Introducing BASE:Biome of Australian Soil Environments.

John R Stephen PhD, AGRF Ltd

A collaborative project to build knowledge for diverse needs

The scale of the question

Australia; 5% of the Earth’s landmass; rainforest, desert, sub-Antarctic…

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

No EMP-high context data

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

BPA, BASE and EMP

Bioplatforms Australia provides services and scientific infrastructure in the specialist fields of genomics, proteomics, metabolomics and bioinformatics.

Coordinating implementation of Systems Biology approaches in Australia.

Wine-making fermentations at Australian Wine Research Institute.

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)

Australian Soil Classification

There are 85 defined Biogeographic Regions in Australia

National Reserve System

Atlas of Australian Soils(and/or geology)

Landscapes

Bioregions (climatic variation)

Define few or many categories to sample the environmental continuum

Primary Stratification

How well does the NRS represent Australian soils?

Soils (Australian Soil Classification)Major farming systems

Inland sheep & beef

Southern dairy

High rainfall sheep & beef

Southern sheep & beef

Major farming systems

Coastal dairy

Inland dairy

Low rainfall cropping

Mixed farming

Medium rainfall cropping

Low rainfall cropping

Inland sheep & beef

Southern dairy

High rainfall sheep & beef

Southern sheep & beef

Sites of interest to rural industries

Coastal dairy

Inland dairy

Mixed farming

Medium rainfall cropping

Crop rotations (SCRIME site) >10 yrs

Crop rotation/stubble retention (Avon site)

>30yrs

Crop rotationsHermitage site (>45yrs)

Crop (tillage/stubble) (Harden site) >20yrs

Grain sites

Livestock sites

Crop lime trials >10 yrs

Grazing trials (Ellinbank) >10 yrs

P fertiliser/grazing trials(Hamilton site) >20 yrs

Urea fertiliser/grazing trials(DemoDairy Terang) >15 yrs

“Enhanced metadata”

Why build a Soil Biodiversity Map for Australia?

1. The Australian economy maintains a large dependence on the primary industries of mining and farming

2. Generate comprehensive survey / audit of Australian soil biodiversity

3. Biodiscovery - add to the known global diversity of key ecological groups

4. Provide a baseline reference dataset to examine effects of land use and management

Soil microbial diversity

• 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 cycling, disease suppression, bioremediation)

• 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

Why generate baseline data?

1. Model relationships between environmental parameters and microbial diversity

2. Examine the importance of microbes in generating ecological complexity, stability and resilience

3. Test broad biogeographical and evolutionary hypotheses regarding microbial evolution and plant-microbe co-evolution

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 ecologyMining remediationMaintain/ Enhance farming productivityHuman impacts (Antarctica)etc

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

Metadata

Indicative Soil Samples

Environment

(including microbial environment)

Vegetation Type

GPS, landscape position, etc

Soil type and Chemistry

+

BPA sequencing /

systems biology & bioinformatics

Collaboration model

Dept. National Parks

Industry (farming)

R&D bodies

Mining companies

Land-managers

CSIRO

Universities

Depts. Primary

Industries

Research bodiessamples

env data

Data analysis - environm

ental, evolutionary and functional m

odelling

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?

Use survey gapanalysis modelingto strategically identify sites to add the most new information

Data accrual and conservation planning – a continuous improvement cycle to guide sampling

Figure from Ferrier S. (2002) Mapping spatial pattern in biodiversity for regional conservation planning: Where to from here? Systematic Biology 51, 331-63.

Looking to a future that includes metagenomic data in decision process

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

Example: Land-use comparison 1: Remnant vs managed)

Remnant vegetation

(MCR)

Wheat crop (MCM)

Dairy pasture (EFM)

Calcarosol

Ferrosol

Mele et al (in preparation)

Soil samples

Recover DNA & Sequence

Extract DNA

PCR 16S& 18S* rRNA regions

ABI 3730 Sanger

50m2 6 x 1 m2

Ecological descriptors (MOTHUR)

Clones Sequences

MCR 4849 9551

MCM 4512 8714

EFM 4864 9554

Sequence reads (M)

MCR 9.13

MCM 9.27

Total 18.40

Shotgun & Titanium 454 pyrosequencer

Annotation and assembly (Celera) (20% frameshift correction to improve

ORF calling)

x 6 & composited

Approaches

Mele et al (in preparation)

Summary of assembly (Titanium 454 Pyrosequencing- Celera assembler)

MCR MCM Combined

Small contig reads

6 633 981 (73%) 6 546 083 (71%) 13 454 718 (73%)

Singleton reads 2 489 007(28%) 2 625 512 (28%) 4 942 562 (26%)

Total Usable Reads

9 133 017 9 265 080 18 482 741

MCMMCR

Mele et al (in preparation)

Restorating & rehabilitating native ecosystems

Major focus on revegetation activities in Australia with a range of goals:- restoring native biodiversity- riverbank stabilization- rehabilitating after mining - managing rare or threatened species- enhancing connectivity (corridors)- restoring landscape function e.g. pumping

water to prevent dryland salinity

Unique challenges… but restoring soil microbial

communities plays a key role in all of these…

Example: Land-use comparison 2

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

Acacia oswaldii Acacia stenophylla

Acacia brachybotrya

Acacia mearnsii

+ rhiz - rhiz + rhiz - rhiz

Restoration trajectory of revegetated soil community

CSIRO.

Soil community relatedness (tRFLPs)

PastureReveg

Remnant

?Inoculate

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

Finally…

Thanks, and Good Luck EMP!