Rhizobium Genomics Group (RHIZOGEN)

Centro de Biotecnología y Genómica de Plantas (CBGP)

UPM-INIA (CSIC), Madrid, Spain

Soil Metagenomics of the

Legume-Rhizobial Symbiosis

Legume and Rhizobia:

A root nodule symbiosis …

… that fixes nitrogen

Agricultural Importance

of Legumes

2nd after cereals (above 11% cultivated land)

Protein and oil-rich: main source of protein foranimal feed

Also used as forage, often in rotation with cereals, where they enrich the soil for the cereal crop

Only major agricultural crops providing a self-sufficient, sustainable input of fixed Nitrogen toagricultural systems

N2 fixation by legumes

The rhizobial-legume symbiosis

Very specific: co-evolution of plants and bacteria

Controlled by the plant, providing an ideal niche for theanaerobic process of nitrogen fixation within the rootnodule

As a result, the legume plant becomes independent of anyexternal source of fixed N

As a result, the rhizobia thrive in a protected environment, thus maintaining and increasing their numbers in soil

O2

PhotosynthateN2

NH4+

Rhizobia as soil bacteria

Rhizobia are soil bacteria devoting a very smallpercentage of their very large genome to the symbioticdeterminants

For any given legume, efficient, inefficient, and non symbiotic rhizobia co-exist in the same soil

Inefficient rhizobia highly adapted to a specific soilusually outperform efficient laboratory strains in theircolonization of their legume plant host. This is a sourceof trouble (inoculation) and a potential area of improvement

Clear-cut case for metagenomic study of soil and rhizospheric rhizobial populations. However …

Rhizobium is a minor soil inhabitant

≈104 R. leguminosarum bv. viciae viable cells per g soil

MPN plant trap method: only symbiotic rhizobia isolated

Direct isolation method: both symbiotic and non-symbiotic rhizobia isolated (1:3 ratio)

This is ≈ 0.1% viable bacteria per g soil

≈105 R. leguminosarum bv. viciae viable cells per g host legume rhizosphere soil

Are standard metagenomic strategies appropriate?

Our current projects. 1

Genomic determinants of rhizobial genotypeselection by the host

R. leguminosarum

bv. viciae, 7.8 Mb

Lens Pisum Vicia sativa Vicia faba Lathyrus

Our current projects. 2

Rhizobial adaptation to a recently descovered lupin species: Lupinus mariae-josephae, growing on basic soils in Eastern Spain: only lupin from basic soils

Not nodulated by rhizobia from other, acidic lupins

Nodulated by novel rhizobia, foundwith the plant in its endemic region, rhizobia nodulating Retama in basicsoils of Northen Algeria, and in basicsoils of Chiapas (Mexico)

Metagenomic, comparative studies of these basic soils are obviouslyinteresting, but will they provide usefulinformation on the rhizobia?

Our current projects. 3

25% electrons fed to nitrogenase end up as H2 as a result of the catalytic mechanismof the enzyme

Hup+ rhizobia (rare) recycle this H2, thusincreasing the energy efficiency of thesymbiosis

However, the production or absence of H2

also has an effect on the soil microbiome(increase in hydrogen-assimilatingbacteria)

Amenable to “standard” soil metagenomicsexperiments

H2

NH4 N2

+

ROOT

ENERGY

organic

N

N2ase

Hup-

N2NH4

+

N2ase

H2

ROOT

ENERGY

organic

N

HUP

Hup+

CENTRO DE BIOTECNOLOGÍA

Y GENÓMICA DE PLANTASUPM – INIA

MONTEGANCEDO (MADRID, SPAIN)

WWW.CBGP.UPM.ES