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

1. Introducing BASE:Biome of Australian Soil Environments. John R Stephen PhD, AGRF Ltd

2. A collaborative project to build knowledge for diverse needs

3. The scale of the question Australia; 5% of the Earth’s landmass; rainforest, desert, sub-Antarctic…

4. Sample selection for BASE - Positives Australian soils have been physically well characterised Characterisation assists sample selection Sample sites (often remote) can be accessed by National Parks Farming R&D bodies Mining R&D University Ecologists

5. No EMP-high context data

6. BPA, BASE and EMP Bioplatforms Australia provides services and scientific infrastructure in the specialist fields of genomics, proteomics, metabolomics and bioinformatics. Pacific Biosciences as EMP sponsor – RS instrument budgeted

7. BPA, BASE and EMP Bioplatforms Australia provides services and scientific infrastructure in the specialist fields of genomics, proteomics, metabolomicsand bioinformatics. Coordinating implementation of Systems Biology approaches in Australia. Wine-making fermentations at Australian Wine Research Institute.

8. EMP association Sample selection for BASE is focussed on Australia’s national interests Here: To understand and ensure compatibility with EMP requirements (MIxS) to maximise the value of the study globally (Information gathering mission)

9. Australian Soil Classification

10. There are 85 defined Biogeographic Regions in Australia

11. National Reserve System Atlas of Australian Soils(and/or geology) Landscapes Define few or many categories to sample the environmental continuum Bioregions (climatic variation) Primary Stratification

12. How well does the NRS represent Australian soils?

13. Major farming systems Soils (Australian Soil Classification)

14. Coastal dairy Inland dairy Southern dairy Southern sheep & beef Inland sheep & beef High rainfall sheep & beef Low rainfall cropping Medium rainfall cropping Mixed farming Major farming systems

15. Inland dairy Southern dairy Southern sheep & beef Inland sheep & beef High rainfall sheep & beef Low rainfall cropping Grain sites Livestock sites Medium rainfall cropping Mixed farming Coastal dairy Sites of interest to rural industries Crop rotations Hermitage site (>45yrs) Crop (tillage/stubble) (Harden site) >20yrs Crop lime trials >10 yrs Crop rotation/stubble retention (Avon site) >30yrs Crop rotations (SCRIME site) >10 yrs P fertiliser/grazing trials (Hamilton site) >20 yrs Grazing trials (Ellinbank) >10 yrs Urea fertiliser/grazing trials (DemoDairy Terang) >15 yrs “Enhanced metadata”

16. Why build a Soil Biodiversity Map for Australia? The Australian economy maintains a large dependence on the primary industries of mining and farming Generate comprehensive survey / audit of Australian soil biodiversity Biodiscovery - add to the known global diversity of key ecological groups Provide a baseline reference dataset to examine effects of land use and management

18. These processes are equally vital for broad ecosystem functions and for sustainable primary production (e.g. nutrient cycling, disease suppression, bioremediation)

19. Involved in symbiotic and pathogenic co-evolutionary relationships with plant hosts e.g legume-rhizobia

20. Likely to play role in determining broad scale patterns of plant species abundance and community resilience

21. Few data on species diversity, composition and abundance of soil microbial communities

23. Primary Deliverable Assessment of Rehabilitation Create a framework for objective & quantitative data to inform restoration of soil communities as part of ongoing broad scale revegetation Restoration ecology Mining remediation Maintain/ Enhance farming productivity Human impacts (Antarctica) etc

24. What will the data look like? It will be layered over existing national and state environmental and vegetation data It will incorporate local environmental data collected from soil sampling sites It will place a metagenomic measurement of biodiversity on three soil microbial communities (fungi, bacteria and archaea) 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

25. Metadata Indicative Soil Samples + Environment (including microbial environment) Vegetation Type Soil type and Chemistry GPS, landscape position, etc

26. Collaboration model Land-managers Research bodies samples Dept. National Parks CSIRO BPAsequencing / systems biology & bioinformatics Industry (farming) R&D bodies Universities Data analysis - environmental, evolutionary and functional modelling Depts. Primary Industries Mining companies env data

27. Carbon Sequestration Biochar can sequester carbon in the soil for hundreds to thousands of years, provide nutrients for plant growth, increase pH… A carbon-negative technology. Interactions with microbial community?

28. Data accrual and conservation planning – a continuous improvement cycle to guide sampling Looking to a future that includes metagenomic data in decision process Use survey gapanalysis modelingto strategically identify sites to add the most new information Figure from Ferrier S. (2002) Mapping spatial pattern in biodiversity for regional conservation planning: Where to from here? Systematic Biology51, 331-63.

29. BPA proposed support Australian Antarctic Division Farming Industry R&D National Parks 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”). 50 – 100 sites per initial question area Deep metagenomics, broader scale Tag profiling

30. Wheat crop (MCM) Example: Land-use comparison 1: Remnant vs managed) Calcarosol Ferrosol Remnant vegetation (MCR) Dairy pasture (EFM) Mele et al (in preparation)

31. Approaches 6 x 1 m2 50m2 Soil samples x 6 & composited Shotgun & Titanium 454 pyrosequencer PCR 16S& 18S* rRNA regions Extract DNA ABI 3730 Sanger Recover DNA & Sequence Annotation and assembly (Celera) (20% frameshift correction to improve ORF calling) Ecological descriptors (MOTHUR) Mele et al (in preparation)

32. MCM MCR Summary of assembly(Titanium 454 Pyrosequencing- Celera assembler) Mele et al (in preparation)

34. riverbank stabilization

35. rehabilitating after mining

36. managing rare or threatened species

37. enhancing connectivity (corridors)

38. restoring landscape function e.g. pumping water to prevent dryland salinityUnique challenges… but restoring soil microbial communities plays a key role in all of these…

39. Acacia mearnsii + rhiz - rhiz + rhiz - rhiz Acacia oswaldii Acacia stenophylla Acacia brachybotrya Restoring Rhizobial communities to improve revegetation outcomes Native plants rely on microbial symbionts for establishment and growth e.g rhizobia, mycorrhizae Loss of native microbial communities can limit revegetation success Identify appropriate microbial symbionts for native species Up to 800% increases in survival and growth Re-establish microbial communities (inoculation) as part of the restoration process

40. Restoration trajectory of revegetated soil community

41. Remnant Pasture Reveg Soil community relatedness (tRFLPs) Inoculate ? CSIRO.

42. Project Champions / Coordinators Prof. Andrew Young Director, Centre for Australian National Biodiversity Research, CSIRO Plant Industry, Canberra Assoc. Prof. Pauline Mele BioSciences Research Division, Dept. Primary Industries, Victoria Anna Fitzgerald, Bioplatforms Australia

43. Finally… Thanks, and Good Luck EMP!