soil microbiology!

www.iita.org A member of CGIAR consortium

Soil Microbiology!

Danny Coyne

24th November 2015

(R4D Week 2015)


Soil Microbiology!

Lots and lots of people

IITA +

R4D Week, Ibadan, November, 2015

A member of CGIAR consortium

THE UNCONVENTIONAL

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


Soil Biodiversity

AMF

Arbuscular

Mycorrhizal

Fungi


Soil Biodiversity

AMF

Benin

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)


Soil Biodiversity


Our knowledge of BENEFICIAL soil biota

in

Africa??

Soil Biodiversity


Production growth will need to come

from intensification

In Africa


Maize-legume farming

systems

• 20% of the cultivated area

Maize-legume crisis

• Soil fertility • Pests and diseases • Low productivity


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)


• Prospecting for Rhizobia:

– What is there

• Selection for performance strains/species :

– best bets

• Local adaptation and suitability:

− From best bet to ‘best fits’

Rhizobiology

Progress in rhizobiology e.g. Kenya

Bio-prospecting

Preliminary screening

Greenhouse assessment

Competitive abilities

Field testing

208 isolates

186

100

24

16


Response to rhizobia

Cowpea biomass


Optimizing N levels

However

Soil Total Nitrogen %


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


N2Africa

Product registration : NAFDAQ approval in 2015


endophytes

Spore

suspension

drench

Biological enhancement of planting

material


endophytes

Delivery of microbial inoculants

with endophytes without endophytes


Striga

www.iita.org


Striga

Wilts


Striga

Wilts

Root Rots


Striga

Wilts

Root Rots

Etc…………


Root-knot nematodes

Effective partnerships


Tropical root-knot nematodes

Targeting

Species delimitation is problematic because they are the result of hybridization!

new species? A C A A C C



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




Molecular identification of root-knot nematodes in

Africa

Benin

Kenya

Nigeria

Tanzania

Uganda


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


THE UNCONVENTIONAL

New Science to Tackle Persistent Problems


AMF

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


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


Selection of the locus (SSU rDNA)

THE UNCONVENTIONAL


THE UNCONVENTIONAL


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


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

Protists


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


PVN delivery



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


Transgenic neuropeptide nematicides

Strongly protective against nematode infection

Neuropeptide genes coordinate crucial behaviors

unconventional


Neuropeptides

Delivery by Rhizobacteria & Microalgae

Re-cap

Productivity – yield gaps

Keating et al., 2010

Production growth will need to come

from intensification

In Africa

Sustainable

Intensification

of

smallholder farming

systems

in

sub‐Saharan Africa


Way forward

”……accurate information on the state of Africa's soils”

Biological control

Delivery - targeted

Quality control

Product development

at scale

It is not always what you see

that matters