ROLE OF SOIL MICROBIOLOGY IN ORCHARD SYSTEM FUNCTION...
Transcript of ROLE OF SOIL MICROBIOLOGY IN ORCHARD SYSTEM FUNCTION...
ROLE OF SOIL MICROBIOLOGY IN ORCHARD SYSTEM FUNCTION & PRODUCTIVITY
Mazzola, M
USDA-Agricultural Research Service, Wenatchee, WA
KEYWORDS microbiome, rhizosphere, suppressive soils, soil-borne pathogens, nutrient cycling, system resilience, “soil health” ABSTRACT Soil microbiology significantly influences the function, efficiency, resilience, sustainability and productivity of all crop production systems including tree fruit orchards. These contributions may be positive, for instance in the cycling and retention of nutrient inputs, or may be negative as is the case for plant/soil-borne pathogen interactions. The composition and activity of the soil and rhizosphere microbiome (entire microbial community) will be determined by numerous factors including environment, management practices and the plant host. However, the microbiology that directly influences root health, and therefore most directly plant productivity, resides in the rhizosphere, a habitat which encompasses the narrow region of soil that is directly influenced by root exudates. The rhizosphere microbiome is vastly different from the same community found in bulk soil (non-rhizosphere soil) in terms of both composition and function. As such, while the management of the rhizosphere microbiome may depend upon indirect actions such as the application of a soil amendment, it can also rely on direct management through selection of the appropriate plant genotype. Our knowledge of how management, or host, influences the form and function of the rhizosphere microbiome has been advanced by novel technologies that enable us to “see” and monitor the entire community whereas in the recent past we were limited to those organisms that could be cultured or were more obvious in their function. As a result, we are well aware of the importance of the well-studied mycorrhizal fungi which extends function of the root by developing relationships that increase phosphorus availability to the plant and may also contribute to root health by limiting pathogen attack. Additional less well known but important components of the rhizosphere microbiome have been shown to enhance drought tolerance, induce flowering, and stimulate root formation. Benefits resolved from active management of the rhizosphere microbiome are most evident in terms of utilizing this microbiological resource for the control of soil-borne plant diseases. The use of biologically active soil amendments and employment of a specific host genotype (rootstock) can result in the recruitment of a specific rhizosphere microbiome which acts as the first line of defense against attack by root infecting pathogens. The capacity to effectively utilize the microbiology resident to orchard soil ecosystems will rely upon clearly defining management goals and greater understanding of the identity and function of the innumerable microorganisms that reside in the plant rhizosphere.
Mark MazzolaUSDA-ARS
Wenatchee, Washington, USA
Role of Soil Microbiology in Orchard System Function & Productivity
A Few Trillion Friends YouNever Knew You Had!
life.org.uk
The Plant Microbiome
Microbiome: The collective of microorganisms that exist in a given environmental niche.
In humans might be considered an additional organ.Gut microbiome-required for metabolismSkin microbiome-protect from pathogensHuman microbiome-exerts control upon the immune system
Phyllosphere microbiome
Rhizosphere soil/rootmicrobiome
Plant Root Development/Function:
Certain protozoa and bacteriadirectly stimulate apple root generation
(Naegleria americana)
Protozoa effects on roots (- protozoa)
(+ protozoa)
What role does microbiology play in crop performance?
Nutrient Cycling/Availability:
Organic matter decomposition/substrate availability
Enhanced P availability (mycorrhizal fungi)
Iron chelation/availability (Pseudomonas)
Nitrogen fixation: symbiotic (Frankia, Rhizobia) or free living (Azospirillum)
What role does microbiology play in crop performance?
Resilience to abiotic stress
Rhizosphere microbiome plays a role in drought tolerance.
What role does microbiology play in crop performance?
Drought sensitive grape rootstocks inoculated with a microbiome from a drought resistant rootstock grew 20-40% greater than non-inoculated plants when grown under drought conditions (ROLLI et al., 2015. Env. Microbiol.)
Program flowering time
What role does microbiology play in crop development?
Rhizosphere microbiomes collected from early and late flowering mustard
These microbiomes were then used to inoculate cultivars
All plants showed a shift in flowering time corresponding with inoculationof an early or late-flowering microbiome
Rootstock genotypes possess different microbiomes?
Could that information be used to optimize flowering time?
(Panke-Buisse et al., 2015. ISME J.)
Micro-site-specific application of rootstock
(e.g. cold-pocket)
What role does microbiology play in crop performance?
Suppress Disease
Disease conducive Disease suppressive
• Strategies to direct soil/rhizosphere microbiology
Tillage
Fertility management
Amendment based selection
Compost
Green manures
Bio-based waste products
Plant driven selection
How to manage the protozoa-root promoting resource?
Bacteria are primary food source
Naegleria americana
10 mm
Naegleria americana
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Canola seed meal amendment amplifies prey and predator densities in rhizosphere soils
Bacterial density
Cohen and Mazzola, 2006
canola meal
mineral fertilizer
Rhizosphere specifically recruits and supports microbes
Rhizo-deposition accounts for 30-40%
of total OM input to soils
Organic acids
polysaccharides
amino acids
Fatty acids
enzymes
Plant-driven modification:
How to manage the rhizosphere microbiome?
NextGen sequence analysis demonstrates that the rhizosphere microbiome recruited from the same soil system differs with rootstock genotype.
M.26 G.210
Community similarity
M.26 ‘recruits’ Rhizobium radiobacter(Agrobacterium tumefaciens), causal agent of crown gall disease, better than G.210
Does rootstock genotype influence rhizosphere microbiome?
Mazzola & Reed, unpublished
Do rootstocks attract different rhizosphere microbiomes that influence subsequent tree health and performance?
Mazzola & Reed, unpublished
G.41 G.935 M.9 Past.
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G.935
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Apple growth and disease were correlated with the rhizosphere microbiome conferred by the previous rootstock.
Do different rootstocks attract different rhizosphere microbiomes that influence subsequent tree health and performance?
Mazzola & Reed, unpublished
Management of the microbiome for disease suppression:
Microbial function vs. Microbial diversity
Increased microbial diversity is associated with enhanced soil system sustainabilityand resistance to disturbance.
Anaerobic Soil Disinfestation (ASD)
Suppression of soil-borne pathogens under anaerobic conditions
Treatment protocol:
I. Incorporate readily available carbon source
II. Irrigate soil to field capacity
III. Tarp with virtually impermeable film
Are specific changes of the soil microbiome associatedwith ASD efficacy?
ASD-Molasses-no effect on yieldASD-Rice bran: significant yield increases
Muramoto, Shennan and Mazzola., unpublished
UTC=controlRB=rice branMol=molasses
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ASD-Rice Bran
Rice Bran
Control
ASD-Mol
NMDS analysis; Bray-Curtis similarity measure
Bacterial Community Similarity: Analysis of NextGen Sequence Data
Are specific biological changes associated with ASD efficacy?
ASD-RB+Mol
Mazzola et al., 2015
Are specific biological changes associated with ASD efficacy?
ASD Molasses-no effect on yield
Bacterial Community Composition Divided by Phyla and Class
Treatment performance
associated with
abundance of specific
bacteria:
Chryseobacterium,
Chitinophaga, Cytophaga,
Sphingobacterium, Flavobacterium
ASD
rice branASD
molasses
ASD
RB/MolRice branControl
8-12% 25-35% 20-32% 14-22% 8-11%
ASD-Rice bran: significant yield increases
Mazzola et al., 2015
Treatment Number of species
ASD-molasses 563b
ASD-Rice bran 472a
Control 523ab
Bacterial diversity
The effective treatment had possessed lower speciesdiversity than the non-effective treatment
Mazzola et al., 2015
Anaerobic Soil Disinfestation (ASD):Identification of effective carbon input (compost or grass)
Hewavitharana, Rudell and Mazzola, 2014
ASD-grassASD-compost
Treatment Number of species Chao1 (diversity) Shannon H (diversity)
ASD-compost 151±14 174±20 4.35±0.34
ASD-grass 54±6 71±8 2.30±0.26
Control 140±7 163±9 4.22±0.15
Fungal Diversity
www.natureworldnews.com
Hewavitharana and Mazzola, 2015
Composition of apple rhizosphere microbiome:
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= control
Specific biological changes areassociated with ASD efficacy
Take Home:
• Microbiology influences many widely recognized (P-acquisition) and relatively unknown (flowering time) attributes of plant development and productivity
• System sustainability/resistance…..more about microbial “function” rather than “diversity”
• Plant genotype can be a powerful tool in managing soil/rhizosphere microbiome.
• Management of the soil/rhizosphere microbiome needs to be undertaken in context of goals and orchard life stage
Acknowledgements:
Organic Grants Program
Methyl Bromide Alternatives Grants Program
Areawide Pest Management Grants Program