role of soil microbiology in orchard system function...

ROLE OF SOIL MICROBIOLOGY IN ORCHARD SYSTEM FUNCTION & PRODUCTIVITY

Mazzola, M

[email protected]

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)


Resilience to abiotic stress

Rhizosphere microbiome plays a role in drought tolerance.


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)


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

0.1

1

10

100

1000

0 15 30 45

mp

n / g

DW

so

il x

10

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Time (d)

MP

N / g

DW

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il x

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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?


G.41 G.935 M.9 Past.

-0.4 -0.3 -0.2 -0.1 0.1 0.2 0.3

Coordinate 1

-0.32

-0.24

-0.16

-0.08

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G.935

G.41

M.9

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?


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

-0.24 -0.16 -0.08 0.08 0.16 0.24 0.32

Coordinate 1

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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


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


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:

-0.4 -0.3 -0.2 -0.1 0.1 0.2 0.3 0.4 0.5

Coordinate 1

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-0.16

-0.12

-0.08

-0.04

0.04

0.08

0.12

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=ASD grass

=ASD compost

= 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

role of soil microbiology in orchard system function...

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