Soil Biotaplants, fungi, microbes, animals

Image: http://www.flickr.com/photos/soilscience/5094927226/ by Soil Science @ NC State. License: CC BY 2.0.

If you remove the 2 scientists and the crop residue, there are still billions of organisms in this picture. Where?

What is soil? Or what isn’t soil?

Illustration by Jon Davis, the author of this presentation

Soil is…

• a habitat• a community• a food web• structured• a resource• a water and nutrient pool• “wealth of a civilization”

Image: http://www.flickr.com/photos/soilscience/5094328371/ by Soil Science @ NC State

Soil is…

• a habitat• a community• a food web• structured• a resource• a water and nutrient pool• fragile• “wealth of a civilization”

Image: http://soils.usda.gov/sqi/concepts/soil_biology/images/A-3.jpgcreated by the USDA and in the public domain.

Plant roots

• Absorb water + nutrients• Need oxygen• Grow throughout warm

seasons• Senesce during cool seasons• Provide food and organic

matter when consumed• stabilize loose soils• break up compact soils• Serve as sites of symbiotic

colonization for important fungi and bacteria

• Structure the “rhizospere”

Image: http://www.flickr.com/photos/peter_curb/5987434485/ License: (CC BY 2.0)

Fine roots

• Roots <2mm in width are considered fine roots and they grow into small spaces in the soil seeking water and nutrients

• These are augmented by the growth of root hairs with are even smaller and explore even smaller spaces

Image http://www.flickr.com/photos/95962343@N04/9079449856/ by Jon Davis, the author of this presentation. License CC BY-SA 2.0

Fine roots and root hairs

Image by Jon Davis, NCSSM, author of this presentation License: CC BY SA 3.0

Root hairs

Image by: http://www.flickr.com/photos/mag3737/1315360188/ by mag3737. License: (CC BY-NC-SA 2.0) Image: http://www.flickr.com/photos/thejcb/4077866037/ by thejcb License: (CC BY-NC-SA 2.0)

Fine roots and root hairs

Image from http://www.flickr.com/photos/ricephotos/8567104993/ by IRRI Images License (CC BY 2.0)

The rhizosphere

Image: http://commons.wikimedia.org/wiki/File:Rhizosphere.svg by Smartse. License: CC-BY-SA 3.0

A=Amoeba consuming bacteria BL=Energy limited bacteria BU=Non-energy limited bacteria RC=Root derived carbon SR=Sloughed root hair cellsF=Fungal hyphae N=Nematode worm

The rhizosphere

• This is the zone immediately around the root• This is the area of greatest biological activity in the

soil below the organic matter layer (O) • The wide array of organisms discussed in this

lesson are found here• The root provides carbohydrates to the microbes,

fungi and animals by exuding sugars or through the consumption of the roots/root hairs themselves

• This is where we will look for organisms

Soil fungi

Image by Jon Davis, NCSSM, author of this presentation. License: CC BY SA 3.0

Soil fungi

• Decompose organic matter, releasing the “mineral” forms of N, P, K and other plant nutrients into the soil solution.

• Terminology: Fungi can be in the form of familiar molds (and yeast), but in soil it is easier to see the threadlike hyphae with the naked eye.

Fungal hyphae

Image http://www.flickr.com/photos/myriorama/2334940947/ by myriorama License: (CC BY-NC-SA 2.0)

If hyphae are belowground, what is above ground? Mushrooms!

Image: http://www.flickr.com/photos/rmb3588photo/8033947949/ by rmb3588photo. License: (CC BY-NC 2.0)

Mycorrhizae• Mycorrhizae are fungi that live

symbiotically on plant roots and extend into the surrounding soil

• The symbiosis is mutualistic, both partners benefit

• The thread-like hyphae of mycorrhizae are much thinner than root hairs

• Thus they can exploit soil resources intensively and extensively (at a distance)

• Mycorrhizae bring nutrients to roots and receive sugars from the plants in exchange

• These symbioses are ubiquitous and ancient

Image: http://commons.wikimedia.org/wiki/File:Mycorrhizal_root_tips_(amanita).jpg from Wikipedia user Thergothon. License: (CC BY 2.5)

Endomycorrhizae

http://www.flickr.com/photos/96794162@N08/8953182093/ by Bio Slide (CC BY-NC-SA 2.0)

Also called Vesicular-Arbuscular (VA) mycorrhizae

Ectomycorrhizae

Image: http://www.flickr.com/photos/96794162@N08/8953182595/ by Bio Slides License: (CC BY-NC-SA 2.0)

Fungal hyphae grow along a root tip

Image by Jon Davis, NCSSM, author of this presentation. License: CC BY SA 3.0

Ectomycorrhizal hyphae extend out from a root

Image by Jon Davis, NCSSM, author of this presentation. License: CC BY SA 3.0

Mycorrhizae in agriculture

• Most crops have endomycorrhizal associations• Ectomycorrhizae are found on a few families of

woody plants• Mycorrhizae occur naturally and should be

protected (minimize antifungal fumigants)• Inoculation of seedlings with mycorrhizal fungi

may be very helpful in establishing them– especially after fumigation with fungicides– especially slower growing woody plants in nurseries.

Bacteria

• Bacteria are as ubiquitous in soil as they are in oceans… and in us!

• And they are diverse. Thousands of species and billions of individuals of bacteria may exist in a single gram of soil.

• In some soils they comprise half the biomass of soil.

Image: http://www.flickr.com/photos/thompsonrivers/4864622390/ by Thompson Rivers. License: CC BY-NC-SA 2.0

4 roles of bacteria in agriculture

• DecomposersThey digest simple compounds in organic matter and root exudates and this make it available to the organisms that eat bacteria

• Mutualistse.g. nitrogen fixing bacteria in root nodules on legumes

• PathogensThey kill plants, but also can be used to genetically transform plants (Agrobacterium tumefaciens)

• Autotrophse.g. cyanobacteria that can capture energy from the sun (appears as a green film on soils) e.g. nitrifying bacteria that can harvest energy from ammonium

Nitrogen fixing bacteria

• Abundant N2 in air is converted to NH3 (ammonia) • Common genus of N-fixing bacteria: Rhizobium.• Because oxygen is toxic these anaerobic bacteria, the

grow in closed chambers-- root nodules.• Leguminous species can be used as cover crops and

tilled under when mature to provide both N and organic matter.

• Common legumes and/or cover crops– peas, beans, alfalfa, clover, peanuts, vetch

Anaerobic root nodules containing N-fixing bacteria

Image: http://www.flickr.com/photos/45796762@N03/5160987294/ by IITA Image Library (CC BY-NC 2.0)

Roles of bacteria in the nitrogen cycle

Image: http://commons.wikimedia.org/wiki/File:Nitrogen_Cycle.svgby Johann Dreo License: CC BY SA 3.0

Nitrogen cycling in soils

• Ammonification: decomposer bacteria convert organic nitrogen (in proteins, DNA, RNA and proteins) to ammonia (NH3)

• Nitrification: nitrifying bacteria convert ammonia (NH3) to nitrite (NO2

-) and then nitrate (NO3

-)

• Nitrate (NO3-) can then be assimilated by plants

and used to make more DNA, RNA and proteins.

Protists

• Protists eat bacteria• Protists are eaten by

animals (e.g. nematodes) and thus energy moves up the food chain.

• Protists can be animal-like, plant like, fungal-like…

• Or none of the above… like slime molds!

• Slim molds are colonial protists

Amoeba

Slime Mold

Image: http://www.flickr.com/photos/aa3sd/4856471557/ by Paul Morris (CC BY-SA-2.0)

Image: http://www.flickr.com/photos/25898159@N07/2695978355/ by Proyecto Agua. (CC BY-NC-SA 2.0)

Earthworms

Image: http://www.flickr.com/photos/goosmurf/3828755105/ by goosmurf .License (CC-BY-2.0)

Earthworms…

• consume organic matter and soil• release castings that are soil aggregates• mix large amounts of soil (carry organic down

and bring mineral soil up)• create openings that permit the aeration,

water infiltration and root growth• Therefore they are very useful for creating a

soil structure that encourages plant growth.

Nematodes

• Very small (1mm) round worms

• There are many species and they are ubiquitous throughout the world.

• The eat bacteria and fungi and are eaten by larger nematodes and arthropods

• Root feeding nematodes can be serious crop pests. They also spread other pathogens between plants.

Image: http://commons.wikimedia.org/wiki/File:Soybean_cyst_nematode_and_egg_SEM.jpg Provided by the USDA in the public domain.

Myriapods

• Centipedes are carnivorous predators• Millipedes are herbivorous decomposers• Neither are serious pests and are often

beneficial

Image: http://www.flickr.com/photos/10728961@N02/3323015953/ by bramblejungle. License: CC-BY-NC 2.0 Image: http://www.flickr.com/photos/82624540@N00/337877683/ by Billy Smith. License: CC BY-NC-SA 2.0

Microarthropods

• Very important for decomposition and mineralization of organic matter

• Most common types: springtails and mites• Almost invisible to the naked eye• Collected with a Berlese funnel• Excellent indicator species of soil health

Microarthropods

Springtails Mites (and one ladybug)

Image: http://www.flickr.com/photos/32977858@N02/5871083123/ by servitude. (CC BY-NC-SA 2.0) Image: http://www.flickr.com/photos/arachnojoe/5514906579/ by Spider Joe (CC BY-NC 2.0)

“Macroarthropods”

• Larger than with microarthropods• More visible with the naked eye • Familiar animals: ants, beetles, pillbugs,

termints, grasshoppers, etc., and their nymphs• Like other soil animals, they alter soil structure

and drive nutrient cycling

How to collect soil arthropods

Image: http://www.flickr.com/photos/snre/6353807883/ by snre (CC BY 2.0)

Image: http://www.flickr.com/photos/snre/6353807425/ by snre (CC BY 2.0)

Image by Jon Davis, NCSSM, author of this presentation. License: CC BY SA 3.0

Planthopper nymph (Cixius sp.)

Image: http://soils.usda.gov/sqi/concepts/soil_biology/images/A-3.jpgcreated by the USDA and in the public domain.