Download Lecture 11, February 24, 2016 - EPSc 413 Introduction to Soil Science

Lecture 11: Soil Flora: Roots and
Fungi; Soil Microbes
Soil Food Web
Plant Roots
Plant Roots
• Occupy ~1% of soil by volume
• Responsible for 25-30% of
respiration in soil
• Supply much of the carbon and
energy for soil fauna and
microflora
• May extend to depths of ~5 m
• Move through soil following path
of least resistance: between peds
and along cracks
The Rhizosphere
Rhizodeposition
Rhizodeposition
• Low molecular weight organic compounds exuded by roots
– Organic acids, sugars, amino acids, phenolic compounds
• High molecular weight organic compounds (mucilage)
secreted by root cap and epidermal cells
– Combines with clay and microorganisms to form mucigel
– Mucigel lubricates root, improves contact with soil, and provides a
home for soil microorganisms
• Root cells continuously shed into soil
• A substantial amount of the organic compounds sent to roots
are deposited in soil through these three mechanisms
– Provide OM and nutrients for other life; the rhizosphere contains 2-10
times as many microorganisms as bulk soil
Complex Signaling and Feedback Loops
in the Rhizosphere
Root exudates (1) stimulates growth of bacteria (2) which are eaten by
protozoa (3); Ammonia excreted by protozoa stimulates nitrifying bacteria (4);
Signal molecules like NO3- are released (5), inducing lateral root growth (6),
leading to release of more exudates (7), subsequent bacterial growth (8), etc.
Image from the European Soil Atlas
-10,000 kPa
-700 kPa
-100 kPa
-80 kPa
-60 kPa
-30 kPa
Water
Transport
in Plants
via a
Gradient in
Water
Potential
Uptake of Water by Plants May Dry
Subsoil
Soil water depletion in summer caused by
water uptake by plants and transpiration
Water Uptake by Roots in Soil:
Root-Water Contact Required for Uptake
Wet Soil (Field Capacity)
• Root expanded
• Substantial water-root contact
• Easy water uptake
Dry Soil (Wilting Coefficient)
• Root contracted
• Little root-water contact
• Water unavailable
Mechanisms of Plant Water Supply
High ψ
Low ψ
Capillary Action
• Uptake by plant roots
reduces the water content
in the surrounding soil
• This drives unsaturated flow
in the direction of the root
Root Extension
• Roots extend to sources of
water
• Only limited by physical
barriers, like compacted
zones or fragipans
Key Concepts on Plant Roots
• Only the roots of plants interact substantially with
soil components
• Roots are the largest single respirers in soil and are
the primary source of organic carbon
• The Rhizosphere is the region near the soil-root
interface with high biological activity
– Rhizodeposition provides a food source for
microorganisms in the rhizosphere
• Water uptake by plant roots is controlled by water
potentials and affects soil hydrology
Soil Fungi
Soil Fungi
• Possibly the most important and diverse class of soil
organisms
• Dominate the biomass in some soils
• Eukaryotic heterotrophs, aerobic, microscopic*
• Decomposers, Mutualists, and Parasites
• Many fungi are filamentous
– Individual filaments are called hyphae
– Many hyphae may twist together to form mycelia
– Reproduce by releasing spores from fruiting bodies
* Fungi can form visible structures (mushrooms, mycelia), but they spend much of their life
in microscopic form
Armillaria solidipes: Humungous
Fungus
• Possibly the largest organism on
Earth is the honey mushroom
fungus
– 1900 to 8500 years old (estimates
vary)
– Occupies 2400 acres in a forest in
Oregon
– Weighs at least 150 metric tons
• Unclear if it is truly a single
organisms or a clonal community
Fungal Activities in Soils
• Decompose virtually all
organic compounds
• Form humus
• Stabilize aggregates
• Continue to decompose
OM after other
decomposers cease
• Recycle nutrients
• Directly impact soil ecology
Fungal Hyphae
• Microscopic, thinner than root hairs
Photo from USDA
Fungal Mycelia
• Intertwined hyphae allow fungus to reach up into
litter layer
Fruiting Bodies
• Macroscopic reproductive structures of
essentially microscopic fungi
Fungal Life Strategies
Decomposers (Saprobic Fungi)
• Decompose dead organic matter, producing fungal
biomass, CO2, and organic acids
• Breakdown complex materials like cellulose and lignin
– Cellulose: Polysaccharide found in all plants
– Lignin: Organic polymer, makes wood hard
• Important for mobilizing and retaining nutrients in
soil
• Increases humic acid-rich soil organic matter
• Primary decomposers in forests
Saprobic Fungi at Work
Photo from USDA
Parasitic Fungi
• Attack and kill living plants and
animals
• Root pathogenic fungi cause
major agricultural losses
• Nematode trapping fungi kill
parasitic nematodes
Sunflower Infected by
Verticillium dahliae
– Bad for nematodes, good for plants
• Fungi that feed on insects may be
useful biological control agents
Photos from Colorado State University and the University of Guelph
Chinch Bug Infected by
Beauveria bassiana
Mycorrhizal Fungi
• Form symbiotic relationships with plant roots
– Most plants have mycorrhizal associations
– Some plants cannot survive without mycorrhizae
– Each fungus species generally only colonizes one plant species
Mycorrhizal Fungi-Plant Interactions
• Mycorrhizal fungi obtain sugar directly from plants
• Mycorrhizal hyphae extend farther into soil and into
smaller pores than root hairs
–
–
–
–
Increase absorption surface area by a factor of 10!
Enhance nutrient (esp. P) and water uptake
Protect plants from soil toxins
Protect plants from infection by producing antibiotics,
altering the root epidermis, and competing with pathogens
for site on root surfaces
• Fossil evidence for mycorrhizal fungi 400 million
years ago
Endomycorrhizae
• Fungal hyphae penetrate cortical root cell walls
• Arbuscular mycorrhize (AM) most common group
(found in 80% of vascular plants)
– Form small, highly-branched structures called arbuscules
– Usually also form vesicles
– Most native plants and agricultural crops have AM
AM Fungi Physiology
• AM fungi begin life through spore germination in soil
– Independent of plant roots, but root exudates can increase
germination rate
• AM fungi then extend hyphae through soil in search
of a host root
– Hyphae display chemotaxis: They can chemically sense the
presence of host roots and low P conditions and alter their
growth, increasing hyphae and the degree of branching
• Once in contact with a root the hyphae colonize
– Further growth into the root requires chemical signals
from the plant
– The plant adjusts root cell structure for the fungus
Ectomycorrhizae
• Primarily associated with trees and shrubs
– Present in ~10% of all plant families
• Coat the surfaces of feeder roots
– Do not penetrate cells
– Stimulated by root exudates
Photo from USDA
Ectomycorrhizal Fungi
• Unlike AM fungi, ectomycorrhizae
typically are both saprotrophic and
biotrophic
– Saprotrophic: Obtain energy from
decomposing organic matter like
wood and leaf litter
– Biotrophic: Obtain energy from
symbiotic host
• Ectomycorrhizal fungi are known to
lure and trap organisms like
springtails for their nitrogen
Ectomycorrhizal fungi coating
a root tip
Importance in Phosphate Uptake
No Addition
Phosphate
Phosphate + Mycorrhizae
• One of the most important roles of mycorrhizal fungi
is their enhancement of P uptake by plants
– Transport P over substantial distances to roots
Hyphal Interconnections
• Some mycorrhizae
can link plants to
enhance nutrient
availability
– AM fungi encourage P
and N exchange
between species
– Ectomycorrhizae
shown to transfer
carbon between trees,
likely coupled to
nutrient exchange
Key Concepts in Soil Fungi
• Soil fungi are essential to soil ecosystems: Primary
decomposers, form soil OM from plant litter, stabilize
soil aggregates, recycle nutrients
– Most important feature of soil fungi are their hyphae
• Fungi are the main organisms that breakdown
cellulose and lignin from plants in aerated soils
• Mycorrhizal fungi are symbiots with plant roots
– Obtain sugars from plants
– In return enhance nutrient and water uptake and protect
the plant from bacteria, predators, and parasites
Key Concepts in Soil Fungi
• Two classes of mycorrhizal fungi:
– Endomycorrhizae: Fungal hyphae directly colonize
root cells; Arbuscular mycorriza (AM) are the most
common group, found in 80% of vascular plants
– Ectomycorrhizae: Coats root surface but does not
penetrate cells; Associated with many trees and
shrubs; Can also gain energy from OM
decomposition in soil without being associated
with a plant
Soil Bacteria and Archaea
Soil Prokaryotes: Archaea and Bacteria
• Most genetic diversity on
earth (and in soils) is in
prokaryotic life
– Bateria 90% microbial
biomass in soils
– Archaea 10% of microbial
biomass in soils
• Small (0.5 to 5 um)
• Billions to trillions in one
gram of soil
• Microbial community
reflects soil environment
Microbes are Everywhere
Microbial Metabolisms
• All metabolic pathways present in bacteria and
archaea
• Heterotrophs dominate soils
– Breakdown easily decomposed organic matter
• In anoxic soils, almost all decomposition is
performed by prokaryotes
– Also produce methane and nitrous oxide, greenhouse
gases, in anoxic soils
Nitrogen Fixation: N2 Gas to Usable Nitrogen
Rhizobium root nodules on soybean roots
Desert soil cyanobacteria
• Only prokaryotes are capable of fixing nitrogen
–
–
–
–
Critical to the existence of higher life forms
Rhizobium: agricultural soils
Actinobacteria: forest soils
Cyanobacteria: rice paddies, wetlands, deserts
Photo from USDA and Garcia-Pichel et al. (2001) Appl. Environ. Microbiol. 67, 1902-1910
Actinobacteria (Actinomycetes)
• Filamentous, initially though to be fungi
• Important in breaking down OM
– Capable of decomposing most resistant compounds:
cellulose, chitin, phospholipids
• Dominant in later stages of decay
Microorganisms in the Rhizosphere
• The rhizosphere contains abundant microbes, up to
109 cells/g soil
• Plant promote the growth of favorable microbes by
releasing root exudates
• Mycorrhizae often modify the plant root exudates to
promote bacteria favorable to post-colonization
conditions
– Enhances the availability of N from N-fixers
– May be important for promoting plant symbiosis with Nfixing microorganisms
Microbiotic Crusts
• Form on undisturbed arid and semi-arid soils
– Dark colored crusts between clumps of grass
• Mutualistic association of algae or cyanobacteria,
fungi, moss, bacteria, lichens
• Protect soil again wind and water erosion
• Improve arid-region ecosystem productivity by:
–
–
–
–
Conserving and cycling nutrients
Fixing nitrogen (cyanobacteria)
Increasing infiltration/reducing evaporation
Producing organic matter through photosynthesis
More Microbiotic Crusts
Photo from USDA
Key Concepts in Soil Microbes
• Bacteria and archaea are the source of much of
soil biomass and genetic diversity
– Display all known metabolic pathways
– Breakdown easily decomposed OM
– Dominant decomposers in anaerobic soils
• Prokaryotes are the only nitrogen fixers on Earth
– Rhizobium in agricultural and grassland soils
– Actinobacteria in forest soils
– Cyanobacteria in rice paddies, wetlands, deserts
Key Concepts in Soil Microbes
• Actinobacteria: Filamentous bacteria,
important decomposers
• Microorganisms are abundant in the
rhizosphere
• Microbiotic crusts:
– Complex association of algae or cyanobacteria,
fungi, moss, bacteria, lichens
– Protects arid soils from erosion
– Improves arid-region productivity