soil biology: what is a healthy soil? -...

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Soil Biology: The role of micro‐organisms in soil fertility and plant health activity

Latvia24 11 1524‐11‐15

Joel WilliamsBioLife Ag

www.biolifeag.com

What is a healthy soil?

What drives a healthy soil?

Chemistry

Physics Biology

SOC

What drives soil organic carbon?

And what drives soil microbes? Soil Biology• Beneath the soil surface contains an immense number of living organisms.– Algae

– Bacteria

– FungiFungi

– Protozoa

– Nematodes

– Micro and Macro Arthropods

– Insects

– Earthworms

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Algae• Range from small single‐celled

forms to complex multi‐cellular forms.

• They contain chlorophyll and f h t th iperform photosynthesis.

• Need light, water and carbon dioxide.

• Good soils have 1 ‐ 10 billion algae per square metre 0‐15 cm deep.

Algae• Algae help to form soil by producing carbonic acids which causes rock to weather.

• Algae excrete sugars which feed fungi and bacteriaand are also eaten by certain nematodes.

• They exude sticky substances which help to bind and y y paggregate soil particles.

Source: Laverstoke Park Laboratories

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Source: Soil Food Web Inc

Bacteria• Microscopic single‐celled organisms.

• More than 1 billion bacteria per teaspoon of soil with more than 30,000 different species.

• Bacteria consume simple carbon compounds.

• Benefits of Bacteria – digest organic matter and improve soil structure;

– recycle, solubilise and retain nutrients,

– produce by‐products that promote plant growth (enzymes, vitamins, hormones);

– protect the plant from disease.



Fungi• Multi‐celled organisms that usually grow as long strands or threads called hyphae.

• Fungi consume complex carbon compounds.

• Organic acids produced by fungi efficiently solubilise nutrients.

• Like bacteria, fungi are – decomposers;

– nutrient cyclers;

– soil structure builders;

– plant protectors.

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Mycorrhizal Fungi

• A group of fungi that form a symbiotic relationship with plants.

• Fungus colonizes plant roots g p(either externally or internally).

• Plant translocates sugars to the fungi in exchange for nutrients, moisture and protection.

Mycorrhizal Fungi

• Critical members of the soil foodweb (for plants) solubilising and supplying often insoluble nutrients – P and Znnutrients – P and Zn.

• Protect the plant from disease.

• Improve soil structure – hyphaeand exudates.

• Key role in carbon sequestration.

Source: Soil Food Web Inc ©

Protozoa• Single‐celled animals that feed primarily on bacteria, and other protozoa, soluble organic matter and fungi.

• 3 different types: Flagellates, Amoebae, Ciliates.

• Play an important role in nutrient cycling ‐Protozoa eat ~10,000 bacteria each day.

• They are also an important food source for other soil organisms (earthworms, nematodes).

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Source: Soil Food Web Inc

Nematodes• Microscopic worms.

• ~20,000 different species are known.

• 4 different types:– Bacterial feeders

– Fungal feeders

– Nematode feeders (Predatory)

– Root feeders (Parasitic)

• Nematodes play an important role in releasing nutrients in plant available form.


• These ecosystem engineers are intimately involved in:– The shredding of organic matter.

– The aeration of the soil.

Earthworms

– The aggregation of soil particles.

– The movement of organic matter and microbes throughout the soil.

– They also increase microbial populations and aid plant root growth.

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Why Microbes?

• A healthy and balanced soil micro biota will:– Digest and cycle organic matter

– Improve soil structure and rooting depth

– Recycle, solubilise and retain nutrients

– Decompose toxins

– Increase water and nutrient holding capacity

– Produce by‐products that promote plant growth

– Protect the plant from disease

– Sequester carbon

Benefits of Soil Biology• Nutrient Cycling

• Disease Suppression

• Soil Structure

• Soil Carbon!

Nutrient Cycling

• Soil microbes solubilise insoluble nutrients (reserves and applied) by exuding:– Organic acids

– Enzymesy

– Carbohydrates

• Decomposer organisms also breakdownsoluble and insoluble organic matter liberating nutrients for subsequent plant uptake.

Nutrient Cycling

• Nutrients are made available for plant growth when:–A microbe dies and its body decomposes releasing nutrients that are stored in itsreleasing nutrients that are stored in its biomass.

–A microbe is consumed by a higher trophic level predator and waste products are excreted from the predator.

Organism Group C:N• Bacteria 5:1

• Fungi 20:1

• People 30:1

• Green Leaves 30:1

• Protozoa 30:1

• Nematodes 100:1

• Brown plant material 150–200:1

• Deciduous wood 300:1

• Conifer wood 500:1

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Protozoa Nematodes

Nutrient and Moisture Access

• AMF are well documented to access soil reserves of P beyond the root zone.

h l i h i• They also assist other macro‐nutrient access – Ca, Mg, K and N.*

• And micro‐nutrients – Zn, Cu, Fe.*

* Gosling, P., Hodge, A., Goodlass, G., and Bending G.D. (2006) Arbuscularmycorrhizal fungi and organic farming. Agriculture, Ecosystems and Environment 113: 17–35

Soil Biology and Carbon

• Plants release ~30% of their total photosynthetic energy into the root zone as root exudates –sugars, carbohydrates etc.

D di h t i h i• Depending on what is happening in the rhizosphere, these exudates can potentially be sequestered into the soil carbon pool.

Bacteria, Fungi and Carbon

• Current understanding suggests fungi are more important than bacteria for carbon sequestration in soils:

1 F i t C i th i bi th b t i1. Fungi store more C in their biomass than bacteria.

2. Fungal metabolites/by‐products are more resistant to degradation.

3. Fungal hyphae promote soil aggregation which physically protects soil organic matter.

* Rillig, M.C. & Mummey, D.L. (2006). Mycorrhizas and soil structure. New Phytologist .171: 41–53* Six, J., Frey, S.D., Thiet, R.K & Batten, K.M. (2006). Bacterial and Fungal Contributions to Carbon Sequestration in Agroecosystems. Soil Sci. Soc. Am. J. 70:555–569.

Mycorrhiza and Glomalin

• AMF also produce an extremely stable compound called glomalin which may resist degradation for up to 40 years*.

• Glomalin is a sticky sugar‐protein which also improves soil aggregation and protects other soil organic matter.

* Six, J., Frey, S.D., Thiet, R.K & Batten, K.M. (2006). Bacterial and Fungal Contributions to Carbon Sequestration in Agroecosystems. Soil Sci. Soc. Am. J. 70:555–569* Wright, S.F. and Upadhyaya, A. (1996) Extraction of an abundant and unusual protein from soil and comparison with hyphal protein of arbuscularmycorrhizal fungi. Soil Science 161: 575–586.

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MICROBIAL AND FUNGALBY‐PRODUCTS GLUE

SOIL PARTICLES TOGETHER

SOIL IN DISPERSED STATE

SOIL IN AGGREGATED STATE

Fungi:Bacteria and Carbon Sequestration

Bacterial Biomass

CO2

Less

Stable C CO2

C InputsStable C 2

Fungal Biomass

CO2

More

Stable CGreater C

Sequestration

‐ Root exudates‐ Plant residues‐ Compost/Manures‐ Green manures

Carbon Protection• The most important ways to preserve soil carbon is to protect it once it has been sequestered!

• Maintaining soil aggregation critical to soil carbon protection.

Mycorrhiza and Soil Structure

• Soil structure is influenced by many factors!

• A long term study found a highly significant correlation with AMF abundance and soilaggregation.gg g

• They also found fungicide applications reduced AMF and water‐stable macroaggregates.

* Wilson, G.W.T., Rice, C.W., Rillig, M.C., Springer, A. and Hartnett, D.C. (2009) Soil aggregation and carbon sequestration are tightly correlated with the abundance of arbuscular mycorrhizal fungi: results from long‐term field experiments. Ecology Letters. 12(5):452–461.

Enhancing AMF ‐ Environment

• Soil Cover – always maintain host plants and a

flow of root exudates (food source) for AMF.

• Avoid fallows or keep them as tight as possible if

unavoidable.

• Mineral Balance – optimise plant nutrient

requirements to ensure adequate photosynthesis

and hence C flow to roots.

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Enhancing AMF – Fertility Ley• Fertility building leys are an ideal method to repopulate soils with AMF.

• Dense seeding rates encourage AMF spread throughout the field through root‐root contact.

• Uncultivated period of time is ideal for AMF establishment.

• Choose strongly mycorrhizal legumes – clovers, medics and vetches.

• Available P (from AMF) enhances N2 fixation if using legumes.

Cultivation• In the absence of inversion and with minimal soil disturbance:– Soil structure is maintained/erosion reduced.

– Soil‐water dynamics are improved (infiltration, WHC).

– Soil biology (earthworms, fungi) improve.

– Soil organic carbon (SOC) levels improve (?).

Tillage and Carbon• Research has highlighted that when compared to conventional tillage, no tillage: – Increases soil C

– Increases C residence time

– Improves the quality of surface layer

• However, this research only investigated surface horizons!

Tillage and Carbon

• More recent research looked at SOC deposition at depth and found no significant difference in total C between till vs no‐till.

• The distribution of that C however, was altered:– No‐Till accumulates C on surface horizon.– Conventional tillage incorporates C more evenly throughout the profile.

* Chatterjee, A. & Lal, R. (2009) On farm assessment of tillage impact on soil carbon and associated soil quality parameters. Soil and Tillage Research. 104: 270‐277.* Salvo, L., Hernandez, J. & Ernst, O. (2010) Distribution of soil organic carbon in different size fractions, under pasture and crop rotations with conventional tillage

and no‐till systems. Soil and tillage Research. 109:116‐122.

Cultivation• There is one thing we know without a shred of doubt:

• Not a single method of cultivation improvessoil aggregation!

• Aggregation is key for soil structural stability and SOC protection and AMF health.

• Conservation tillage must be considered/investigated/integrated or offset!

• Practicalities?

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To till or not to till?

• Some evidence suggests that…

• soil amendments such as animal and green manures; and

• plant diversity (crop rotations/mixedplant diversity (crop rotations/mixed cropping)

… may be more important in maintaining soil microbial activityand diversity than conservation tillage in monocultural systems.

* Dick, R.P. (1992). A review: long‐term effects of agricultural systems on soil biochemical and microbial parameters Agriculture, Ecosystems & Environment. 40 (1‐4): 25‐36.

Crop residuesCover Crops

Animal manureCrop residues

20 years of similar tillage intensity and C inputsbut contrasting types of organic inputs

Soil Carbon Sequestration• It is estimated that there is presently 3‐4 times more carbon stored in soils than there is in all terrestrial plant biomass.*

• Hence, soil represents a vast potential for i b ( i ll id i SOCsequestering carbon (especially considering SOC

have declined since intensive agriculture).

• Agro‐ecosystems must play a key role in this process.

• Understanding soil microbial processes in our agricultural soils is fundamental to achieving this.

* Stockman, U. (2011) Managing the soil‐plant system to mitigate atmospheric CO2. Soil Carbon Sequestration Summit

* Powlson, D. S., Whitmore, A.P. & Goulding, K .W.T. (2011) Soil carbon sequestration to mitigate climate change: a critical re‐examination to identify the true and the false. European Journal of Soil Science (62) 42–55.

Future Research

• What are the most suitable methods to: – Optimise microbial abundance in agro‐ecosystems?

– Optimise sequestration of plant biomass and/or root exudates into the stable carbon pool?

– Optimise microbes’ ability to acquire and supply nutrients?p y q pp y

• What are the optimum soil characteristics that shift microbial communities toward these processes (chemistry, physics, biology)?

• What are the key microbe groups that are most efficient for these processes and how best to use them in agro‐ecosystems?

Sustainable Agriculture

• A quote to summarise:

“The achievement of sustainable agriculture was ‘let down’ in the 20th century when

h f d l il h i lresearch focused strongly on soil chemical and physical factors, and neglected biological factors”

• Lets not waste anymore time!

* Sherwood, S. & Uphoff N. (2000) Soil health: Research, practice and policy for a more regenerative agriculture. Applied Soil Ecology. 15:85‐97.

Thank you

Summary and Questions?Questions?

[email protected]

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Nutrients and Carbon

• Every single time any nutrients are applied, they should be combined with a carbon source (liquid or dry).

• The carbon binds to the nutrients• The carbon binds to the nutrients chelating and complexing them, stabilising them, buffering them and improving uptake by plants.

Carbon Protects Biology• Research findings investigating soil life recovery after: – Fumigant application vs

– Fumigant + composted manure

• Fumigant: little recovery of soil function 12 weeks later.

• Fumigant + compost: normalbiological activity observed within 8‐12 weeks.

* Dungan, R.S., Ibekwe, A.M. And Yates, S.R. (2003). Effect of propargyl bromide and 1,3‐dichloropropene on microbial communities in an organically amended soil. FEMS Microbiology Ecology. 42: 75‐87.

Fertilisers – Organic vs Inorganic

• 200 kg/ha of nitrogen was added to the soil in the form of:– Ammonium nitrate, or

– Dairy manure

• Soil respiration and enzyme activity were higher in the organically amended soil*.

• Increasing carbon in your fertiliser program will increase microbial health irrespective of nutrient content.

* Marinari, S., Masciandaro, G., Ceccanti, B. and Grego, S. (2000) Influence of organic and mineral fertilisers on soil biological and physical properties. Bioresource Technology. 72: 9‐17.

Nutrients and Biology

• Excess nutrients can interfere with healthy soil biological function.

• Nutrients should be applied in a timelyand appropriate fashion to ensureand appropriate fashion to ensure surplus nutrition is not flushing through the system having a negative impact on soil life.

Organic and Inorganic

• Organic inputs buffer Inorganic inputs.

• The message is simple:

• Increasing carbon in your fertiliser programs will increase nutrient efficiency and microbial h lth tt h t d ti thealth no matter what production system you use!

• Just combine it with Carbon!

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The Biological Link to Foliar Applied Nutrition

• Foliar applied nutrients is actually all about microbial stimulation.

• When calculated back, the amount of nutrient applied via foliar applications is very small.

• But those small amounts stimulate photosynthesis and hence sugar production.

• Those sugars etc are sent to the roots and exuded to feed soil microbes.

• Soil microbes in return, solubilise much more nutrient from the soil and feed the plant.

Photosynthesis

6CO2 + 6H2O ‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐> C6H12O6 (sugar) + 6O2

minerals/enzymes• Complex sugars• CarbohydratesA i A id

C6H12O6 (sugar) ‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐>minerals/enzymes

• Amino Acids• Proteins• Fats & Oils• Hormones• Vitamins• Phyto‐nutrients• Protective Compounds

/ y

• Bacterial Foods– Simple sugars and carbohydrates

– Molasses, Sugars, Fulvic acid

• Fungal Foods– Complex carbohydrates and complex organic molecules

– Fish Hydrolysate, Fish Oils

Feeding Soil Microbes

– Fish Emulsions– Seaweed/Kelp Extracts

• Protozoa Foods– Bacteria

– Seaweed/Kelp Extracts– Humic acid

• Nematode Foods– Bacteria and Fungi

• Earthworm Foods– Protozoa and Fungi

Biofertilisers• Apply new populations of soil organisms

– Composts

– Liquid Compost Extracts

– Commercial inoculums

– Manures


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Biological Disease Management• A combination of:

– Nutrition• Balanced nutrient supply

• Management of key ‘disease fighter’ nutrients

– Biology– Biology• Viable, active and diverse population

• Key antagonistic species

– Crop Management• Inducing resistance

– nutrition and biology

Nutrition• Plants require a balanced supply of allmineral nutrients.

• Macro and micro nutrients are equally important.

N t i t th t l t f h t th i• Nutrients are the catalyst for photosynthesis –the process by which the plants immune system is fuelled.

Photosynthesis

6CO2 + 6H2O ‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐> C6H12O6 (sugar) + 6O2

minerals/enzymes• Complex sugars• CarbohydratesA i A id

C6H12O6 (sugar) ‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐‐>minerals/enzymes

• Amino Acids• Proteins• Fats & Oils• Hormones• Vitamins• Phytonutrients• Protective Compounds

/ y

Disease Fighters

• Although a balanced nutrient supply is necessary, key ‘disease fighting’ nutrients can also be specifically and intentionally managed:– Silicon

– Calcium

– Potassium

– Copper

– Nitrate (excess)

Disease Prevention• Competitive Exclusion

– Competition for space, food sources, nutrients etc

• Antagonism/Antibiosis– Production of antibiotic, ,antifungal and other inhibitory compounds

• Predation/Parasitism– Direct predation of disease causing organisms

• Induced Resistance

What happens when microbes are applied?

• The increase in microbial biomass on root and leaf surfaces:– Protects the plant

– Feeds the plant (N‐fixation etc)– Feeds the plant (N‐fixation etc)

– The plant feeds the microbes

• Induces resistance– Microbes release compounds that turn the plants immune system on strengthening its disease resistance.

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Early Blight

Pathogen Challenged

Tomato

Unchallenged Tomato

6 defense genes were activated

Biology and Disease• Plants can ‘pick and choose’ different microbes species they need around root systems.

• Plants under foliar pathogen attack have been shown to release the root exudate, malic acid – a known food source for Bacillus subtilis.

• B. subtilis then colonises the root system and triggers the plants immune system further to aid the attack against the foliar pathogen.

* Thimmaraju Rudrappa, Kirk J. Czymmek, Paul W. Paré and Harsh P. Bais (2008) Root‐Secreted Malic Acid Recruits Beneficial Soil Bacteria. Plant Physiology November (148) 3: 1547‐1556

Photosynthesis and Plant Defence

• Nutrients catalyse photosynthesis.

• Photosynthesis fuels the plants own protective defence systems.

P i D f h i l• Passive Defences – physical

• Active Defences – biochemical

Induced Resistance ‐How it Works

SAR ISR

A weak signal or lack of energy to respond to pathogen signal causes infection.

Barley sprayed with ISR elicitor (yeast derived). Far right = control, left 3 sets treated with different elicitor formulations

How do we ‘Induce’ Systemic Resistance?

• Kelp ‐ cytokinins involved in ISR

• Silicon – promotes accumulation of phenolics in infected host epidermal cells & increases number of cells that respond.

• Promote soil life diversity ‐many ISR responses happen at the root/soil interface with specific microbes such as:

• Bacillus sp• Trichoderma sp• Pseudomonas sp• Compost teas – species & exudate variety

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The Argument against Chemical Pest Control

• By using a chemical to control a pest, the rich suite of biological compounds that the plant would have naturally synthesised in order to protect itself will not be produced.

• Therefore flavour, nutritional & medicinal properties of produce will be compromised.produce will be compromised.

The beneficial bio‐chemicals are replaced by potentially toxic man made chemicals. You are in essence restricting the full expression of the plant’s potential.

• Minerals?– Ca, Si, K, Cu, NO3

‐

• Microbes?– Diversity/specific species

In Summary

• Soil/Plant Balance?

• Ask the plant what it requires?

• Watch and listen to what the plant is telling you.

• Learn from your mistakes.

soil biology: what is a healthy soil? -...

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