Soil biology - latest messages for advisers

Pauline Mele, Department of Economic Development, Jobs, Transport and Resources, Victoria.

GRDC project codes: UWA00138, DAV00102, DAS00111, UWA00142, DAV00120, UWA00139, CSP00138, DAV00106, UA00119, UA00128, UWA00150, UWS00008, DAW00201, DAQ00164, CSP00135, DAV00105

Keywords: disease suppression, monitoring, soil quality, nitrogen cycle.

Take home messages

www.soilquality.org.au is now available as a national database and decision support tool.
Nine new DNA tests for beneficial nematodes have been developed for the PreDicta B platform and will be available for trial this year.
Free living N fixation can deliver a large additional amount of N into crops. It ranges from less than 0.2 kg/ha/day, up to ~3kg/ha/day.
Specific management strategies can be applied to ‘make’ bacterial N fixers and mineralisers of organic N work harder to access ‘free-N’.
Farmers can manage soils to suppress Rhizoctonia and root lesion nematode (RLN) diseases by stimulating biological turnover through organic matter additions; even a 10% addition of field soil to sterilised soil is sufficient to achieve RLN suppression
Rhizoctonia suppression can be attributed to a unique bacterial and fungal communities that act in a variety of ways including production of antimicrobial agents

Background

The Soil Biology Initiative (SBI) funded 15 R&D projects from 2010 to June 2014. Projects were organised into three broad theme areas; Soil quality monitoring (www.soilquality.org.au); Nutrient management; and Disease suppressive soils-traits and transferability. SBI deliberately set out to have a mix of foundational and translational R&D. This paper summarises some of the messages to emerge focussing on those that are more readily translatable into practice change in the immediate to medium term. It should also be noted that there are broadly accepted management ‘rules of thumb’ on how to improve general soil biological functions that can be applied across all cropping zones. If the end game is to reduce inputs by making soil biota work harder, then these rules of thumb do not go far enough. The adoption of more sophisticated technologies now provides unprecedented insights into who is doing what in the soil and most importantly how we can manipulate this through management.

Methodology

Table 1 summarises the projects funded, the location of the research and the key methods employed in the research effort. Worth noting is the wide adoption of DNA based approaches to elucidate the complexities within the soil biota. These approaches are now the tools of trade in soil biology R&D.

Table 1. Summary of projects including sampling locations and key methods to measure soil biology.

Project Title, Project Code, Project Leader (PL)	Sampling Locations	Methods
A National Soil Quality Monitoring Framework (UWA00138, PL-D. Murphy)	National- SCaRP sites	Minimum data set chosen by expert panels; workshops to roll out www.soilquality.org.au
Monitoring soil biology with high resolution genomic technologies (DAV00102, PL-C. Bath)	SR and WR	DNA fragment patterns and sequencing of fungi, bacteria and archaea
DNA tests for nematode community analysis (DAS00111, PL-K. Ophel-Keller)	National	DNA methods to target different groups
Molecular indicators for soil quality (UWA00142, PL- Tony O’Donnell)	SR and WR	DNA fragment patterns and sequencing of fungi, bacteria and archaea
Harnessing the nitrogen cycle through novel solutions (UWA00139, PL-D. Murphy)	WR-WA (Liebe trial)	DNA sequencing of ammonium oxidising bacteria and archaea; ¹⁵N isotope dilution method, NanoSIMS
Free living N fixing bacteria (CSP00138, PL- G. Vadakattu)	SR-SA, Vic, NSW	DNA sequencing of bacteria with N-Fixation gene; acetylene reduction, ¹⁵N isotope dilution method
Managing soil biology to improve nitrogen supply in grain production systems (DAV00106, PL- L. Phillips)	SR-Vic (SCRIME trial)	DNA sequencing of fungi, bacteria and archaea, ¹⁵N isotope dilution method, NMR for C fraction analysis
Assessing management options for enhanced soil phosphorus availability using rotations (UA00119, PL- A. McNeill)	SR- SA, Vic, NSW	³³P-labelling of break crop residues, available P tests (DGT, Colwell)
Can arbuscular mycorrhizal (AM) fungi be harnessed to enhance P nutrition and grain yield in rotations? (UA00128, PL- A. Smith)	SR-SA	AM Fungal bioassays, ³³P-labelling of crop residues and to assess P transfer
Management of microorganisms to unlock the phosphorus bank in soil (Murphy FT) (UWA00150, PL- D. Murphy)	WR- WA	DNA sequencing of fungi, bacteria and archaea
Carbon storage: Identifying microbial drivers and key modulators in grain cropping systems (UWS00008, PL-B. Singh)	SR	Aggregate size separation, DNA sequencing of fungi, bacteria and archaea
Identification and characterisation of disease suppressive soils in the Western Region (DAW00201, PL-W. McLeod)	WR-WA	In-field root disease assessments at tillering, Pot bioassays, PreDicta B tests
Biological Suppression of Root-lesion Nematodes in Grain-growing Soils (DAQ00164, PL- N. Seymour)	NR- Qld, NSW	Pot bioassays, root examination and scoring
A molecular approach to unravel the dynamics of disease suppressive microbial communities (Rhizoctonia) (CSP00135, PL- G. Vadakattu)	SR- NSW, SA (Avon)	DNA sequencing of fungi and bacteria to identify potential antagonists to Rhizoctonia;
Suppressive soils: Can we find a microbial finger-print using 'omics' technology? *(Rhizoctonia) (DAV00105, PL-H. Hayden)*	SR-SA (Avon)	DNA and RNA to identify potential antagonists to Rhizoctonia; NMR and LCMS for antimicrobials

Results and discussion

A summary of some of the messages emerging from projects is provided in Tables 2 and 3. Some of these will be highlighted in more detail in my presentation.

Table 2. A selection of messages arising from the Soil Biology Initiative that are translatable.

Theme 1: Monitoring soil quality	Theme 2: N management	Theme 3: Disease suppressive soils
www.soilquality.org.au is now available as a national database and decision support tool. New tests are available this year for beneficial nematodes. The majority of nematodes do not cause disease. The diversity of these groups indicate the health (or resilience) of our cropping soils. Nine new DNA tests for beneficial nematodes have been developed for the PreDicta B platform.	Free living N fixation can deliver a large additional amount of N into crops. It ranges from less than 0.2 kg/ha/day, up to ~3kg/ha/day. Wet soils with a high clay content are better able to support N fixation. Make free living N fixers work harder by: Retaining stubble; Crop type: Wheat > cereal rye > canola Lower N fertiliser rates: > 25kg N/ha reduces fixation but this varies with soil type Promoting summer active grasses e.g. Rhodes grass and Panicum species Make bacteria that mineralise N from plant residues (‘free-soil N’) work harder by: adding less fertiliser N; this suppresses the release of stored organic-N (from legumes) by favouring bacteria that process fertiliser-N over those that process stored organic N strategic tillage to mix residues can speed up the process Make it harder for bacteria that cause loss of N by: cutting of food (NO3--N ) supply by using chemical inhibitors to slow mineralising bacteria; inhibitors can now work at higher temperatures (40°C) strategic tillage; oxygenating the soil to suppress the anaerobic processes that N loss bacteria enjoy controlled traffic and wide row spacing; keeps pore structure open so that rainfall can drain away (again keeps soil oxygenated)	Farmers can manage soils to suppress diseases but it takes time to develop (after 3 years). The soils may or may not be active against all pathogens in every situation/site. *A more active soil biota will suppress Rhizoctonia* and root lesion nematode disease incidence by at least 10%. This can be done by:** adding or retaining organic matter (don’t burn graze or bale); in the Southern region, Rhizoctonia suppression can be achieved on farms in continuous cropping systems where crop residues are maintained (e.g. >70% sites from Mallee to Ceduna). adding organic matter deeper; Root lesion nematode suppression is currently largely confined to surface soils

Theme 1:

Monitoring soil quality

Theme 2:

N management

Theme 3:

Disease suppressive soils

www.soilquality.org.au is now available as a national database and decision support tool.

New tests are available this year for beneficial nematodes. The majority of nematodes do not cause disease. The diversity of these groups indicate the health (or resilience) of our cropping soils. Nine new DNA tests for beneficial nematodes have been developed for the PreDicta B platform.

Free living N fixation can deliver a large additional amount of N into crops. It ranges from less than 0.2 kg/ha/day, up to ~3kg/ha/day. Wet soils with a high clay content are better able to support N fixation.

Make free living N fixers work harder by:

Retaining stubble; Crop type: Wheat > cereal rye > canola
Lower N fertiliser rates: > 25kg N/ha reduces fixation but this varies with soil type
Promoting summer active grasses e.g. Rhodes grass and Panicum species

Make bacteria that mineralise N from plant residues (‘free-soil N’) work harder by:

adding less fertiliser N; this suppresses the release of stored organic-N (from legumes) by favouring bacteria that process fertiliser-N over those that process stored organic N
strategic tillage to mix residues can speed up the process

Make it harder for bacteria that cause loss of N by:

cutting of food (NO3--N ) supply by using chemical inhibitors to slow mineralising bacteria; inhibitors can now work at higher temperatures (40°C)
strategic tillage; oxygenating the soil to suppress the anaerobic processes that N loss bacteria enjoy
controlled traffic and wide row spacing; keeps pore structure open so that rainfall can drain away (again keeps soil oxygenated)

Farmers can manage soils to suppress diseases but it takes time to develop (after 3 years). The soils may or may not be active against all pathogens in every situation/site.

A more active soil biota will suppress Rhizoctonia and root lesion nematode disease incidence by at least 10%. This can be done by:

adding or retaining organic matter (don’t burn graze or bale); in the Southern region, Rhizoctonia suppression can be achieved on farms in continuous cropping systems where crop residues are maintained (e.g. >70% sites from Mallee to Ceduna).
adding organic matter deeper; Root lesion nematode suppression is currently largely confined to surface soils

Table 3. A selection of messages arising from the Soil Biology Initiative that, as yet, are not readily translatable (but help raise awareness and understanding).

Theme 1: Monitoring soil quality	Theme 2: N management	Theme 3: Disease suppressive soils
At the large scale the key factors driving soil biology (abundance, diversity and activity) are known: soil texture, climate, pH At the small scale (i.e. where these factors are constant), trials and survey data show that soil biology is affected by management practices (tillage, liming, fertilisation) New DNA testing procedures for beneficial microbes verifies the influence of soil type, pH and organic matter in maintaining critical functions	The diversity of bacteria involved in free living N fixation is variable depending on location. The number of groups capable of N fixation in Colonsay (NR) was almost double the number in Buntine (WR) Bacteria rather than archaea are responsible for most nitrification but archaea are more dominant at depth in a semi-arid WA subsoil. This is associated with pH where more acidic soils support a more abundant archaeal community N cycle is a biological cycle that we can measure precisely. Biological N-release (nitrification), biological storage (immobilisation) and biological loss (denitrification) functions are controlled by water, temperature, previous rotation (C:N ratio of residue) and N fertiliser regime	General suppression involves a distinct community of bacteria, and fungi , archaea that act in a variety of ways against soil-borne pathogens of wheat Unique antimicrobial substances have been detected in Rhizoctonia suppressive soils A 10% addition of field soil to sterilised soil is sufficient to achieve RLN suppression Specific suppression also occurs. A fungal endophyte that reduced RLN multiplication by 40% was isolated and identified from wheat roots. A bacterial parasite that is known to kill RLN, Pasteuria spp, co-locates with RLN The reduction in RLN caused by biological suppression is of the same order of magnitude as using resistant wheat varieties.

Theme 1:

Monitoring soil quality

Theme 2:

N management

Theme 3:

Disease suppressive soils

At the large scale the key factors driving soil biology (abundance, diversity and activity) are known: soil texture, climate, pH

At the small scale (i.e. where these factors are constant), trials and survey data show that soil biology is affected by management practices (tillage, liming, fertilisation)

New DNA testing procedures for beneficial microbes verifies the influence of soil type, pH and organic matter in maintaining critical functions

The diversity of bacteria involved in free living N fixation is variable depending on location. The number of groups capable of N fixation in Colonsay (NR) was almost double the number in Buntine (WR)

Bacteria rather than archaea are responsible for most nitrification but archaea are more dominant at depth in a semi-arid WA subsoil. This is associated with pH where more acidic soils support a more abundant archaeal community

N cycle is a biological cycle that we can measure precisely. Biological N-release (nitrification), biological storage (immobilisation) and biological loss (denitrification) functions are controlled by water, temperature, previous rotation (C:N ratio of residue) and N fertiliser regime

General suppression involves a distinct community of bacteria, and fungi , archaea that act in a variety of ways against soil-borne pathogens of wheat

Unique antimicrobial substances have been detected in Rhizoctonia suppressive soils

A 10% addition of field soil to sterilised soil is sufficient to achieve RLN suppression

Specific suppression also occurs. A fungal endophyte that reduced RLN multiplication by 40% was isolated and identified from wheat roots. A bacterial parasite that is known to kill RLN, Pasteuria spp, co-locates with RLN

The reduction in RLN caused by biological suppression is of the same order of magnitude as using resistant wheat varieties.

Conclusion

The soil biota of Australian cropping soils no longer represents a ‘black box’. We now have significantly greater knowledge and capacity to describe microbial and nematode communities across Australian grain growing regions through the adoption of DNA profiling and other precision tools. A snapshot of this knowledge is reiterated here:

www.soilquality.org.au is now available as a national database and decision support tool.
Nine new DNA tests for beneficial nematodes have been developed for the PreDicta B platform and will be available for trial this year.
Free living N fixation can deliver a large additional amount of N into crops. It ranges from less than 0.2 kg/ha/day, up to ~3kg/ha/day.
Specific management strategies can be applied to ‘make’ bacterial N fixers and mineralisers of organic N work harder to access ‘free-N’.
Farmers can manage soils to suppress Rhizoctonia and RLN diseases by stimulating biological turnover through organic matter additions; even a 10% addition of field soil to sterilised soil is sufficient to achieve RLN suppression.
Rhizoctonia suppression can be attributed to a unique bacterial and fungal communities that act in a variety of ways including production of antimicrobial agents.

This knowledge is being translated into farmer and adviser training packages to raise general awareness and to provide actionable information. Further validation needs to occur to capture regional conditions and farming systems and to quantify the economic contribution of specific biological functions and management actions at the operational scale.

Contact details

Pauline Mele
GRDC Soil Biology Initiative coordinator
AgriBio; 5 Ring Rd, Bundoora Vic
03 9032 7083
pauline.mele@depi.vic.gov.au

GRDC Project Code: UWA00138, DAV00102, DAS00111, UWA00142, DAV00120, UWA00139, CSP00138, DAV00106, UA00119, UA00128, UWA00150, UWS00008, DAW00201, DAQ00164, CSP00135, DAV00105,

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