SummaryRoot nodule symbioses (RNS) allow plants to acquire atmospheric nitrogen by establishing an intimate relationship with either rhizobia, the symbionts of legumes or Frankia in the case of actinorhizal plants. In legumes, NIN (Nodule INception) genes encode key transcription factors involved in nodulation.Here we report the characterization of CgNIN, a NIN gene from the actinorhizal tree Casuarina glauca using both phylogenetic analysis and transgenic plants expressing either ProCgNIN::reporter gene fusions or CgNIN RNAi constructs.We have found that CgNIN belongs to the same phylogenetic group as other symbiotic NIN genes and CgNIN is able to complement a legume nin mutant for the early steps of nodule development. CgNIN expression is correlated with infection by Frankia, including preinfection stages in developing root hairs, and is induced by culture supernatants. Knockdown mutants were impaired for nodulation and early root hair deformation responses were severely affected. However, no mycorrhizal phenotype was observed and no induction of CgNIN expression was detected in mycorrhizas.Our results indicate that elements specifically required for nodulation include NIN and possibly related gene networks derived from the nitrate signalling pathways.

Root endosymbioses are mutualistic interactions between plants and the soil microorganisms (Fungus, Frankia or Rhizobium) that lead to the formation of nitrogen-fixing root nodules and/or arbuscular mycorrhiza. These interactions enable many species to survive in different marginal lands to overcome the nitrogen-and/or phosphorus deficient environment and can potentially reduce the chemical fertilizers used in agriculture which gives them an economic, social and environmental importance. The formation and the development of these structures require the mediation of specific gene products among which the transcription factors play a key role. Three of these transcription factors, viz., CYCLOPS, NSP1 and NSP2 are well conserved between actinorhizal, legume, non-legume and mycorrhizal symbioses. They interact with DELLA proteins to induce the expression of NIN in nitrogen fixing symbiosis or RAM1 in mycorrhizal symbiosis. Recently, the small non coding RNA including micro RNAs (miRNAs) have emerged as major regulators of root endosymbioses. Among them, miRNA171 targets NSP2, a TF conserved in actinorhizal, legume, non-legume and mycorrhizal symbioses. This review will also focus on the recent advances carried out on the biological function of others transcription factors during the root pre-infection/pre-contact, infection or colonization. Their role in nodule formation and AM development will also be described.

BackgroundTrees belonging to the Casuarinaceae and Betulaceae families play an important ecological role and are useful tools in forestry for degraded land rehabilitation and reforestation. These functions are linked to their capacity to establish symbiotic relationships with a nitrogen-fixing soil bacterium of the genus Frankia. However, the molecular mechanisms controlling the establishment of these symbioses are poorly understood. The aim of this work was to identify potential transcription factors involved in the establishment and functioning of actinorhizal symbioses.ResultsWe identified 202 putative transcription factors by in silico analysis in 40 families in Casuarina glauca (Casuarinaceae) and 195 in 35 families in Alnus glutinosa (Betulaceae) EST databases. Based on published transcriptome datasets and quantitative PCR analysis, we found that 39% and 26% of these transcription factors were regulated during C. glauca and A. glutinosa-Frankia interactions, respectively. Phylogenetic studies confirmed the presence of common key transcription factors such as NSP, NF-YA and ERN-related proteins involved in nodule formation in legumes, which confirm the existence of a common symbiosis signaling pathway in nitrogen-fixing root nodule symbioses. We also identified an actinorhizal-specific transcription factor belonging to the zinc finger C1-2i subfamily we named CgZF1 in C. glauca and AgZF1 in A. glutinosa.ConclusionsWe identified putative nodulation-associated transcription factors with particular emphasis on members of the GRAS, NF-YA, ERF and C2H2 families. Interestingly, comparison of the non-legume and legume TF with signaling elements from actinorhizal species revealed a new subgroup of nodule-specific C2H2 TF that could be specifically involved in actinorhizal symbioses. In silico identification, transcript analysis, and phylogeny reconstruction of transcription factor families paves the way for the study of specific molecular regulation of symbiosis in response to Frankia infection.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-014-0342-z) contains supplementary material, which is available to authorized users.

Actinorhizal symbioses are mutualistic interactions between plants and the soil bacteria Frankia spp. that lead to the formation of nitrogen-fixing root nodules. The plant hormone auxin has been suggested to play a role in the mechanisms that control the establishment of this symbiosis in the actinorhizal tree Casuarina glauca. Here, we analyzed the role of auxin signaling in Frankia spp.-infected cells. Using a dominant-negative version of an endogenous auxin-signaling regulator, INDOLE-3-ACETIC ACID7, we established that inhibition of auxin signaling in these cells led to increased nodulation and, as a consequence, to higher nitrogen fixation per plant even if nitrogen fixation per nodule mass was similar to that in the wild type. Our results suggest that auxin signaling in Frankia spp.-infected cells is involved in the long-distance regulation of nodulation in actinorhizal symbioses.

The phytohormone jasmonic acid (JA) and its derivatives, collectively referred to as jasmonates, regulate many developmental processes, but are also involved in the response to numerous abiotic/biotic stresses. Thus far, powerful reverse genetic strategies employing perception, signalling or biosynthesis mutants have broadly contributed to our understanding of the role of JA in the plant stress response and development, as has the chemical gain-of-function approach based on exogenous application of the hormone. However, there is currently no method that allows for tightly controlled JA production in planta. By investigating the control of the JA synthesis pathway in bacteria-infected cotton (Gossypium hirsutum L.) plants, we identified a transcription factor (TF), named GhERF-IIb3, which acts as a positive regulator of the JA pathway. Expression of this well-conserved TF in cotton leaves was sufficient to produce in situ JA accumulation at physiological concentrations associated with an enhanced cotton defence response to bacterial infection.

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Maize is part of the essential food security crops for which yields need to tremendously increase to support future population growth expectations with their accompanying food and feed demand. However, current yield increases trends are sub-optimal due to an array of biotic and abiotic factors that will be compounded by future negative climate scenarios and continued land degradations. These negative projections for maize yield call for re-orienting maize breeding to leverage the beneficial soil microbiota, among which arbuscular mycorrhizal fungi (AMS) hold enormous promises. In this chapter, we first review the components relevant to maize-AMF interaction, then present the benefits of arbuscular mycorrhizal symbiosis (AMS) to maize growth and yield in terms of biotic and abiotic stress tolerance and improvement of yield and yield components, and finally summarize pre-breeding information related to maize-AMF interaction and trait improvement avenues based on up-to-date molecular breeding technologies.

Rhizosphere microbial communities are important components of the soil-plant-atmosphere continuum in paddy field ecosystems where they contribute to nutrient cycling and rice productivity. However, the rhizosphere microbial sensitivity to anthropic soil disturbance across plant growth stages remains little investigated. Here, we tracked the effects of long-term (> 25 years) N and NPK-fertilization on bacterial and archaeal community inhabiting the rice rhizosphere at three growth stages (tillering, panicle initiation and booting). Our results reveal that the effect of long-term inorganic fertilization on rhizosphere microbial communities varied with growth stage and that the bacterial and archaeal community differed in their response to N and NPK-fertilization. The microbial communities inhabiting the rice rhizosphere at the panicle initiation appear to be more sensitive to long-term inorganic fertilization than those at the tillering and booting stage. However, the effect of growth stage on microbial sensitivity to long-term inorganic fertilization was more strongly pronounced for bacterial than archaeal community. Furthermore, our results reveal dynamics of bacteria and archaea co-occurrence patterns in the rice rhizosphere, with differentiated bacterial and archaeal pivotal roles in the microbial inter-kingdom networks across growth stages. Hence, our study brings new insights on rhizosphere bacteria and archaea co-occurrence and sensitivity to long-term inorganic fertilization across growth stages in field-grown rice. By identifying one of the critical rice growth stages during which rhizosphere microbial communities are highly sensitive to inorganic fertilization, our results open new avenues for developing appropriate strategies in microbiome engineering to mitigate biotic and abiotic stress and improve crop yields.