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The rhizosphere community represents an “ecological interface” between plant and soil, providing the plant with a number of advantages. Despite close connection and mutual influence in this system, the knowledge about the connection of plant and rhizosphere diversity is still controversial. One of the most valuable factors of this uncertainty is a rough estimation of plant diversity. NGS sequencing can make the estimations of the plant community more precise than classical geobotanical methods. We investigate fallow and crop sites, which are similar in terms of environmental conditions and soil legacy, yet at the same time are significantly different in terms of plant diversity. We explored amplicons of both the plant root mass (ITS1 DNA) and the microbial communities (16S rDNA), determined alpha- and beta-diversity indices and their correlation, and performed differential abundance analysis. In the analysis, there is no correlation between the alpha-diversity indices of plants and the rhizosphere microbial communities. The beta-diversity between rhizosphere microbial communities and plant communities is highly correlated (R = 0.866, p = 0.01). ITS1 sequencing is effective for the description of plant root communities. There is a connection between rhizosphere communities and the composition of plants, but on the alpha-diversity level we found no correlation. In the future, the connection of alpha-diversities should be explored using ITS1 sequencing, even in more similar plant communities—for example, in different synusia.

The rhizosphere community represents an “ecological interface” between plant and soil, providing the plant with a number of advantages. Close connection and mutual influence in this communication allow to talk about the self-adjusting “plant-rhizosphere community” system, which should be be studied in connection. Diversity estimation is one of the ways of describing both bacterial and plant communities. Based on the literature, there are two assumptions of how the diversity of plant communities related to the diversity of bacterial communities: 1) an increase in the species richness of plants leads to an increase in the number of available micro-niches, and increasing of microbial diversity, 2) an increase in the species richness of plants is accompanied by the predominant development of bacteria from highly productive specific taxa and decreasing in the diversity of microorganisms. Experimental studies show controversial results.We analyzed field sites (rye crop field and two fallow sites), using DNA isolation of both the plant root mass (followed by sequencing of the ITS1 region) and rhizosphere microorganisms (followed by sequencing of the 16s rDNA V4 region). This allowed us to 1) accurately determine the abundance and taxonomic position of plant communities; 2) extract information about both plant and microbial communities from the same sample.There was no correlation between alpha-diversity indices of plants and rhizosphere communities. Alpha-diversity connection should be explored in similar plant communities, such as synusia. We hypothesize, that the significant differences in plant abundances lead to significant changes in exudation profiles, and the loss of diversity connection. The beta-diversity between rhizosphere communities and plant communities is highly correlated, in particular in terms of the abundance of taxa. This can be explained by a potential correlation (as reported in the literature) or by the presence of statistical artifacts.

In the N2-fixing symbionts of legumes (rhizobia), the evolution of (altruistic) characters that are useful for a host occurs in the populations colonizing the subscellular compartments of nodules (infection threads, symbiosomes). These compartments appear as a result of the coevolution of partners, which is associated with the complication of the trophic and regulatory interactions determining the ecological efficiency of symbiosis. Their analysis allows us to study the correlation of the mechanisms of the adaptive and progressive evolution of symbiosis, which is still unclear for free-living organisms.

The mathematical model is constructed which describes the impacts of chaotically changing environment on the frequencies and productivity of partners in the legume-rhizobia symbiosis. The most sensitive for external impacts are the adaptively prospective bacteria strains which are specific with respect to hosts and are capable for the intensive evolution towards an improved symbiotic efficiency. An increased stability of these strains in symbiotic system may be an important factor of its evolution for the improved efficiency of partners’ interaction.

In N2-fixing symbionts of leguminous plants (rhizobia) evolution of the host-beneficial (“altruistic”) traits occurs in populations colonizing the subcellular compartments in nodules (infection threads, symbiosomes). These compartments are developed as a result of partners’ coevolution related to complications of trophic and regulatory interactions elevating the ecological efficiency of symbiosis. Their analysis enables us to study correlations between genetic mechanisms of adaptive and progressive symbiosis evolution which remain obscure in free-living organisms

Using the example of nodular legume-rhizobia symbiosis (LRS), we discuss the evolution in plant micro-symbionts of mutualistic traits that are apparently host-beneficial and therefore the products of inter-species evolution. These traits include: in planta activation of N2 fixation machinery; exporting the products of nitrogenase reaction into the plant cells/tissues; and the terminal differentiation of bacteria into non-reproductive N2-fixing bacteroids. It seems probable that such adaptive traits evolved by natural selection within the populations of endosymbiotic bacteria that colonize the extra- and intra-cellular compartments provided by the hosts (i.e., infection threads and symbiosomes). This evolution would occur under the impacts of group (inter-deme, kin) selection pressures induced by the partners’ metabolic and regulatory feedbacks that ensure the high activity of symbiotic N2 fixation. These important feedbacks include: progressive allocation of C compounds into N2-fixing nodules; maintenance of micro-aerobic intracellular environments that are indispensable for intensive N2 fixation; and stringent control by the host over bacterial reproduction in planta. A computational simulation of the associated co-evolutionary processes reveals the trade-off between inter-species and individual species components of progressive and adaptive LRS evolution. This is expressed as a correlated increase of ecological efficiency, functional integrity and genotypic specificity of mutualistic symbiosis. Thus, the evolution of rhizobia in symbiosis may be represented by a progressive multi-level scenario based on increasing the dependency of bacteria on the host-provided nutrients accompanied by increasing complexity of the bacterial genomes and of the symbiosis-encoding gene networks.

Based on the knowledge on the structural and functional organization, ecological potential, and evolution of symbiotic complexes, we suggest to formulate the subject, aims, and methodology of symbiogenetics as a science studying the genetic control of interspecies interactions. It is based on the view on the superspecies system of variation and heredity (symbiogenome) controlling the development of novel properties lacking in the unitary organisms and radically extending their adaptive potentials. Investigation of symbiogenomes represents the first step toward genetic analysis of microbiomes and metagenomes, which are superspecies hereditary systems responsible for developing the multicomponent complexes of biocenotic type, such as rumen microflora, endophytic and rhizospheric communities, soil microbial consortia. The approaches of symbiogenetics can be used for developing biotechnologies of integration of plants or animals with beneficial microbes ensuring host nutrition and development as well as resistance to biotic and abiotic stresses.

The methodology is suggested for analyzing the variability and heredity in super-organism genetic systems of different complexity ranging from two-component plant-microbe and animal-microbe symbiosis to the endosymbiotic and soil microbial communities. The approaches based on symbiogenetics and metagenomics may be used for development of highlyproductive ecologically sustainable agrocenoses based on the substitution of agrochemicals (mineral fertilizers, pesticides) by the microbial preparations. A possibility is emphasized to use the natural analogs of agrocenoses for development of models to implement the directed construction and improvement of productivity in the sustainable agricultural systems.

Legumes develop different mutually beneficial microbial-root symbioses such as arbuscular mysorrhiza (AM), rhizobium-legume symbiosis (RLS) and epiphytic or endophytic associations with plant growth-promoting bacteria (PGPB) which are distinguished in level of integration of the partners. Evidences of the role of AM as ancestral form of symbiosis which might be a source of the legume pre-adaptation to form some RLS are demonstrated. The RLS is supposed to evolve for a few times in ancient legumes in parallel ways based on the universal organization and regulatory mechanisms of the plant genetic material. Associations of plant roots with PGPB probably are the vestige of the early stages of evolution in morphologically differentiated RLS. Also, it is quite possible that 'first' rhizobia have originated from bacterial endosymbionts of AM fungi; then AM fungi might operate as effective vectors for introducing bacteria into the plants. Thus, the legume root symbioses may be considered as a single 'evolutionary plant-microbial continuum'. The acquired knowledge about evolution of plantmicrobe symbioses would contribute to the creation of new commercial varieties of plants with the use of both bio-engineered methods and traditional plant breeding. An original conception of legume breeding to improve their symbiotic effectiveness is proposed.

The development of symbioses ensures formation of the super-organism systems for heredity (symbiogenomes) which represent the products of joint adaptations of partners towards an unfavorable environment. Using the examples of symbioses which enable plants and microorganisms to cooperatively overcome the limitations in the major biogenic elements (C, N, P) or impacts of the biotic and abiotic stresses we demonstrate that symbiosis involves not only the de novo formation (epigenesis) by plant of the ecological niches for hosting the microsymbionts, but also the reorganizations of relevant genetic systems in accordance to the partners’ genotypes and environmental conditions. A possibility to address the ongoing processes in terms of epigenetics is evident when the microsymbionts occurring in the novel niches are included into the host reproduction cycle ensuring a stable maintenance of novel adaptation in the next generations suggesting that the newly formed symbiogenome have acquired the properties of a system for inheritance of the newly acquired adaptive traits.

Simulation of evolution in the legume-rhizobial symbiosis allowed us to suggest the mathematical criterion (index) for the functional integrity of symbiosis (FIS). Calculation of FIS index is based on analysis of the covariance matrix of partners’ frequencies influenced by fluctuations of the systemic parameters. The positive correlations of FIS with ecological efficiency of symbiosis (its impact on the seed productivity of plants) and a negative correlation with the partners’ diversity indices were demonstrated. The revealed dependences allow us to explain the increasing of structural-functional integrity in mutualistic symbiosis byoperation of the natural selection in favor of an improved ecological efficiency of partners’ interactions.

Inactivation of genes involved in the dicarbyxylic acid transport in alfalfa rhizobia, Sinorhizobium meliloti (structural gene of succinate permease dctA and its transcriptional regulators dctBD, nifA, ntrA) resulted in the full or partial loss of Nsub2/sub-fixing activity while amplifications of these genes - in its improvement. It lead to the marked increases of N and C accumulation in alfalfa while its shoot mass was increased by a much lesser degree due to the incomplete N translocation from the roots. Factorial analysis suggested that dctABD amplification was important for improving the symbiotic efficiency in all trials while the effects of dctA, nifA and ntrA amplifications depend on the plant genotypes and growth conditions.

The model is suggested for evolution of Nsub2/sub-fixing legume-rhizobia symbiosis implemented under the conditions of multi-strain bacteria competition for inoculation of symbiotic habitats (rhizosphere, nodules). Competitiveness of each strain is characterized by the power coefficients which reflect the operation of frequency-dependent selection in the rhizobia population. When polymorphic bacteria populations are interacting with the dimorphic plant population, the selective pressures in favor of hostspecific symbionts (forming Nsub2/sub-fixing nodules only with one of the available plant genotypes) are higher than the pressures in favor of non-host-specific symbionts (forming these nodules with both plant genotypes). The highest mutualism efficiency is reached under an intermediate level of plant population diversity.

The molecular mechanism of the agronomically important nutritional and defensive plantmicrobe symbioses are reviewed. These symbioses are based on the signaling interactions which result in the development of novel tissue/cellular structures and of extended metabolic capacities in the partners which improve greatly the adaptive potential of plants due to an increased tolerance to biotic or abiotic stresses. The molecular, genetic and ecological knowledge on plant-microbe interactions provide a strategy for a sustainable crop production based on substituting the agrochemicals (mineral fertilizers, pesticides) by the microbial inoculants. An improvement of plantmicrobe symbioses should involve the coordinated partners' modifications resulted in complementary combinations of their genotypes. The research presented in this paper is supported by grants from Russian Foundation of Basic Research (04-04-48457, 06-04-48800, 06-04-89000NWO); NWO Centre of Excellence: 047. 018. 001.

The mathematical model for evolution of legume-rhizobia mutualism based on the partners' positive feedbacks resulted from their metabolic (C-N) exchange is presented. Negative FDS in rhizobia population, combined with the partners' positive feedbacks ensure anchoring or even domination of the mutants which either acquired the mutualistic traits or changed the specificity in their expression with different host genotypes. The created model allows us to consider the mutualistic symbiosis as of a finely balanced population system in which the equilibrium may be shifted in favor of beneficial microbial genotypes due to natural selection for an improved symbiotic efficiency implemented in plant population. Research is supported by RFBR grant 06-04-48800a.

The purpose of the course "Genetic mechanisms of individual and cooperative adaptation" (12 semester 18 hours) - is to provide students with a broad view in population mechanisms of the different types of adaptation. The problem of the course consists in benchmark analysis of the ways and mechanisms of the origin of these adaptations, as well as in their possible macroevolution consequence. The individual adaptation is considered on model of stressful influence on populations. Cooperative adaptation is considered basically on model of symbiosis, whose formation associates with origin of new traits, which greatly increase evolution potential of biological species. The course develops the knowledge obtained from prerequisite courses, such as "General genetics" "Symbiogenetics", "General ecology" and "Theory of evolution".

The method for mathematical simulation is suggested to analyze the balanced polymorphism in rhizobia population generated due to the interplay of Darwinian and frequency-dependent selection. Analysis of the model suggested that this polymorphism is determined not only by the selection pressures but also by the capacities of ecological niches occupied by bacteria in the «plant-soil» system. The model may be used for analyzing the selective processes in various symbiotic systems and for predicting the consequences of releasing of genetically modified plant symbionts into environment.

We present the concept of symbiogenetics defined as a branch of general genetics which investigates the Super-Organism Genetic Systems (SOGS) formed due to functional integration of partners' genes during symbiotic interactions. The minimal hereditary unit within SOGS involves no less than a pair of genes that belong to different partners and interact according to the models of complementation or epistasis. Using the examples of plant-microbe interactions we demonstrate that the integrity of SOGS is maintained due to tight signal interactions between partners and is manifested as formation of common biochemical pathways and as development of special symbiotic structures. Using the models of nodule development we demonstrate that the origin of SOGS involves recruiting of genes, which performed diverse functions in free-living organisms, into the symbiotic regulatory networks. The progressive evolution of nodule structures in different dicot lineages was based on the parallel recruiting of genes from the ancestral gene pool into symbiotic regulatory networks. The majority of mutualistic and antagonistic plant-microbe symbioscs represent the components of an evolutionary continuum that originated early in land plants and underwent intensive transformations due to high plasticity of SOGS based on inter- and intra-gene recombination.

Formation of the cultured flora resulted in a decrease of plant symbiotic potential based on interactions with beneficial microorganisms. This decrease leads to transformation of plant micro-symbionts into the non-adaptive forms caused by: а) blocking the selection in favor of mutualistic strains; б) horizontal gene transfer in the microbial communities resulted in formation of virulent “symbiotic cheaters”. Mathematical simulation suggests that these tendencies may be overcome by formation of the optimal population structures in symbiotic system which should possess a high integrity and specificity of partners’ interactions as well as by a tolerance to the invasions of non-active aboriginal strains from the local soil populations.

Symbiosis, or “coexistence of diverse organisms”, is the term which was proposed firstly by Anton de Bary (1879). Roughly, there are three types of symbiosis: commensalism (an interaction which is beneficial for one symbiotic partner but neutral for the other), antagonism (or parasitism, where one symbiont develops to the detriment of another – see elsewhere in this Book) and mutualism (where both symbionts benefit from mutual coexistence). Mutualism is a special ecological and evolutionary strategy for two (or more) dissimilar organisms to share (allocate) all of their physiological functions between them rather than them being separated. This is distinguished principally from individual adaptations which are dependent on morpho-physiological and behavioural reactions of one free-living organism. Here there is an evolutionary opportunity to develop certain functions and possibly lose others leading to genetic and metabolic integration according to a dialectical law “negation of negation” which may be applicable to evolution. As a result some intimate genetic and metabolic cooperation between the symbiotic partners of complicated super-organismic systems develop resulting in new adaptations (functions) with their environments. In mutualistic (mutually beneficial) symbioses between plants and microbes, novel types of cells and tissues (physiologically and/or structurally) and even organs have often evolved (Douglas 1994; Tikhonovich and Provorov 2007)