Microbial Ecology of Rhizosphere Bacteria in Brazilian Maize as Influenced by Plant Genotype and...
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Microbial Ecology of Rhizosphere Bacteria in Brazilian Maize as Influenced by Plant Genotype and Soil Environment David Morris Johnston Monje Plant Agriculture,
Microbial Ecology of Rhizosphere Bacteria in Brazilian Maize as
Influenced by Plant Genotype and Soil Environment David Morris
Johnston Monje Plant Agriculture, University of Guelph Advisor:
Manish Raizada Brazilian Partner: Dra. Veronica Reis (EMBRAPA
Agrobiologica) Funding: Manish Raizada and IICA Canada
Slide 2
Maize has been important all over the Americas for thousands of
years... Mayan maize god Yumil Kaxob Zapotec maize god Pitao Cozobi
Moche culture Peru Mitchell Corn Palace, USA 2
Slide 3
Where does maize come from? Developed 9,000 years ago In
Oaxaca, Mexico 3 Distinct genotypes and soils, yet unresearched
Already researched genotypes and soils (by Dr. Johnston)
Slide 4
Dramatic differences in soil may have forced maize to develop
novel bacterial surface populations 4
Slide 5
Dramatic Physiological Change in Plants May Have also Altered
Bacterial Populations Domestication, breeding, and migration have
altered plant and seed architecture while forcing maize to grow in
different environments and to be completely dependent on humans.
5
Slide 6
Obvious structural or environmental differences may coincide
with changes to the microbial ecology 6
Slide 7
Plants have been shown to have large numbers of bacteria inside
their bodies and on their surfaces Plant root surfaces interact
with soil, absorbing all the water and nutrients needed for growth
and metabolism. Bacteria living on this surface or inside the plant
are able to influence both absorption and metabolism of these
compounds. Discovering new rare bacteria with capacity to improve
plant growth, nutrient acquisition and metabolism posses great
potential for productive, environmental agriculture Previous work
done by Dr. David Johnston Monje suggests that bacteria living
inside the plant are not rare or influenced by the external
environment. Are root or leaf surface bacteria rare or influenced
by external environment? What are these microbes and can we use
them in agriculture? What are plant associated bacteria and why
study their ecology in maize plants? 7
Slide 8
Rare New Strains May Help Agriculture Rhizobial bacteria first
patented and sold as Nitragin in the United States in 1895
Burkholderia phytofirmans PsJN from rotting onions can promote
plant growth. High levels of nitrogen fixation found in Brazilian
sugarcane thanks to Gluconacetobacter diazotrophicus. Nitrogen
fixing Klebsiella pneumonii isolated from wild maize shown to
improve wheat growth. (Dalton and Kramer 2006) 8
Slide 9
Previous Research on Maize Bacteria? 99% microbes in the world
are believed to have not yet been cultured. Chelius and Triplett
(2001) studied 16S rDNA (a bacterial gene used for barcoding) from
in Wisconsin grown maize roots of genotype Pioneer 3751. 74
phylotypes in 6 bacterial divisions including were found by
culture-independent analysis, as opposed to 27 cultured phylotypes
in 4 divisions. It is impossible to accurately use only culturing
to study bacteria in corn!!! 9
Slide 10
How can DNA identify bacteria? All life contains ribosomes:
protein/RNA complexes responsible for production of protein using
information coded in DNA A ribosomal gene called 16S is found in
all bacteria, although it has accumulated diagnostic mutations in
different species over evolutionary time Each sequence can be
compared bioinformatically to reference sequences to predict what
species it is from 10
Slide 11
TRFLP is one way to comprehensively view a microbial community
using DNA Extract DNA from the community PCR label with a
fluorescently labelled rRNA forward primer Restriction Digest of
PCR Product Fragment separation in sequencing gel Recognition of
labelled fragments Relative fluorescence Outline of the terminal
restriction fragment length polymorphism method 11
Slide 12
How can a DNA fingerprint like TRFLP be interpreted
statistically? Based on 99 microsatellites Principle Component 1
Principle Component 2 Matsuoka et al. (2002) 12
Slide 13
Objectives Objective 1: Isolate novel microbes from Brazilian
corn grown on diverse and stressful soils such as contaminated mine
tailings. These would be transported back to Canada for further
testing and eventually developed as biofertilizers for corn
agriculture. Objective 2: Establish whether different soils do
dramatically alter the surface bacterial populations of maize
plants. This is a basic research question with implications for
future sampling strategies. 13
Slide 14
Methodology Employed Maceration in buffer DNA extraction
Molecular fingerprinting (TRFLP) Modern Ancient Surface
sterilization: bleach and ethanol Multivariate Statistics Collect
washings from roots and shoots Growth of an ancient and one modern
Brazilian maize genotype on a sterile sand, a mining residue, and
black amazonian soil Isolating novel bacteria 14
Slide 15
Significance of the internship to recipient and home
country/region Dr. Johnston Monje completed a PhD at the University
of Guelph (microbial ecology of maize in Mexico and Canada) just
before the internship took place in Brazil, so the proposed
research was a way to immediately continue the research started
during the doctorate Maize is a tropical plant which made it to
tropical South America thousands of years ago, where it may have
maintained or developed unique and beneficial microbial
relationships no longer present in temperate climates like Canada
15
Slide 16
Brazilian ecological agricultural research is world famous, so
experience and networking within EMBRAPA is invaluable for future
collaboration or even career opportunities Specifically important,
the lab of Dr. Reis is the same lab Dr. Dobreiner ran for many
years, arguably the most famous grass-bacterial research lab in the
world 16 Significance of the internship to recipient and home
country/region Dr. Dobreiner Dr. Reis
Slide 17
Expected and achieved results 17 Sterile sand Iron mine subsoil
Amazonian black earth of the Indians Can I acquire interesting,
diverse Brazilian soils? After loosing support from the Canadian
mine partner in Brazil and having negotiated with EMBRAPA Soils for
1.5 months, I got deep iron mine soil and Amazonian dark earth for
my experiment. The sand was heat sterilized and was included as a
negative control. (note the pre-Colombian pottery shard I found in
the Amazonian soil)
Slide 18
Expected and achieved results 18 Sterile sand Iron mine subsoil
Amazonian black earth of the Indians Are there bacterial
differences in different Brazilian soils? Based on simple plate
culturing, you can see there is.
Slide 19
Expected and achieved results 19 Can I acquire interesting
maize genotypes to study? Although Dr. Reis told me there was too
much red-tape to get the exact types I wanted, there was a relevant
pre- Colombian variety in their collection called Lehna. This was
contrasted to a modern variety found to be highly responsive to
bacterial innoculation. Lehna
Slide 20
20 Can I isolate bacteria and DNA to ship to Canada for further
study? I was able to sign a material transfer agreement between the
University of Guelph and EMBRAPA, allowing me to transport DNA back
to Canada. I was unable to buy DNA extraction kits with EMBRAPA
(importation fees and times were prohibitive) so my supervisor in
Guelph bought the MoBio kit and mailed it so that it arrived 2
weeks before I left Brazil. Export of live bacteria, seeds or soil
were absolutely out of the question Dr. Reis told me, as there
would be years of paperwork involved. I never isolated any
bacterial strains since I could not do any further analysis.
Expected and achieved results
Slide 21
21 Expected and achieved results
Slide 22
22 Expected and achieved results Extracted DNA from leaf and
root surfaces, and root interiors from 5 plants per genotype per
soil treatment. Also extracted DNA from soil samples, water in
empty cups in the greenhouse, and washes from seed surfaces. These
120 tubes were put in my lugagge and flown back to Canada for
analysis. X120
Slide 23
Lessons Learnt and Next Steps 23 I had big intentions to
conduct a experiment in Brazil, sourcing biological materials from
all over the world, sending biological materials back to Canada,
and discovering biological novelty for international agriculture
and my own personal glory I learnt that Brazilians are very
paranoid about biopiracy and have implemented many rules to protect
and restrict access of biological materials. The prehistoric
Amazonian soil I selected to use is world famous, and very highly
regulated for transportation and research purposes.
Slide 24
Lessons Learnt and Next Steps 24 Beurocracy, taxation, and
uncertainty figure prominently in the mindset and reality of
scientific research in Brazil (as they might in many developing
countries). Research products are often imported with over 100%
import taxes, huge wait times, and the need for lying/cheating to
expedite delivery. Only Brazilians can currently apply for jobs at
the Brazilian ministry of agriculture (this might be changing so as
to lure more international talent to Brazil)
Slide 25
Lessons Learnt and Next Steps A huge competitive advantage
exists for companies to develop scientific products for sale within
Brazil importation taxes and delivery times are very effective
tariffs. EMBRAPA is not very international. Few people speak
English (although all claim to want to) and Brazilians have to
leave the country to gain exposure to international research.
25
Slide 26
Next Steps I am in the process of doing analysis of DNA at my
NSERC Funded Post-doc at the start up soil microbiology company,
A&L Biologicals in London, Ontario. I have made a partnership
with Dr. Jeff Dangl at the University of North Carolina, Chapel
Hill, who will generate additional data with the DNA using
pyrosequencing. Great opportunities to partner A&L Biologicals
with EMBRAPA to research soil borne plant diseases such as yellow
death of oil palm, which would be a boon to many countries all over
the world. Well just need to find money and time to do this...
26
Slide 27
Future budget and future requirements This internship/project
would not have been possible without IICA funding. I was to have
recieved additional funding from two other sources, but neither
came through and I had to cover some personal and profesional
expenses using pocket money Additional experiments are planned, but
these are to be funded by my current employer and my collaborator
at the University of North Carolina. I hope IICA will consider
funding future students who may wish to visit the University of
Guelph or A&L Biologicals to learn about Canadian research on
soil microbiology. 27
Slide 28
Thank you! IICA Canada for funding agricultural cooperation and
this project! Dr. Manish Raizada for co-writing the grants and
purchasing DNA extraction kits Dr. Veronica Reis for hosting me and
helping me conduct this experiment in Brazil All my new colleagues
and friends in Seropedica, Rio de Janeiro, Brasilia, Salvador and
Sao Paolo 28