The establishment of apple orchards as temperate forest garden systems and their

93 Pages·2015·1.77 MB·English

The
 establishment
 of
 apple
 orchards
 as
 temperate
 forest
 garden
 systems
 and

their
 impact
 on
 indigenous
 bacterial
 and
 fungal
 population
 abundance
 in

Southern
 Ontario,
 Canada

by

Paul
 Wartman

A
 Thesis

Presented
 to

The
 University
 of
 Guelph

In
 partial
 fulfilment
 of
 requirements

for
 the
 degree
 of

Master
 of
 Science

in

Plant
 Agriculture

Guelph,
 Ontario,
 Canada

©
 Paul
 Wartman,
 May,
 2015
ABSTRACT

THE
 ESTABLISHMENT
 OF
 APPLE
 ORCHARDS
 AS
 TEMPERATE
 FOREST
 GARDEN

SYSTEMS
 AND
 THEIR
 IMPACT
 ON
 INDIGENOUS
 BACTERIAL
 AND
 FUNGAL

POPULATION
 ABUNDANCE
 IN
 SOUTHERN
 ONTARIO,
 CANADA

Paul
 Wartman
  Co-­‐Advisors:

University
 of
 Guelph,
 2015

 Rene
 Van
 Acker

 Ralph
 Martin

This
  thesis
  investigated
  soil
  microbial
  abundances
  affected
  by
  different

ground
 management
 systems
 in
 establishing
 apple
 (Malus
 domestica
 cv.
 Idared,
 M9)

orchards
 in
 Ontario.
 Four

 treatments
 including
 forest
 garden
 systems
 with
 and

without
 compost
 (FGSC
 and
 FGS)
 and
 grass
 understory
 systems
 with
 and
 without

compost
 (GC
 and
 G)
 were
 established,
 sampled
 and
 analyzed
 over
 the
 establishing

two
 years
 for
 gene
 copy
 abundance
 of
 soil
 arbuscular
 mycorrhizal
 (AM)
 fungi,
 total

fungi,
 and
 total
 bacteria
 using
 quantitative
 real-­‐time
 polymerase
 chain
 reactions.

From
 Spring2013
 to
 Fall2014
 soil
 bacterial
 abundance
 decreased
 by
 -­‐0.78,
 -­‐0.84,
 -­‐
0.86,
 and
 -­‐0.88
 ± 0.08
 Log
 16S
 gene
 copies
 g-­‐1
 dry
 soil,
 total
 soil
 fungal
 abundance

increased
 by
 2.12,
 1.86,
 1.82,
 and
 1.78
 ± 0.15
 Log
 ITS
 gene
 sequence
 copies
 g-­‐1
 dry

soil,
 and
 AM
 fungal
 abundance
 decreased
 by
 -­‐1.73,
 -­‐2.15,
 -­‐2.23,
 -­‐2.04
 ± 0.55
 Log

AML
 gene
 sequence
 copies
 g-­‐1
 dry
 soil
 within
 respective
 treatments
 FGSC,
 FGS,
 GC,

and
 G.
iii

Acknowledgements

I
 would
 like
 to
 acknowledge
 that
 this
 research
 was
 conducted
 on
 the
 traditional

territory
 of
 the
 Attawandaron
 and
 the
 Mississaugas
 of
 the
 New
 Credit
 First
 Nations

peoples,
 and
 offer
 respect
 to
 them
 and
 their
 ancestors.
 I
 hope
 that
 the
 food
 systems

that
 support
 us
 can
 contribute
 to
 the
 reconciliation
 of
 the
 harm
 caused
 to
 your

communities
 and
 our
 shared
 environment.
 Ecological
 farmers
 in
 southern
 Ontario

area
 who
 are
 practicing
 regenerative
 food
 production
 on
 the
 land
 that
 they
 are

stewarding
 inspired
 this
 work.
 Thank
 you
 all
 and
 I
 hope
 this
 work
 can
 support
 you.

I
 am
 extremely
 grateful
 to
 my
 co-­‐advisors,
 Rene
 Van
 Acker
 and
 Ralph
 Martin,
 for

their
  initial
  interest
  in
  this
  topic,
  and
  their
  generous
  financial,
  technical,
  and

emotional
  support
  throughout
  this
  process.
  Your
  commitment
  to
  regenerative

agriculture
 is
 inspiring!
 Thank
 you
 so
 much
 to
 the
 amazingly
 supportive
 folks
 at
 the

School
 for
 Environmental
 Sciences:
 Kari
 Dunfield,
 who
 sat
 on
 my
 committee
 and

greatly
 assisted
 in
 the
 whole
 process,
 Kamini
 Khosla,
 who
 provided
 so
 much
 lab

support
 and
 laughter,
 Crystall
 McCall,
 who
 showed
 me
 “the
 ropes”
 of
 molecular

analysis,
 and
 John
 Drummelsmith,
 who
 analyzed
 soil
 microbes
 with
 great
 dexterity!

Armfuls
  of
  thanks
  to
  Ecosource
  in
  Mississauga
  for
  their
  donation
  of
  land
  and

logistical
 support,
 to
 Martha
 and
 Martin
 from
 the
 Guelph
 Centre
 for
 Urban
 Organic

Farming
 in
 Guelph
 for
 their
 donation
 of
 land
 and
 logistical
 support,
 and
 to
 Ignatius

Farm
  for
  logistical
  support!
  So
  much
  love
  and
  thanks
  to
  my
  Mum,
  Dad,
  Sister,

Brother,
 and
 Ilana
 for
 emotional
 and
 physical
 support
 over
 the
 two
 years.
 I
 give

boundless
 appreciation
 for
 my
 housemates
 and
 friends
 who
 joined
 me
 on
 countless

conversations,
 outdoor
 adventures,
 and
 board
 games
 when
 I
 felt
 challenged.

 To
 all
iv

of
 you
 who
 helped
 to
 set
 up
 and
 maintain
 this
 project,
 my
 heartfelt
 thanks!
 Thanks,

also,
 to
 Arthur
 D.
 Latornell
 and
 family
 for
 their
 offering
 of
 a
 graduate
 scholarship
 in

support
  of
  conservation
  and
  remediation.
  Finally,
  I
  acknowledge
  myself
  for

committing
 to
 this
 project
 and
 following
 through
 with
 what
 I
 wanted
 to
 do.
 It
 took
 a

lot
 of
 asking
 for
 help
 and
 self-­‐care,
 and
 I
 did
 it!
v

TABLE
 OF
 CONTENTS

Acknowledgements

 iii

Table
 of
 Contents

 v

1.0
 Introduction

 1

1.1 Introduction

 1

1.2 Literature
 Review

 4

1.2.1 Introduction

 4

1.3 Land
 Acknowledgement
 of
 Southern
 Ontario

 5

1.4 Development
 of
 Temperate
 Forest
 Garden
 Systems

 8

1.4.1 Beginning
 and
 History

 8

1.4.2 Present
 and
 Future
 Growth
 Opportunities
 in
 Academia

 12

1.5 Holistic
 Conceptual
 and
 Practical
 Design
 Frameworks

 13

1.6 Orchards
 as
 a
 Base
 for
 FGS

 14

1.6.1 Soil
 Microbe-­‐Plant
 Communities
 and
 Interactions

 17

1.6.2 Apple
 Orchard
 Plant-­‐Microbe
 Interactions

 20

1.6.3 Agroforestry
 Plant-­‐Microbe
 Interactions

 22

1.7 Perennial
 Contributions
 to
 Agricultural
 Systems

 25

1.7.1 Internal
 System
 Inputs

 26

1.7.2 Biodiversity
 and
 Balance

 32

1.8 Interactions
 Between
 Plants
 and
 Management

 36

1.9 Future
 Work

 38

2.0 Materials
 and
 Methods

 39

2.1 Site
 Description

 39

2.2 Experimental
 Design

 41

2.3 Sampling
 and
 Laboratory
 Analysis

 50

2.4 Statistical
 Analysis

 53

3.0 Results

 54

3.1 Abundance
 of
 soil
 bacteria
 and
 fungi

 54

3.2 Tree
 Growth

 58

3.3 Soil
 Nutrients

 58

4.0 Discussion

 63

5.0 Conclusions

 73

6.0 Summary
 and
 Final
 Thoughts

 75

7.0 Literature
 Cited

 78

8.0
 Appendix
 A

 86
1

1.1
 Introduction

Agriculture
 is
 going
 through
 a
 transition
 on
 a
 global
 scale.
 External
 input-­‐
intensive
 practices
 have
 led
 to
 great
 accomplishments
 in
 some
 regards
 but
 now,

with
 reflection,
 effects
 of
 these
 practices
 on
 the
 environment
 and
 on
 some
 groups
 in

society
  demonstrate
  a
  need
  to
  evolve
  these
  practices
  or
  look
  for
  alternative

practices

 (Bainard
 et
 al.,
 2011A;
 Foley
 et
 al.,
 2005;
 FAO,
 2013;
 Tomich
 et
 al.,
 2011;

Tsonkova,
 et
 al.,
 2012;
 Van
 Acker,
 2008).
 In
 temperate
 areas
 of
 North
 America,
 such

as
 Southern
 Ontario,
 our
 landscapes
 have
 largely
 been
 transformed
 from
 forest
 and

grassland
  to
  urban
  development
  and
  cultivation
  agriculture
  (Ontario,
  2014).

Consequences
 of
 such
 a
 large-­‐scale
 change
 in
 landscape
 include
 loss
 of
 biodiversity,

soil
  erosion,
  contributions
  to
  climate
  change,
  water
  contamination,
  hydrological

imbalances,
 and
 dependence
 on
 fossil
 fuels
 for
 management
 practices
 (Graves
 et
 al.,

2014;
 Tomich
 et
 al.,
 2011).
 Academics
 have
 been
 researching
 these
 issues
 for
 many

years
 and
 governments
 have
 created
 policies
 that
 support
 the
 transition
 towards

reconciling
  the
  issues
  of
  the
  21st
  century,
  but
  the
  actions
  are
  slow
  and,

comparatively,
 under-­‐supported
 (FAO,
 2014;
 Wotherspoon
 2014;
 UNCTD,
 2013).

The
 shift
 away
 from
 late
 20th
 century
 agricultural
 practices
 towards
 systems,

such
 as
 forest
 garden
 systems
 (FGS),
 which
 are
 regenerative,
 locally
 appropriate,

holistic
 in
 design,
 and
 resilient,
 is
 occurring
 (Ferguson
 and
 Lovell,
 2014;
 Tomich
 et

al.,
 2011).
 Indigenous
 communities,
 grass
 roots
 organizations,
 private
 and
 public

research
 institutions,
 and
 ecological
 farmers
 are
 the
 leading
 practitioners
 of
 forest

garden
  systems.
  They
  are
  applying
  indigenous
  knowledge,
  western
  scientific

knowledge,
  and
  nature-­‐mimicked
  frameworks
  of
  system
  design
  to
  achieve
  this.
2

Academics
  have
  a
  great
  opportunity
  to
  support
  the
  development
  of
  resilient,

regionally
 appropriate,
 community-­‐based
 food
 systems
 by
 providing
 research
 and

data
 on
 system
 performance.

A
  forest
  garden
  system
  (FGS)
  can
  be
  described
  simply
  as
  “a
  perennial

polyculture
 of
 multipurpose
 plants”
 (Jacke
 and
 Toensmeier,
 2005).
 Similar
 to
 some

agroforestry
  concepts,
  FGS
  support
  ecosystem
  services,
  provide
  environmental

benefits,
 and
 diversify
 economic
 products
 as
 a
 multi-­‐functional
 landscape
 (Jose,

2009).
 Agroforestry
 has
 been
 defined
 as
 a
 land-­‐use
 system
 where
 trees
 and/or

shrubs
 are
 introduced
 into
 agricultural
 cropping
 and
 livestock
 systems
 or
 where

crops
 are
 planted
 into
 forest
 systems.
 FGS
 expands
 this
 approach
 to
 land-­‐use
 and

production
 systems
 designed
 primarily
 with
 diverse,
 multi-­‐strata
 perennials
 and

self-­‐sowing
  annuals
  that
  mimic
  the
  structure
  of
  natural
  forest,
  woodland,
  and

savannah
 ecosystems.
 The
 goals
 of
 FGS
 are
 to
 achieve
 a
 state
 of
 abundant
 diverse

yields,
 self-­‐fertilization,
 self-­‐maintenance,
 and
 self-­‐renewal
 (Jacke
 and
 Toensmeier,

2005;
 Wiersum,
 2004).
 In
 temperate
 climates,
 FGS
 are

 increasing
 in
 popularity
 for

the
 production
 of
 food,
 medicine,
 fodder,
 fuel,
 fibre,
 and
 recreation,
 and
 the
 practice

of
 these
 systems
 is
 increasing
 on
 smallholder
 farms
 in
 North
 America
 and
 the
 UK

(M.
 Crawford,
 personal
 communication,
 August
 27
 2014;
 E.
 Toensmeier,
 personal

communication,
 August
 29
 2014).
 FGS
 are
 noted
 as
 an
 area
 of
 great
 opportunity
 in

agroforestry
  research
  and,
  although
  current
  scientific
  literature
  is
  lacking
  in

temperate
 FGS,
 it
 is
 being
 practiced
 around
 the
 world.
 There
 is
 novel,
 larger-­‐scale,

participatory
  research
  on
  FGS
  occurring
  at
  the
  University
  of
  Illinois
  (Savana

Institute,
 2013;
 Wiersum,
 2004).
3

The
 purpose
 of
 this
 study
 was
 to
 initiate

 research
 in
 temperate
 forest
 garden

systems
 with
 goals
 of
 measuring
 the
 effects
 that
 establishing
 an
 apple-­‐based
 FGS

with
 varying
 amounts
 of
 compost
 has
 on
 the
 abundance
 of
 soil
 bacterial
 and
 fungal

communities
  (integral
  components
  of
  a
  self-­‐sufficient
  ecosystem)
  in
  Southern

Ontario,
 Canada.
 The
 overall
 null
 hypothesis
 is
 that
 newly
 established
 apple-­‐based

FGS
 and
 newly
 established
 apple
 trees
 with
 mixed-­‐grass
 understories,
 both
 with
 an

without
 compost,
 will
 have
 the
 same
 shift
 in
 soil
 bacterial
 and
 fungal
 population

abundance,
 SOM,
 tree
 growth
 and
 soil
 chemistry
 over
 two
 years.
 The
 alternative

hypothesis
  is
  that
  newly
  established
  apple-­‐based
  FGS
  with
  compost
  will
  have

different
 soil
 fungal
 and
 bacterial
 abundance,
 different
 tree
 growth,
 and
 different

soil
  nutrients
  compared
  to
  newly
  established
  apple
  trees
  with
  mixed-­‐grass

understories
 after
 the
 first
 two
 establishing
 years.
 The
 specific
 objectives
 of
 this

study
 were
 to
 measure
 and
 compare
 1)
 the
 abundance
 of
 indigenous
 total
 bacterial,

total
 fungal,
 and
 arbuscular
 mycorrhizal
 fungi
 populations
 in
 the
 soil,
 2)
 soil
 organic

matter,
 3)
 apple
 tree
 growth,
 and,
 4)
 chemical
 properties
 (i.e.,
 the
 nutrients
 K,
 Mg,

P),
  between
  newly
  established
  apple-­‐based
  FGS
  plots
  and
  grass
  understory

managed
 apple
 plots,
 both
 with
 and
 without
 compost
 amendments.
4

1.2
 Literature
 Review

1.2.1
 Introduction

  In
 the
 tropics,
 FGSs,
 which
 are
 characterized
 as
 forest-­‐analogous
 agroforests

(i.e.,
 a
 cross
 between
 natural
 forests
 and
 specialized
 tree
 crop
 plantations)
 that
 have

been
  established
  by
  indigenous
  peoples
  (Wiersum,
  2004).
  FGSs
  are
  currently

practiced
 to
 a
 large
 extent
 using
 systems
 developed
 by
 local
 communities
 with
 a

goal
 of
 conserving
 the
 forests
 on
 which
 they
 depend
 for
 a
 livelihood
 (Wiersum,

2004).
 In
 temperate
 regions,
 forest
 ecosystems
 have
 been
 and
 still
 are
 an
 integral

component
  of
  indigenous
  livelihood
  and
  they
  produce
  products
  for
  the
  global

market
 (Uprety
 et
 al.,
 2012).
 Some
 forest
 functions
 provide
 direct
 value
 to
 people

(e.g.
 food
 and
 medicine)
 while
 others
 are
 more
 indirect
 such
 as
 what
 we
 may
 now

refer
 to
 as
 ecosystem
 services,
 such
 as
 water
 filtration
 (Kimmins,
 2004;
 Uprety
 et
 al.,

2012).

There
 are
 many
 agroforestry
 systems
 that
 domesticate
 specific
 components

of
  forest
  ecosystems
  for
  particular
  yields,
  for
  example,
  the
  use
  of
  trees
  in

silvopasture,
 intercropping
 with
 alley
 crops,
 and
 orchards
 (Nerlich
 et
 al.,
 2013).
 The

land-­‐use
 practice
 of
 FGS
 in
 temperate
 climate
 regions
 is
 relatively
 new
 but
 it
 mimics

aspects
 from
 regional
 ecosystem
 models
 that
 have
 developed
 over
 centuries.
 FGSs

provide
 opportunities
 for
 producing
 multiple
 human-­‐use
 yields,
 such
 as
 food,
 fibres,

medicines,
 and
 fuel,
 while
 simultaneously
 preserving,
 or
 regenerating
 aspects
 and

processes
 prevailing
 in
 undisturbed
 forests
 (Wiersum,
 2004).
 Choosing
 to
 study
 our

regional
 environments
 and
 the
 benefits
 of
 implementing
 FGS
 is
 a
 vital
 decision.
 With

more
 understanding
 of
 these
 systems,
 and
 how
 farmers
 might
 adopt
 the
 practices
 to
5

establish
 and
 manage
 them,
 we
 can
 begin
 to
 transition
 away
 from
 systems
 of
 low

diversity
 that
 require
 high
 external
 inputs
 towards
 holistic
 production
 systems.

  In
 this
 review
 of
 the
 literature
 I
 first
 acknowledge
 the
 history
 and
 ecology
 of

the
 land
 in
 Ontario
 and
 present
 the
 development
 of
 FGS
 as
 a
 practice
 and
 science.

Second,
 I
 present
 conceptual
 aspects
 of
 permaculture
 and
 agroecology
 from
 which

FGS
 can
 be
 designed.
 The
 main
 focus
 of
 the
 latter
 section
 is
 on
 the
 relationships

between
  diverse
  perennial
  plants
  and
  soil
  microorganism
  communities
  which

informs
 questions
 around
 how
 FGS
 function
 and
 where
 research
 is
 most
 required.

1.3
 Land
 Acknowledgement
 of
 Southern
 Ontario

The
 temperate
 regions
 of
 the
 world
 have
 different
 conditions
 that
 support

diverse
 ranges
 of
 ecosystems
 which
 can
 be
 mimicked
 to
 create
 systems
 that
 provide

for
  humans,
  non-­‐human
  species,
  and
  the
  environment.
  For
  example,
  Canada’s

temperate
 land
 mass
 is
 approximately
 50%
 forest
 cover,
 containing,
 among
 others,

the
  deciduous
  forest
  biome
  (McCartney,
  2011).
  Southern
  Ontario’s
  landscape
  is

made
 up
 of
 the
 mixed-­‐wood
 plains
 ecozone
 in
 the
 north
 and
 stretching
 up
 from
 the

south
 is
 the
 Carolinian
 ecozone,
 which
 is
 the
 most
 tree
 species-­‐diverse
 zone
 in

Canada
 with
 more
 than
 1600
 plant
 species
 (McCartney,
 2011).
 Figure
 1
 shows
 the

19th
 century
 land
 cover
 in
 S.
 Ontario:
 large
 areas
 of
 forest
 types
 including
 maple

(Acer
 spp.
 L.)
 and
 beech
 (Fagus
 grandifoloia
 L.)
 which
 covers
 most
 of
 S.
 Ontario,
 with

larger
 patches
 of
 black
 ash
 (Fraxinus
 nigra
 Marshall)
 swamps,
 oak
 (Quercus
 spp.
 L.)

forest,
 and
 interspersed
 patches
 of
 hemlock
 (Tsuga
 spp.
 Carriere),
 willow
 (Salix
 spp.

L),
 tamarack
 (Larix
 spp.
 (Du
 Roi)
 K.
 Koch),
 chestnut
 (Castanea
 spp.
 L.),
 birch
 (Betula

spp.
 L.),
 cedar
 (Cedrus
 spp.
 L.),
 spruce
 (Picea
 spp.
 Mill.),
 pine
 (Pinus
 spp.
 L.),
 poplar