Table Of ContentThe
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
Description:Second, I present conceptual aspects of permaculture and agroecology from which .. producers to replant old apple orchards with apples, sometimes
