Soil biology for soil health

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1 Soil biology for soil health Sarah Hargreaves, PhD PFI Annual Conference 2015 Healthy Soil for Health Crops Short Course

2 Outline 1. What is a microbe anyway? 2. Why do microbes matter? i.e. What do microbes do to promote to soil health? 3. What does a healthy microbial community look like? 4. How does what we do on our farms affect microbes? Nitrogen, tillage, crop choice & rotation 5. How do we measure soil microbes?

3 1. What is a microbe?

4 1. What is a microbe? (http://www.denniskunkel.com/)

5 100 million - 1 billion bacteria in a teaspoon of soil David Schefif

6 1. What is a microbe? https://sites.google.com/a/apaches.k12.in.us/mr-evans-science-website/fungi

7 1-100 yards of fungi in a teaspoon of soil Worldpress

8 2. Why do microbes matter? Microbes promote soil health in 3 ways: i) Biological ii) Physical iii) Chemical

9 2. Why do microbes matter? i) Biological: Microbes are a critical part of the soil food web

10 2. Why do microbes matter? ii) Physical: Microbes are important to the physical structure of soil Bacterial biofilms and fungal glomalin ( glue ) help bind aggregates together Fungal networks mycelia contribute to stabilization of aggregates

11 2. Why do microbes matter? iii) Chemical: Microbes perform important chemical transformations in soil Decomposition = microbial digestion

12 2. Why do microbes matter? iii) Chemical: Microbes perform important chemical transformations in soil Decomposition = microbial digestion Extracellular enzymes = Digestive enzymes Organic matter (dead leaves, roots, organisms) = Food

13 2. Why do microbes matter? Microbes perform important chemical transformations in soil Decomposition of organic matter via extracellular enzymes Mineralization or release Inorganic nutrients to plant and other microbes

14 2. Why do microbes matter? Microbes perform important chemical transformations in soil Decomposition of organic matter via extracellular enzymes Mineralization or release Soil organic matter formation Inorganic nutrients to plant and other microbes Nutrient and water retention Long-term suitability of soil to life (e.g. reduced soil erosion)

15 2. Why do microbes matter? Microbes perform important chemical transformations in soil Decomposition of organic matter via extracellular enzymes Mineralization or release Soil organic matter formation Inorganic nutrients to plant and other microbes Nutrient and water retention Long-term suitability of soil to life (e.g. reduced soil erosion)

16 3. What does a good microbial community look like? A diversity community of bacteria and fungi Diversity of functions Diversity of growth rates Why? Greater chance a plant will find a microbial friend Nutrient release evenly across a field and over a season Resistance, resilience and recovery

17 3. What does a good microbial community look like? More fungi than bacteria i.e. high fungal: bacterial ratios Why? Mycelium = decomposition and aggregate formation Slower growing = greater N retention and release Internet of the soil

18 Outline 1. What is a microbe anyway? Diversity of bacteria, archaea, fungi 2. Why do microbes matter? What do microbes do to promote to soil health? Integral to food web Help build soil structure Decompose organic matter into nutrients and soil organic matter 3. What does a good microbial community look like? Diverse, predominance of fungi

19 Outline 1. What is a microbe anyway? 2. Why do microbes matter? What do microbes do to promote to soil health? 3. What does a good microbial community look like? 4. How does what we do on our farms affect microbes? Nitrogen, chemical use, tillage, crop choice & rotation 5. How do we measure soil microbes?

20 4. How does what we do on our farms affect microbes? In general: Decisions to till, the type and amount of organic fertilizer, and crop choice and rotations act together to affect microbial communities. However, inorganic nitrogen and chemical use have effects on microbes that are hard to overcome, irrespective of other on-farm decisions.

21 4. How does what we do on our farms affect microbes? Fertilizer use Inorganic Microbial biomass, size of community Diversity Important groups of bacteria (Verrucomicrobia) Fast growing bacteria = fast release of nutrients Fungal: bacterial ratios Decomposition (i.e. nutrient release and SOM)

22 4. How does what we do on our farms affect microbes? Fertilizer use Inorganic Organic? Microbial biomass, size of community Diversity Important groups of bacteria (Verrucomicrobia) Fast growing bacteria = fast release of nutrients Fungal: bacterial ratios Decomposition (i.e. nutrient release and SOM)

23 4. How does what we do on our farms affect microbes? Tillage Disruption of soil structure Soil aggregates Turnover, aeration Microbial habitat Microbial stimuli

24 4. How does what we do on our farms affect microbes? Chemical use Most research is on glyphosate, and is still limiting. All or nothing response. Glyphosate is a potent microbiocide Root colonization by mycorrhizae Fungal spores Beneficial bacteria Pathogenic bacteria

25 4. How does what we do on our farms affect microbes? Crop species and rotation Different plant-microbe linkages Jim Richardson, National Geographic

26 4. How does what we do on our farms affect microbes? Crop species and rotation Plant growth Time

27 5. How do we measure soil microbes? i) Measure microbes directly: Ingham microscope method Microbial biomass Phospholipid fatty acids (PLFA) Diversity (DNA sequencing) ii) Measure what microbes do (decomposition, mineralization): Haney test

28 5. How do we measure soil microbes? Method What it tells you Price Difficulty Main advantage Service lab Ingham microscope method Coarse count of morphological groups of bacteria and fungi $ * Ease Microbial biomass Size (in carbon) of microbial community $ ** Long-term data to compare Phospholipid fatty acid Size of biochemical groups of bacteria and fungi; Fungal: bacterial ratio $$ *** Fungal: bacterial ratio is very good indicator of function Diversity Diversity of community; who s there $$$$$ ***** Detailed analysis Haney test Mineralization rates (digestion rates), products $$ ** Soil function; data to compare; standards

29 Outline 4. How does what we do on our farms affect microbes? Nitrogen has long-term affects on soil diversity Aggregate stability is critical to diversity Plant-microbe interactions are critical to diversity 5. How do we measure soil microbes? Measure microbes and/or what they do And many others...

30 I hope you know a little more about: 1. What a microbe is, 2. Why microbes matter, 3. What a good microbial community looks like, 4. How our farming affects microbes, 5. How we measure soil microbes

31 Caroline Homer 2011

32 Decomposition via extracellular enzymes Soil organic matter formation Mineralization Nutrient and water retention Long-term suitability of soil to life Release of inorganic nutrients for plant and microbial growth

33 2. Why do microbes matter? Microbes are responsible for important chemical transformations in soil release N - nitrogen P -phosphorus C - sugars decomposition

34 Microbial communities have spatial structure Plants, in part, structure microbial communities The rhizosphere ( soil gut ) is a hotspot for change Change in relative abundance Turner et al The ISME Journal, 7:

35 Corn Switchgrass Prairie?

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