Presentation during IITA R4D week 2015 (23 - 27 Nov. 2015). By: Danny Coyne.

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Soil Microbiology!
Danny Coyne
24th November 2015
(R4D Week 2015)

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Soil Microbiology!
Lots and lots of people
IITA +
R4D Week, Ibadan, November, 2015

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THE UNCONVENTIONAL

6. The Soil
“If we are to feed growing populations and
cope with climate change, we need accurate
information on the state of Africa's soils”
Nteranya Sanginga
TSBF-CIAT
On the announcement of a $18 million project to map soils

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Soil Biodiversity
AMF
Arbuscular
Mycorrhizal
Fungi

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Soil Biodiversity
AMF
Benin

9. AMF species biodiversity potential??
Total identified:
8 genera
59 species
Six new species described:
Racocetra beninensis n.sp.
Racocetra tropicana n.sp.
Acaulospora sieverdingii n.sp
Acaulospora minuta n.sp.
Acaulospora spinosissoma n.sp.
Acaulospora fossa n.sp.
Revision of the Glomeromycotes, with description of two
new families and eight new genera and organization of glomoid species
BOTANISCHES INSTITUT
DER UNIVERSITÄT BASEL (SCHWEIZ)

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Soil Biodiversity

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Our knowledge of BENEFICIAL soil biota
in
Africa??
Soil Biodiversity

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Production growth will need to come
from intensification
In Africa

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Maize-legume farming
systems
• 20% of the cultivated area
Maize-legume crisis
• Soil fertility
• Pests and diseases
• Low productivity

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Enhancing legume productivity
 Major efforts through two projects
• Putting nitrogen fixation to work for smallholder
farmers in Africa (N2Africa)
• Institutionalization of quality assurance and
dissemination of high quality commercial
products (COMPRO-II)

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• Prospecting for Rhizobia:
– What is there
• Selection for performance strains/species :
– best bets
• Local adaptation and suitability:
− From best bet to ‘best fits’
Rhizobiology

17. Progress in rhizobiology e.g. Kenya
Bio-prospecting
Preliminary screening
Greenhouse assessment
Competitive abilities
Field testing
208 isolates
186
100
24
16

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Response to rhizobia
Cowpea biomass

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Optimizing N levels
However
Soil Total Nitrogen %

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COMPRO
 >100 products evaluated
 ~ 3000 trials in 2015
 mainly bio-fertilizers, bio-pesticides,
 ≥ 90% have been found sub-
standard or ineffective
Promotion of quality products through COMPRO and N2Africa
increase farmer confidence and adoption of biological products

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N2Africa
Product registration : NAFDAQ approval in 2015

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endophytes
Spore
suspension
drench
Biological enhancement of planting
material

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endophytes
Delivery of microbial inoculants
with endophytes without endophytes

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Striga
www.iita.org

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Striga
Wilts

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Striga
Wilts

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Striga
Wilts
Root Rots

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Striga
Wilts
Root Rots
Etc…………

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Root-knot nematodes
Effective partnerships

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Tropical root-knot nematodes
Targeting
 Species delimitation is problematic because
they are the result of hybridization!
new species? A C A A C C
new species? A C A A C C
new species? A C A A C C
sister species A C C T G G
sister species A C C T G G
sister species A C C T G G
other species1 A T C A G C
other species1 A T C A G C
other species1 A T C A G T
other species2 C T C A G C
other species2 C T C A G C
other species2 C T C A G C

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Molecular identification of root-knot nematodes in
Africa
Benin
Kenya
Nigeria
Tanzania
Uganda

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Molecular identification of root-knot nematodes in
Africa
Targeting
Pagan, C., Coyne, D., Carneiro, R., Kariuki, G., Luambana, N., Affokpon,
A., and Williamson, V. M. 2015. Mitochondrial haplotype-based
identification of ethanol-preserved root-knot nematodes from Africa.
Phytopathology 105:350-357
Janssen, Karssen, Verhaeven, Coyne and Bert. 2015. Mitochondrial coding
genome analysis of tropical root-knot nematodes (Meloidogyne)
supports haplotype based diagnostics and reveals evidence of recent
reticulate evolution. Scientific Reports Nature
Effective partnerships

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THE UNCONVENTIONAL
New Science to Tackle Persistent Problems

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AMF
A MICROBIAL REVOLUTION:
improving mycorrhizal fungi to increase
cassava productivity in Africa

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AMF
 Selection of progeny from parents with genetic variability
AMF Inoculated
Selection of the locus (SSU rDNA)
 will support a greater range of responses in cassava

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Selection of the locus (SSU rDNA)
THE UNCONVENTIONAL

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THE UNCONVENTIONAL

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Novel Delivery - Protists
 single-celled, e.g. ciliates, protozoans
 ingest micro-particles or bacteria
 move through unsaturated soils
 can chemotact toward the root tips
Protists

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Particulates may include:
- beneficial bacteria
or - encapsulated chemicals
or - encapsulated nutrients
Protists

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 SO – can we exploit them for plant protection?
 Viral nanoparticles serve as applications in medicine
Red clover necrotic mosaic virus-based
plant viral nanoparticle (PVN) carrier
unconventional

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PVN delivery
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enhanced delivery of anthelminthic compounds
at low rates using PVN carrier
Abamectin (Abm) is a strong biological
pesticide
BUT
poor mobility in the soil
PVN delivery

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Transgenic neuropeptide nematicides
 Strongly protective against nematode infection
 Neuropeptide genes coordinate crucial behaviors
unconventional

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Neuropeptides
Delivery by Rhizobacteria & Microalgae

46. Re-cap

47. Productivity – yield gaps
Keating et al., 2010
Production growth will need to come
from intensification
In Africa

48. Sustainable
Intensification
of
smallholder farming
systems
in
sub‐Saharan Africa

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Way forward
”……accurate information on the state
of Africa's soils”
 Biological control
 Delivery - targeted
 Quality control
 Product development
 at scale

50. It is not always what you see
that matters