Growing Crops with Microbiology- Endophytes and Rhizophagy Cycle.pdf

Mid-Atlantic Fruit and Vegetable Convention
‘Growing Crops with Microbiology:
Endophytes and Rhizophagy Cycle’
James F. White
Department of Plant Biology, Rutgers University, New Brunswick, NJ, USA
jwhite3728@gmail.com; 848-932-6286
2/1/2024

Chemical Inputs Chemical Inputs
Products
Conventional Agriculture
Environment and Human Health Degradation
Biological Agriculture Products
Plant, Environment and Human Health Regeneration
Conventional Agriculture Assumptions: 1) Crops managed by chemistry alone; 2) Yield is the most important criterion; 3) Microbes must
be killed and controlled.
Biological Agriculture Assumptions: 1) Crops managed by managing plant and soil microbiology; 2) Soil, plant and human health the
most important criteria; 3) Communities of microbes must be propagated and increased in soils and plants.

Endogenous Nutrient
Supply Using
Endophytic Bacteria
K
K
N
P
N
N
Bacteria
Bacteria
Bacteria
Plant Cell Plant Cell
N
N
K
N
N
N
P
N
N
P N
K
K
P
K
N
N
N
K
P
N
Exogenous Nutrient
Supply
P
N
N
N
P
N
N
P
N
K N
Chemical Fertilizer is
30-40% Efficient in Transfer to
Plant Cells.
100% Efficiency of Nutrient
Transfer to Plant Cells.

What makes a soil
healthy?
Elaine Ingham
Rick Bieber
Kelly and Deanna Lozensky John Kempf Gabe Brown

Non pathogen microbes in plants are are
endophytes?
(Botany): Endophytic/endosymbiotic non-pathogenic microbes
(fungi, bacteria or algae) present asymptomatically for all or part
of their life cycles in tissues of plants.
6
Fungal hyphae of endophyte in stem tissue of tall fescue grass.

Potatoes contain endophytic microbes!

The depressions on tubers around the buds hold soil and microbes!

Growing Crops with Microbiology- Endophytes and Rhizophagy Cycle.pdf

Endophytic microbes intimately enter
into plant nuclei and affect plant DNA
expression.

Potato root cell showing bacterial endophytes emerging from
nucleus (arrows).
Bacteria in nucleus are encapsulated.

Nuclear symbiosis (Hosta sp.)
Nitrate stain (blue) Stained for ethylene (blue)

We need endophytes to create new
climate resilient crop cultivars.

Plants engage in Habitat-Adaptive Symbiosis
with soil microbes/endophytes.
Rusty Rodriguez Regina Redman

Plant microbes alter genetics of the
host plants and stimulate adaptation
to the environment!
1) Bacteria produce ethylene and nitrate in and
around plant nuclei that serve as nucleomodulins to
stimulate plant chromosome replication (process of
‘endoreduplication’). Highly microbial plants have a
“wild-look” due to their high variability.
2) Microbes regulate development of plant cells and
tissues through altering gene expression in the
plant.
3) Microbes provide nutrients that support plant
growth.
4) Microbes cause an increase in pollen production.

Bacteria within the pollen mother cell (left;
arrow) and pollen grain (right; arrow) of corn.
Pollen Mother Cell
Pollen Grain

Uniformity of conventional crop production
Non-uniformity of biological crop production

Plant microbes are:
1) Soil microbes
2) Seed vectored

Bacterial symbiosis: germinating tall fescue seed showing
seed-transmitted bacteria (Bacillus spp., Pseudomonas sp.,
etc..)
Small communities of bacteria of 3-4
species are vectored on seeds.
The bacteria that vector on seeds appear to be
Important for seedling development and survival.
Richard Chen

Bacterial endophytes colonize
seeds.

Microbes vectored on seeds and
within seeds are vulnerable to our
seed treatments.
Seeds should be treated in a way to
preserve the internal and surface
microbiology.

Tomato seedling root tip showing high ethylene areas
to either side of the root tip meristem.
Root Tip Meristem/
Bacterial Entry Zone
Bacterial Cell Wall Removal/
Nutrient Extraction Zone
Stained with 1% Ammonium Molybdate (Blue or Purple Color Indicates Ethylene)
For stain: Lang and Hubert (2012) A colour ripeness indicator for apples. Food Bioprocess Technology 5: 3244-3249.

Close-up of Micrococcus tetrads in periplasmic space of
root meristematic cells.

The Rhizophagy Process in Roots

Figure 1. Roots of axenically grown Arabidopsis and tomato were incubated with E coli or
yeast expressing green fluorescent protein (GFPE. coli or GFPyeast).
“Rhizophagy”
Do plant roots
consume
bacteria to
obtain
nutrients?
Paungfoo-Lonhienne C et al. 2010.
Turning theTable: Plants Consume Microbes as a Source of Nutrients.
PLoS ONE 5(7): e11915, doi:10.1371/journal.pone.0011915
Chany Paungfoo-Lonhienne
Suzanne Schmidt

Soil algae (e.g., Chlorella spp.)
Yeasts (e.g., Saccharomyces)
Bacteria (e.g., Bacillus spp.)
What soil microbes are internalized in the rhizophagy process?

Plant Cell Entry Zone
(Microbes Become Intracellular in Meristem Cells
as Wall-less Protoplasts.)
Microbe Exit Zone
(Microbes Stimulate Elongation
of Root Hairs and Exit at the Tips
of Hairs Where Walls are Thin.
Microbes Reform Cell Walls Once
Outside Root Hair.)
RHIZOPHAGY
CYCLE
Nutrients Extracted from Microbes
By Reactive Oxygen Produced by
NOX on Root Cell Plasma
Membranes
Microbes Exit Root
Hairs Exhausted of
Nutrients
meristem
Bacteria (arrow) in root
parenchyma cell
near root tip meristem.
.
Bacteria (arrow) emerging
from root hair tip of millet
seedling.
Microbes Recharge with Nutrients
in the Rhizosphere
Microbes Enter Root
Cell Periplasmic
Spaces Carrying
Nutrients
From Soil
1
A
B
C
Kate Kingsley

Grass roots show numerous roots tip meristems. These
root tip meristems are the sites of internalization of
microbes and extraction of nutrients from microbes in
the rhizophagy cycle.
Illustration of a root system of corn (Illustration by Botanist John E. Weaver, 1927)

Bacteria entering root epidermal cells in the ‘zone on intracellular
colonization’ at the root tip meristem. A cloud of bacteria (arrows) is
seen around the root tip meristem where intracellular colonization is
occurring. The blue stain is aniline blue.

Zone of bacterial entry and cell wall loss
Zone of bacterial protoplast replication
Poa annua root inoculated with Bacillus sp. (crystal violet)

Bacteria lose cell walls after they enter plant cells. Irregular shapes that stain densely
with crystal violet are bacterial cell walls (arrows). Bacterial L-forms replicate rapidly
in root cells.

Phragmites root stained with diaminobenzidine DAB to visualize reactive oxygen around bacterial protoplasts
(arrows). Reactive oxygen is visualizable as brown or red coloration around bacteria. The reactive oxygen is
the result of superoxide produced by NADPH oxidases on the root cell plasma membranes. The reactive oxygen
extracts nutrients from the bacteria (mostly pseudomonads) that are symbiotic with Phragmites.

Celeste Zhang
Confocal Microscopy:
Pseudomonas sp. tagged with
M-Cherry and inoculated into
clover plants. Bacteria fluoresce
red in the root cap cells.
Blue = calcofluor white (plant
cell walls)
Green = syto13 (nucleic acid)
Red = mCherry tagged bacteria

2O-
Root Cell Wall
2O-
(Superoxide)
Cyclosis*
2O-
2O-
2O-
2O-
2O-
Periplasmic Space
Periplasmic Space Periplasmic Space
Bacterium Bacterium
2O-
2O-
2O-
2O-
2O-
2O-
2O- 2O-
2O- 2O-
2O-
2O-
2O-
2O-
2O-
2O-
Plasma Membrane
Root Cell Cytoplasm
Cyclosis* Central Vacuole
Bacterial Protoplasts in Periplasmic Space are Subjected to Host-Produced Superoxide.
*Cyclosis = Cytoplasmic Movement

REACTIVE OXYGEN DEFENSE RESPONSE OF THE ROOT CELL
INVOLVES MEMBRANE-BOUND NADPH OXIDASES (NOX)
Molecular oxygen
(from atmosphere)
Superoxide

Bacteria with cell walls (rods) Spherical bacterial protoplasts
(no cell walls)
Bacterium Bacillus subtilis
Reactive oxygen
(superoxide)
Inside root cells superoxide strips cell walls off of the microbes!
Bacterial protoplasts
are called L-forms.

Rhizophagy cycle microbes modulate
development of seedlings
• Microbes trigger root hair elongation
• Microbes trigger the gravitropic response in
roots
• Microbes increase root branching
• Microbes increase root and shoot elongation

Bermuda grass seedling root in
agarose without microbes showing
absence of root hairs
Root tip
More developed region of seedling root

Bermuda grass root containing Pseudomonas (bacterium)
Bacteria
(from seed coat)
Colonize root
tip meristem
(enter cells)
Intracellular
in root parenchyma
Bacteria stimulate
root hair formation
In root epidermis
Bacteria emerge to
surface of hair as the
hair elongates
Route of endophyte colonization of root
at root tip and reentry to rhizosphere from root hairs
Bacteria colonize soil
rhizosphere
Bacteria acquire nutrients
in rhizosphere
RHIZOPHAGY CYCLE

Bermuda grass seedling root containing
Pseudomonas endophyte.
All brown spots in roots are intracellular
bacteria.

Pseudomonas sp. (arrows) in root hairs
of Bermuda grass seedling.
Bacterial protoplasts shown in hairs.

No antibiotic treatment
Streptomycin treated
Experiment: All seeds surface disinfected for 20 mins in 4% sodium hypochlorite—then washed.
½ seeds treated with streptomycin (100 mg/L) for 24 hours to inhibit growth of endophytic
bacteria.
Results: Where bacteria are present I seedlings, tomato seedlings (3-days-old) show root hair
formation (arrow); and where antibiotic limits bacterial growth no hairs form.
Mode of action: Streptomycin binds to the small 16S rRNA bacterial ribosome and inhibits protein synthesis.
Streptomycin treatment of tomato seedlings

C
A
B
Tomato Root Hair Initial Without
Internal Microbes Do Not Elongate.
NO MICROBES IN HAIR INITIAL
MICROBES PRESENT IN HAIR INITIAL
Root hair growth is linked to presence of
microbes in hair initials.

Why is root hair growth linked to
presence of intracellular bacteria?

Bacterium present
(Pseudomonads fluorescens inoculated
onto disinfected seeds.)
No microbes in
seedlings
(Seeds disinfected rigorously.)
Xiaoqian (Ivy) Chang
Experiments to test the ‘Microbial Stimulated Cell Growth Hypothesis’

What stimulates the plant root hairs to elongate?
Microbe Produced Hormones Hypothesis
Microbial Ethylene and Nitric Oxide Stimulate Root Cell Growth
Ethylene
Nitric oxide/
Nitrate
Root Hair Elongates
Microbes in root hair tip
produce ethylene and nitric oxide Ethylene and nitric oxide
act as a hormones,
causing root hair to elongate

Plant grows in pits and crevices of limestone or in sand along high salt
Caribbean shore environments.
Sedge (Fimbristylis cymosa)

Root hair showing microbes circulating along interior of hair
Root hair stained to show microbes (arrows) in periplasmic space of hair
Constant cyclosis of microbes enables efficient nutrient exchange
between microbe and root cells and reduces exposure to
superoxide (permitting microbe replication and N fixation).

Clusters of replicating bacteria within periplasmic
space of root hair of sedge Fimbristylis cymosa.
The red coloration around clusters of bacterial
protoplasts (arrows) is indicative of reactive
oxygen secreted by the root cell plasma membrane
to induce nutrient leakage from bacteria (stained
with DAB/aniline blue).
Plants increase the numbers of
microbe protoplasts prior to
releasing microbes back into the soil.

Microbes
accumulating in
hair tip.
Microbes circulating along length
of root hair.
This constant circulation may be a way to induce
replication in the microbe protoplasts.
Root hair of sedge Fimbristylis cymosa
Cyclosis was measured
to move microbes at a
rate of 8-11
micrometers/second in
root hairs of the sedge
Fimbristylis cymosa.
Qiang Chen

Root hair of sedge (Fimbristylis cymosa) showing
expulsion of bacteria (large arrow) from the soft-
walled hair tip. Red-staining bacterial protoplasts
are seen in root hair. A wave of expansion of the
hair protoplast propagates from base to tip of hair
and this wave forces microbes through pores that
form in the hair tip.

Sequence of periodic build-up and
ejections of bacteria from root hairs.
Red bacteria are active in antioxidant nitrogen secretion while blue bacteria
are active in nitrogen fixation.

Nitrogen-transfer symbiosis in plant
hairs
Nitrogenous antioxidants like nitric oxide are secreted by the bacteria to
neutralize superoxide. Nitric oxide combines with superoxide to form
nitrate. Nitrate is absorbed directly into the plant.

Root hairs of Bermuda grass (Cynodon dactylon) infected with endophytic bacterium Bosea
thiooxidans (initially from Japanese knotweed). Bacteria emerge from the tip at regular
intervals leaving the bacterial clusters in dark-stained flat deposits (black arrows) on the
outer surface of the root hair wall. The root hair then elongates to the side of the bacterial
deposit, creating zig-zag pattern to the hair. The hair tip is seen to proliferate past the latest
Microbe ejection appears to be periodic rather than continuous. Microbes may
be ejected in clusters rather than 1 at a time. This may be the result of ethylene-
triggered growth spurts. A growth spurt occurs after a critical mass of bacteria in
hair tips secrete enough ethylene to cause hair elongation.
Incomplete ejection of microbes in hairs suggest periodic ejection.

This ejection of microbes (arrows) occurs
rapidly with a wave of expansion in the
hair cell that begins in the hair base and
moves to the tip. This forces microbes
through pores in the hair tips.
Sofia Dvinskikh
1
3
2

Nutrient Absorption Function
of the Rhizophagy Cycle:

Plant nutrient sources
1) Nutrients that are dissolved in soil water
2) Nutrients that must be oxidatively extracted
from soil microbes within root cells
3) Nutrients obtained from mycorrhizae
Ivy Chang

Sequence of oxidative extraction for nutrients:
Mn > Fe > Ca> Mg > S > Cu> N > Zn > P > K
Rhizophagy Nutrients:
Micronutrients tend to be favored in
oxidative extraction from bacteria in the
rhizophagy cycle.

Nitrogen Fixation by Endophytes
The first land plants (Bryophyta)
internalized bacteria into their cells
(hairs) to obtain nitrogen from them!
In plant hairs plants cultivate and
extract nitrogen from nitrogen-fixing
bacteria.

Moss (Physcomitrella patens) gametophytes
have chloroplasts and do photosynthesis, but
they also have non-photosynthetic tissues
where nitrogen-transfer endosymbiosis
occurs. Achlorophyllous filaments termed
‘caulonemata’ contain bacteria that transfer
nitrogen to the moss gametophyte.
The brown filaments (arrow) in this image are caulonemata.
Chloronemata are photosynthetic filaments; while
caulonemata function to fix atmospheric nitrogen and
transfer it to the photosynthesizing gametophyte.
Nicole Vaccaro
Lena Struwe Blair Young

Caulonemata of moss stained for ethylene (blue color) around
intracellular bacteria (arrows). Stain is ammonium molybdate.
For histochemical staining protocols see: Chang X, Kingsley KL, White JF. 2021.
Chemical Interactions at the Interface of Plant Root Hair Cells and Intracellular
Bacteria. Microorganisms. 9(5):1041.
https://doi.org/10.3390/microorganisms9051041
Moss filaments are the earliest versions of plant hairs (trichomes) and they function to
extract nitrogen from bacteria.

The very first land plants used endophytic microbes for
nutrients from the start. These endophytes are about
delivering nitrogen to plants.
Liverwort (Riccia sp.)
Plant lacks leaves and roots-but has
non-photosynthetic filaments that contain
bacteria (white arrow).
Stained for nitrate
(purple color)

Invasive Tree-of-heaven (Ailanthus
altissima)

Symbiosis in pitted filamentous
trichomes of tree-of-heaven
Pitted trichome of tree-of-heaven (Ailanthus altissima) showing bacteria. A. Developing trichome stained with acidified
diphenylamine showing nitrate (blue color) around bacteria (arrow) in the tip of the trichome (Bar = 10 µm). B.
Trichome stained with sulfur monochloride to show bacteria (arrow) emerging from lateral pits in wall (Bar = 10 µm).

Trichome
of tree-of-heaven stained with iron sulfate
showing bacteria (arrows) emerging from hairs
through channels.

Cyclosis occurs within trichomes. Trichome cell walls
are thickened and hardened with silica and calcium
carbonate to prevent bending and damage to the
cytoskeleton.
Root hairs have thin walls.
Bending the hair stops
nitrogen fixation by
stopping cyclosis.
K-silicate has been shown to increase stress tolerance and nitrogen-use efficiency in many
plants. Hemp growers report more THC in plants with silica use.
Deus, A.C.F., de Mello Prado, R., de Cássia Félix Alvarez, R. et al. Role of Silicon and Salicylic Acid in the
Mitigation of Nitrogen Deficiency Stress in Rice Plants. Silicon 12, 997–1005 (2020).
https://doi.org/10.1007/s12633-019-00195-5.
Neu, S., Schaller, J. & Dudel, E. Silicon availability modifies nutrient use efficiency and content, C:N:P
stoichiometry, and productivity of winter wheat (Triticum aestivum L.). Sci Rep 7, 40829 (2017).
https://doi.org/10.1038/srep40829.

Nitrogen Fixation Symbiosis in
Plant Cells

NH1-4 + 2O- ONOO- NO3
-
Reduced nitrogen Superoxide Peroxynitrite Nitrate
O2
NADPH oxidase
(in root cell
plasma membrane)
Functions as
antioxidant to
protect bacteria
from oxidation
CO2 catalyst
CO2 product of reaction of
ethylene and superoxide
Absorbed into
root cells
N2
Molecular nitrogen and oxygen (air)
Nitrogenase
(in bacteria)

Table. From Micro-Array Study by Dr. Ivelisse Irizarry
Enriched pathways in cotton seedling roots colonized by Bacillus amyloliquefaciens
(n=24).
GO term Description p-value FDR
GO:0042126 nitrate metabolic process 2.10E-
05
0.003
GO:0042128 nitrate assimilation 2.10E-
05
0.003
GO:0034641 cellular nitrogen compound metabolic process 1.40E-
05
0.003
GO:0020037 heme binding 0.0013 0.036
GO:0005507 copper ion binding 0.00026 0.013
GO:0031988 membrane-bounded vesicle 0.00016 0.0037
GO:0015630 microtubule cytoskeleton 0.0022 0.034
GO:0007018 microtubule-based movement 0.00037 0.031
Data from: Irizarry, I., J. F. White. 2018. Bacillus amyloliquefaciens alters gene
expression, ROS production, and lignin synthesis in cotton seedling roots. J. Applied
Microbiology 124: 1589-1603. doi:10.1111/jam.13744
Dr. Ive Irizarry

Hemp leaves bear trichomes that
contain endophytic bacteria.
April Micci

Hemp glandular trichomes unstained

Hemp-NBT stained showing bacterial rods (arrows) around
trichome cells. Blue color indicates presence of superoxide.

Nitrogen
fixation
zone
Nitrogen
transfer zone
(superoxide)
Trichome cells
Basal cells with chloroplasts
produce the sugars that fuel the
process of nitrogen fixation.
Hemp Glandular Trichome

Model for how glandular trichomes
work

Cannabinoids and terpenoids as
oxygen scavengers

Hops photo showing inflorescences (arrows) composed of whorls
of bracts that bear trichomes.
April Micci

Hops stained with nitro blue tetrazolium to show
superoxide (blue) around bacteria (arrows).

Hops glandular trichome stained for
nitrate.

• Rhizophagy cycle activity in plants is a key part
of NUE.
• Higher NUE corresponds to higher titer of
nitrogen fixing bacteria in plants.
• Nitrogen fixation in trichomes on leaves is an
important source of NUE.
• Colonization of chloroplasts by endophytes
may be another source of NUE??
Comparative study of corn types
differing in nitrogen use efficiency
(NUE)

Rhizophagy
Cycle
N Fixation
In Leaf Trichomes
N Fixation
In Leaf Epidermis Cells
N Fixation In
Root Hairs
Mn > Fe > Ca> Mg > S >
Cu > N > Zn > P > K
High NUE in corn is the result of microbes all over plants.

Developing N-fixing corn by breeding and microbiome
transfer from highly nitrogen-efficient landraces
Dr. Walter Goldstein (Plant Breeder)
Mandaamin Institute, WI

Total NLFA
Landrace/Conventional
PFLA + NLFA average
Landrace/Conventional
NLFA/PLFA
Conventional
NLFA/PLFA
Landrace
Total Biomass 0.8 0.9 6.26 4.77
Diversity Index 0.7 0.8 1.83 1.51
Bacteria % 2.8 1.2 0.22 0.74
Total Bacteria Biomass 15.4 3.2 0.17 2.57
Gram (-) % 2.9 1.2 0.21 0.73
Gram (-) Biomass 19.1 3.2 0.14 2.56
Rhizobia % 1.1 1.1 14.17 14.25
Rhizobia Biomass 7.6 6.6 5.39 34.19
Total Fungi % 1.1 0.9 0.20 0.25
Total Fungi Biomass 15.5 1.9 0.06 1.04
Saprophytic % 1.1 0.9 0.20 0.25
Saprophytes Biomass 15.5 1.9 0.06 1.04
Protozoan % 37.5 13.2 0.50 20.06
Protozoa Biomass 12.9 10.7 4.41 57.58
Gram (+) Biomass 0.8 0.8 11.63 6.92
Gram (+) % 0.4 0.6 3.75 1.49
Undifferentiated % 0.8 0.9 2.22 1.41
Undifferentiated Biomass 0.6 0.7 15.57 7.89
Fungi:Bacteria 1.0 4.3 0.36 0.06
Predator:Prey 0.5 0.6 57.15 4.96
Gram(+):Gram(-) 0.2 0.2 178.22 7.31
Sat:Unsat 0.5 0.5 10.94 3.43
Mono:Poly 2.6 2.0 1.79 4.69
Microbial Load In N-Fixing Landrace Corn vs Conventional Corn
*Data with obtained from leaves with collaboration of Ward Labs in Nebraska. Four conventional cultivars from
Monsanto and Pioneer were selected as conventional; 5 cultivars derived from N-fixing Landraces were used.
High NUE corn plants contain a rich community of microbes!

Endophytic and soil microbes
protect plants from fungal
diseases.

Disease Protection Experiment
Summary
Removing surface microbes from basil seeds
resulted in:
1. Seedlings that grew slower than seedlings
with surface microbes present;
2. Seedlings that were more susceptible to
disease caused by Fusarium (evidenced by
low seed germination, slow root growth, root
tissue browning due to necrosis; see Table 1).

Basil seedlings with microbes intact Basil seedlings with microbes + Fusarium
Basil seedlings without microbes Basil seedlings without microbes + Fusarium

Soil/Endophytic Bacteria Modulate
Virulence of Facultative Plant Pathogens.
Facultative Plant Pathogens (Fusarium sp.)
Symbiotic
bacteria
present
Symbiotic
bacteria
absent
Plant Disease Saprotrophy

Bacterial endophytes of fungi change
behavior of fungi (e.g., Fusarium spp.)
• We dipped a sterile probe
into the soil in between
seedlings and then streaked
it onto plates to see if the
bacteria were going out into
the soil.
• Pseudomonas sp. (Sandy LB
4) on the left
• Pseudomonas sp. (West 9)
on the right
• Pseudomonas sp. (Sandy LB
4) reduces sporulation and
growth rate of Fusarium

Bacterium + Fusarium Fusarium only
Soil with bacteria
and fungus (left
photo) appears
darker because soil
moisture is retained,
and the surface
mycelium is
suppressed.
Kate Kingsley

Project with Jimmy Emmons, Willie Pretorius, Ray Ward, Patrick Freeze and Terry Buettner.

Biofilm composed of fungal hypha and bacteria.
Biofilm (arrow) from symbiosis
between fungus (Alternaria sp.)
and bacterium.

Endohyphal bacteria (endophytes) in
mycelium of Alternaria sp.
Stained with nuclear stain SYTO13 to show internal bacteria Hyphae without internal bacteria

Bacteria emerging from hyphae
Stained with nuclear stain SYTO13 to show internal bacteria
Biogels = Biofilms

Bacteria emerging from hyphae.

Bacteria (arrows) emerging from hyphae of
saprophytic zygomycete Absidia glauca.

Even mushrooms carry endophytes in
their hyphae.

Reishi Mushroom (Ganoderma sp.)

Nitrate stain: Acidified diphenylamine
Bacteria (arrows) appear to be encapsulated.

Nitrate stain
Fungal ‘nodules’
rich in nitrate

Fungal ‘nodules’ are composed of a knot of hyphae
and filled with bacteria.

2. Increased oxidative stress
tolerance in plants
Increased reactive oxygen
activity in root cells
The soil microbial community
liberates and absorbs nutrients
from soil.
Rhizophagy cycle
microbes take nutrients
from microbial community.
The plant takes nutrients
from rhizophagy cycle microbes, and
provides photosynthate
to soil microbes.
3. Soil fungal pathogens have
reduced virulence
Soil fungi drained of nutrients
by rhizophagy cycle microbes
1. Plants absorb nutrients
from microbes
Rhizophagy microbes enter
plant roots with nutrients
A. Three Beneficial Outcomes of Rhizophagy Symbiosis
B. Nutrient Flow
3

Jeff Lowenfels with MicroBIOMETER
founder Judy Fitzpatrick

Kate Kingsley
Monica Torres
Qiang Chen
Peerapol Chiaranunt
Celeste Zhang
Fernando Velazquez
Gianna Pecorella
Marshall Bergen
Chris Zambell
Mariusz Tadych
Mohini Pra Somu
Ray Sullivan
Haiyan Li
Ivy Chang
Ivelisse Irizarry
Marcos Antonio Soares
Surendra Gond
April Micci
Satish K. Verma
Kurt Kowalski
Shuai Zhao
Sadia Bashir
Judy Gatei
Xiang Yao
Amy Abate
Shanjia Li
Jiaxin Lu
New Jersey Agric. Exp. Sta.;
USDA NIFA Multistate 3147;
Rutgers Center for Turfgrass Science;
USGS-Rutgers U (CESU Study Agreement)

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