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