Streptomyces are ubiquitous bacteria representing alone about 10% of the microbial soil flora (Janssen, 2006) and are found in all the terrestrial as well as marine ecosystems. In forest soils, they are found in the mineralosphere, the mycorhizosphere and the rhizosphere, and even in the endorhizosphere in the case of alder (Liu et al., 2009). They modulate the plant defences towards pathogenic agents either by favouring invasion of the roots by the pathogen, or by stimulating local and systemic defence and favouring plant growth (Lehr et al., 2008). They also behave as auxiliary of symbiosis between trees and ectomycorhizial fungi (Tarkka et al., 2008). At last, in some cases, Streptomyces are recruited as symbionts by insects such as in ants where they protect cultivated fungi from pathogenic ones (Currie et al., 1999).
This high capacity to colonize multiple niches and interact with other organisms such as fungi is directly linked to their life style and growth form (mycelium growth and spore formation) and their rich secondary metabolism. This latter includes secreted enzymes and a vast array of metabolites. Extracellular enzymes allow them to degrade complex vegetal, animal and fungal polymers such as lignin and chitin (McCarthy et Williams, 1992). If the role of secondary metabolites as weapon is likely (Chater, 2006), they could also act as molecular signalling in cellular communication (Linares et al., 2006; Davies, 2006) and interfere with gene transfer phenomena. These metabolites are then expected to have a strong impact on the structuration of the soil microbial communities.
Streptomyces are possessing one of the largest bacterial genomes with an 8-10 Mb linear chromosome. While the central part of the linear chromosome shows a global conserved organization, the terminal regions, over several hundreds of kilobases (10 to 20% of the genome), are highly variable and specific. Analysis of the gene functions encoded in these regions recently revealed that they mainly correspond to xenologues, i.e. paralogues derived from HGT. Moreover, when a function could be ascribed, it suggested a possible adaptative role of these genes. For example, the presence of gene clusters involved in the biosynthesis of secondary metabolites typifies the terminal regions (Bentley et al., 2002). Thus, Streptomyces show a strong delimitation of ‘core’ and ‘accessory’ genomes roughly corresponding to ‘vertical’ versus ‘horizontal’ inherited gene pools. Previous comparative genome analyses at the interspecific level highlighted specific evolutionary schemes that would have diversified the pool of adaptation genes in Streptomyces (Choulet et al., 2006a). A close analysis of the frontiers between the conserved and specific regions revealed that this zone corresponds to a synthenic region riddled with multiple short insertions and deletions (indels of 1-10 genes). Interestingly, these frontiers between the conserved and specific regions seem to “move” towards the inner regions of the central core part when the phylogenetic distance between the compared species is increasing. Consequently, the conserved region tends to reduce in size when comparing distantly related species. Thus, the gene flux progressively erased the common ancestral organization of the chromosome ends and tends to reduce the size of the conservedr region. Conjugation is most probably involved in gene fluxes in Streptomycetes in the absence of known natural competence and transducing phages. The conjugation machinery is actually much simpler with a single membrane-associated ATPase (Tra) similar to DNA translocases, such as SpoIIIE of Bacillus subtilis (Wu and Errington, 1997), sufficient for plasmid transfer. A plasmid-borne cis-acting sequence of about 50 bp, called clt, is recognized by Tra (Reuther et al, 2006). Another original feature is the transfer of double-stranded DNA (Possoz et al., 2001). In contrast to the recent knowledge on plasmid transfer in Streptomyces, chromosomal DNA mobilization is very poorly documented, except that it was proven that conjugative elements stimulate chromosomal DNA transfer (Pettis and Cohen, 1994).
Thus, Streptomyces constitute an interesting model to study the impact of biotic stimuli on gene fluxes in soil especially in the frame of biotic interactions in fungi/bacteria/plants consortia (Tarkka et al., 2009). While several hot-spots for conjugal gene transfer have been identified in the plant rhizosphere (Lilley et al., 2004), the phylloplane (Normander et al., 1998) and the spermosphere (Sorensen and Jensen, 1998), nothing is known about conjugation events in the mycorhizosphere (soil surrounding mycorrhizal roots) and the pathosphere (soil surrounding diseased roots). In addition, gene echange seems stimulated in niches where bacterial communities can reach high densities (such as biofilms, Sorensen et al., 2005).
In addition, their remarkable genetic organization, i.e. compartmentalization, separating ‘core’ and ‘accessory’ genomes provides an interesting situation to study their relative evolution processes.