Plant-Microbe Symbiosis

Arbuscular mycorrhizal fungi (AMF) form symbioses with most plant species. They are ecologically important determinants of plant growth and diversity. Considerable genetic variation occurs in AMF populations. Thus, plants are exposed to AMF of varying relatedness to each other. Very little is known about either the effects of coexisting AMF on plant growth or which factors influence intraspecific AMF coexistence within roots. No studies have addressed whether the genetics of coexisting AMF, and more specifically their relatedness, influences plant growth and AMF coexistence. Relatedness is expected to influence coexistence between individuals, and it has been suggested that decreasing ability of symbionts to coexist can have negative effects on the growth of the host. We tested the effect of a gradient of AMF genetic relatedness on the growth of two plant species. Increasing relatedness between AMFs lead to markedly greater plant growth (27% biomass increase with closely related compared to distantly related AMF). In one plant species, closely related AMF coexisted in fairly equal proportions but decreasing relatedness lead to a very strong disequilibrium between AMF in roots, indicating much stronger competition. Given the strength of the effects with such a shallow relatedness gradient and the fact that in the field plants are exposed to a steeper gradient, we consider that AMF relatedness can have a strong role in plant growth and the ability of AMF to coexist. We conclude that AMF relatedness is a driver of plant growth and that relatedness is also a strong driver of intraspecific coexistence of these ecologically important symbionts.

Phosphorus is the second important key element after nitrogen as a mineral nutrient in terms of quantitative plant requirement. Although abundant in soils, in both organic and inorganic forms, its availability is restricted as it occurs mostly in insoluble forms. The P content in average soil is about 0.05 % (w/w) but only 0.1 % of the total P is available to plant because of poor solubility and its fixation in soil (Illmer and Schinner, Soil Biol Biochem 27:257-263, 1995). An adequate supply of phosphorus during early phases of plant development is important for laying down the primordia of plant reproductive parts. It plays significant role in increasing root ramification and strength thereby imparting vitality and disease resistance capacity to plant. It also helps in seed formation and in early maturation of crops like cereals and legumes. Poor availability or deficiency of phosphorus (P) markedly reduces plant size and growth. Phosphorus accounts about 0.2 - 0.8 % of the plant dry weight.To satisfy crop nutritional requirements, P is usually added to soil as chemical P fertilizer, however synthesis of chemical P fertilizer is highly energy intensive processes, and has long term impacts on the environment in terms of eutrophication, soil fertilility depletion, carbon footprint. Moreover, plants can use only a small amount of this P since 75--90% of added P is precipitated by metal--cation complexes, and rapidly becomes fixed in soils. Such environmental concerns have led to the search for sustainable way of P nutrition of crops. In this regards phosphate-solubilizing microorganisms (PSM) have been seen as best eco-friendly means for P nutrition of crop. Although, several bacterial (pseudomonads and bacilli) and fungal strains (Aspergilli and Penicillium) have been identified as PSM their performance under in situ conditions is not reliable and therefore needs to be improved by using either genetically modified strains or co-inoculation techniques. This review focuses on the diversity of PSM, mechanism of P solubilization, role of various phosphatases, impact of various factors on P solubilization, the present and future scenario of their use and potential for application of this knowledge in managing a sustainable environmental system.

There is a concerted understanding of the ability of root exudates to influence the structure of rhizosphere microbial communities. However, our knowledge of the connection between plant development, root exudation and microbiome assemblage is limited. Here, we analyzed the structure of the rhizospheric bacterial community associated with Arabidopsis at four time points corresponding to distinct stages of plant development: seedling, vegetative, bolting and flowering. Overall, there were no significant differences in bacterial community structure, but we observed that the microbial community at the seedling stage was distinct from the other developmental time points. At a closer level, phylum such as Acidobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria and specific genera within those phyla followed distinct patterns associated with plant development and root exudation. These results suggested that the plant can select a subset of microbes at different stages of development, presumably for specific functions. Accordingly, metatranscriptomics analysis of the rhizosphere microbiome revealed that 81 unique transcripts were significantly (P<0.05) expressed at different stages of plant development. For instance, genes involved in streptomycin synthesis were significantly induced at bolting and flowering stages, presumably for disease suppression. We surmise that plants secrete blends of compounds and specific phytochemicals in the root exudates that are differentially produced at distinct stages of development to help orchestrate rhizosphere microbiome assemblage.

The leaves of fescue grasses are protected from herbivores by the production of loline alkaloids by the mutualist fungal endophytes Neotyphodium sp. or Epichloë sp. Most bacteria that reside on the leaf surface of such grasses can consume these defensive chemicals. Loline-consuming bacteria are rare on the leaves of other plant species. Several bacterial species including Burkholderia ambifaria recovered from tall fescue could use N-formyl loline as a sole carbon and nitrogen source in culture and achieved population sizes that were about eightfold higher when inoculated onto plants harboring loline-producing fungal endophytes than on plants lacking such endophytes or which were colonized by fungal variants incapable of loline production. In contrast, mutants of B. ambifaria and other bacterial species incapable of loline catabolism achieved similarly low population sizes on tall fescue colonized by loline-producing Neotyphodium sp. and on plants lacking this endophytic fungus. Lolines that are released onto the surface of plants benefiting from a fungal mutualism thus appear to be a major resource that can be exploited by epiphytic bacteria, thereby driving the establishment of a characteristic bacterial community on such plants

Cell walls are deeply involved in the molecular talk between partners during plant and microbe interactions and their role has been extensively investigated in mycorrhizae, i.e., the widespread symbiotic associations established between plant roots and soil fungi (Bonfante and Genre 2010). All mycorrhizal interactions achieve full symbiotic functionality with the development of an extensive contact surface between the plant and fungal cells, where nutrients and signals are exchanged. In more detail, the exchange of molecules from the fungal to the plant cytoplasm and viceversa takes place through both partners’ plasma membranes and cell walls, defining a functional compartment known as the symbiotic interface (Bonfante 2001; Harrison 2005). Plant cell walls form a dynamic extracellular matrix that actively controls plant growth and development (Sattelmacher and Horst 2007). An analogous condition is found in fungi, where the cell wall determines hyphal growth, shape and responses (Durán and Nombela 2004). Not surprisingly, cell wall organization and composition within the interface compartment has attracted strong attention, both in ecto- and endomycorrhizae (Balestrini and Bonfante 2005; Balestrini et al. 1996; Genre and Bonfante 2012). 
The aim of this review is to provide a general overview of the current knowledge integrating morphological observations which have illustrated cell wall features in ecto- and endomycorrhizae with the today data produced by the genomics and transcriptomics approaches. 
Among all symbiotic interfaces, the complex intracellular interface of arbuscular mycorrhizal (AM) symbiosis has received large attention since its first description. Here in fact the host plasmamembrane invaginates and proliferates around all the developing intracellular fungal structures and cell wall material is laid down between this membrane and the fungal cell surface (Balestrini and Bonfante 2005). Transcriptome analysis, on roots colonized by AM fungi, revealed up-regulation of many genes directly or indirectly involved in cellular reorganization events, which may be required for fungal accommodation, including several genes involved in cell wall metabolism (Guether et al. 2009). On the other side, in ectomycorrhizae (ECM), where the fungus grows outside and among the root cells, plant and fungal cell walls are always in direct contact and form the interface between the two partners (Martin 2007). In recent years, thanks to the genome/transcriptome projects of several fungal species, the analysis of the cell wall-degrading enzymes present in the genome has offered information on their own specialized lifestyles and their adaptation capacity (Balestrini et al. 2012). It has been recently reported that the ECM fungi Laccaria bicolor and Tuber melanosporum genomes contains a reduced gene set involved in the production of enzymes that are active on the plant cell wall polysaccharides (Martin et al. 2008; Martin et al. 2010), compared to saprotrophic and pathogenic fungi (Martin and Selosse 2008). T. melanosporum and L. bicolor may use different gene sets for plant cell wall degradation, which would seem to suggest differences in the mode of interaction with the respective host plants (Martin et al. 2010). A lack of expression of hydrolitic enzymes acting on plant cell wall polysaccharides has been reported also in the AM fungus Rhizophagus irregularis (syn. Glomus intraradices), revealing a similarity with obligate biotrophic pathogens. By contrast, a large set of genes encoding enzymes involved in fungal cell wall metabolism were expressed, suggesting a role in remodeling the fungal cell wall during growth and symbiosis (Tisserant et al. 2012). 
In conclusion, advances in mycorrhizal fungal genome/transcriptome sequencing is suggesting that the strict regulation of the cell wall-related genes from both the partners, together with the reciprocal remodeling of their cell walls at the interface and the production of signaling molecules (Genre et al. 2013), is one of the key element to understand biotrophism.