovery - add to the known global diversity of key ecological groups<br />Provide a baseline reference dataset to examine effects of land use and management <br />
    17. 17. Soil microbial diversity<br /><ul><li>Microbial communities are primary drivers of soil ecological processes
    18. 18. These processes are equally vital for broad ecosystem functions and for sustainable primary production (e.g. nutrient cycling, disease suppression, bioremediation)
    19. 19. Involved in symbiotic and pathogenic co-evolutionary relationships with plant hosts e.g legume-rhizobia
    20. 20. Likely to play role in determining broad scale patterns of plant species abundance and community resilience
    21. 21. Few data on species diversity, composition and abundance of soil microbial communities
    22. 22. Metagenomics now provides an opportunity to investigate and quantify soil communities at large scales</li></li></ul><li>Why generate baseline data?<br />Model relationships between environmental parameters and microbial diversity <br />Examine the importance of microbes in generating ecological complexity, stability and resilience<br />Test broad biogeographical and evolutionary hypotheses regarding microbial evolution and plant-microbe co-evolution<br />
    23. 23. Primary Deliverable<br />Assessment of Rehabilitation <br />Create a framework for objective & quantitative data to inform restoration of soil communities as part of ongoing broad scale revegetation<br />Restoration ecology<br />Mining remediation<br />Maintain/ Enhance farming productivity<br />Human impacts (Antarctica)<br />etc<br />
    24. 24. What will the data look like?<br />It will be layered over existing national and state environmental and vegetation data<br />It will incorporate local environmental data collected from soil sampling sites<br />It will place a metagenomic measurement of biodiversity on three soil microbial communities (fungi, bacteria and archaea)<br />It will allow a metagenomic assessment of functional diversity data from soil samples e.g. “redundancy” of nitrogen and phosphorus cycle genes; relationship to carbon sequestration<br />
    25. 25. Metadata<br />Indicative Soil Samples<br />+<br />Environment <br />(including microbial environment)<br />Vegetation Type<br />Soil type and Chemistry<br />GPS, landscape position, etc<br />
    26. 26. Collaboration model<br />Land-managers<br />Research bodies<br />samples<br />Dept. National Parks<br />CSIRO<br />BPAsequencing / systems biology & bioinformatics<br />Industry (farming) R&D bodies<br />Universities<br />Data analysis - environmental, evolutionary <br />and functional modelling <br />Depts. Primary Industries<br />Mining companies<br />env data<br />
    27. 27. Carbon Sequestration<br />Biochar can sequester carbon in the soil for hundreds to thousands of years, provide nutrients for plant growth, increase pH… A carbon-negative technology.<br />Interactions with microbial community?<br />
    28. 28. Data accrual and conservation planning – a continuous improvement cycle to guide sampling<br />Looking to a future that includes metagenomic data in decision process<br />Use survey gapanalysis modelingto strategically identify sites to add the most new information<br />Figure from Ferrier S. (2002) Mapping spatial pattern in biodiversity for regional conservation planning: Where to from here? Systematic Biology51, 331-63.<br />
    29. 29. BPA proposed support<br />Australian Antarctic Division<br />Farming Industry R&D<br />National Parks<br />Terrestrial Ecosystems Research Network (TERN) (“Eco-informatics Strategy:  data sets covering flora, fauna, and biophysical properties captured at sites or areas, from genetic to landscape scales”).<br />50 – 100 sites per initial question area<br />Deep metagenomics, broader scale Tag profiling <br />
    30. 30. Wheat crop (MCM)<br />Example: Land-use comparison 1: Remnant vs managed)<br />Calcarosol<br />Ferrosol<br />Remnant vegetation (MCR)<br />Dairy pasture (EFM)<br />Mele et al (in preparation)<br />
    31. 31. Approaches<br />6 x 1 m2<br />50m2<br />Soil samples<br />x 6 & composited<br />Shotgun & Titanium 454 pyrosequencer<br />PCR 16S& 18S* rRNA regions<br />Extract DNA<br />ABI 3730 Sanger<br />Recover DNA & Sequence<br />Annotation and assembly (Celera) (20% frameshift correction to improve ORF calling)<br />Ecological descriptors (MOTHUR)<br />Mele et al (in preparation)<br />
    32. 32. MCM<br />MCR<br />Summary of assembly(Titanium 454 Pyrosequencing- Celera assembler)<br />Mele et al (in preparation)<br />
    33. 33. Example: Land-use comparison 2<br />Restorating& rehabilitating native ecosystems<br />Major focus on revegetation activities in Australia with a range of goals:<br /><ul><li>restoring native biodiversity
    34. 34. riverbank stabilization
    35. 35. rehabilitating after mining
    36. 36. managing rare or threatened species
    37. 37. enhancing connectivity (corridors)
    38. 38. restoring landscape function e.g. pumping water to prevent dryland salinity</li></ul>Unique challenges… but restoring soil microbial communities plays a key role in all of these…<br />
    39. 39. Acacia mearnsii<br />+ rhiz<br />- rhiz<br />+ rhiz<br />- rhiz<br />Acacia oswaldii<br />Acacia stenophylla<br />Acacia brachybotrya<br />Restoring Rhizobial communities to improve revegetation outcomes<br />Native plants rely on microbial symbionts for establishment and growth e.g rhizobia, mycorrhizae<br />Loss of native microbial communities can limit revegetation success<br />Identify appropriate microbial symbionts for native species<br />Up to 800% increases in survival and growth<br />Re-establish microbial communities (inoculation) as part of the restoration process <br />
    40. 40. Restoration trajectory of revegetated soil community<br />
    41. 41. Remnant<br />Pasture<br />Reveg<br />Soil community relatedness (tRFLPs)<br />Inoculate<br />?<br />CSIRO. <br />
    42. 42. Project Champions / Coordinators<br /> Prof. Andrew Young<br /> Director, Centre for Australian National Biodiversity Research, CSIRO Plant Industry, Canberra<br />Assoc. Prof. Pauline Mele<br />BioSciences Research Division, Dept. Primary Industries, Victoria<br />Anna Fitzgerald, Bioplatforms Australia<br />
    43. 43. Finally…<br />Thanks, and Good Luck EMP!<br />
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