Use of Frankia and actinorhizal plants for degraded lands reclamation

Endophytic microbiota and ectomycorrhizal structure of Alnus glutinosa Gaertn. at saline and nonsaline forest sites

The tolerance of European alder (Alnus glutinosa Gaertn.) to soil salinity can be attributed to symbiosis with microorganisms at the absorptive root level. However, it is uncertain how soil salinity impacts microbial recruitment in the following growing season. We describe the bacterial and fungal communities in the rhizosphere and endosphere of A. glutinosa absorptive roots at three tested sites with different salinity level. We determined the morphological diversity of ectomycorrhizal (ECM) fungi, the endophytic microbiota in the rhizosphere, and the colonization of new absorptive roots in the following growing season. While bacterial diversity in the rhizosphere was higher than that in the absorptive root endosphere, the opposite was true for fungi. Actinomycetota, Frankiales, Acidothermus sp. and Streptomyces sp. were more abundant in the endosphere than in the rhizosphere, while Actinomycetota and Acidothermus sp. dominated at saline sites compared to nonsaline sites. Basidiomycota, Thelephorales, Russulales, Helotiales, Cortinarius spp. and Lactarius spp. dominated the endosphere, while Ascomycota, Hypocreales and Giberella spp. dominated the rhizosphere. The ECM symbioses formed by Thelephorales (Thelephora, Tomentella spp.) constituted the core community with absorptive roots in the spring and further colonized new root tips during the growing season. With an increase in soil salinity, the overall fungal abundance decreased, and Russula spp. and Cortinarius spp. were not present at all. Similarly, salinity also negatively affected the average length of the absorptive root. In conclusion, the endophytic microbiota in the rhizosphere of A. glutinosa was driven by salinity and season, while the ECM morphotype community was determined by the soil fungal community present during the growing season and renewed in the spring.

Comparative analysis of nitrogen content and its influence on actinorhizal nodule and rhizospheric microorganism diversity in three Alnus species

Alnus spp. (alder) are typical nonleguminous nitrogen-fixing trees that have a symbiotic relationship with Frankia. To explore the differences in nitrogen-fixing microorganisms between three alders (A. cremastogyne, A. glutinosa, and A. formosana) with different chromosome ploidies, the community structure and compositional diversity of potential nitrogen-fixing microorganism in root nodules and rhizosphere soil were comparatively analyzed using 16S rRNA and nitrogenase (nifH) gene sequencing. The nitrogen contents in the root nodules and rhizosphere soil were also determined. The results showed that the contents of total nitrogen and nitrate nitrogen in the root nodules of the three alders are significantly higher than those in the rhizosphere soils, while the ammonium nitrogen content show the opposite trend. The family, genus, and species levels showed obviously differences between root nodules and rhizosphere soils, while there were no significant differences at the classification level between the three alders. At the phylum level, the dominant phyla from 16S rRNA and nifH gene data in the root nodules and rhizosphere soil of the three alders are phylum Actinomycetota and phylum Pseudomonadota, respectively. The LEfSe results showed that there are significant differences in the dominant groups in the root nodules and rhizosphere oil of the three alders. The relative abundances of dominant groups also showed obvious differences between the root nodules and rhizosphere soils of three alders. The relative abundances of Frankia and unclassified_Frankia in root nodules are obviously higher than those in rhizosphere soils, and their relative abundances in A. glutinosa root nodules are significantly higher than those in A. cremastogyne and A. formosana at the genus and species levels. The diversity of potential nitrogen-fixing microorganism from 16S rRNA and nifH gene data in the A. glutinosa root nodules and rhizosphere soils are all higher than those in A. cremastogyne and A. formosana. The results of functional prediction also showed that the OTUs for nitrogen fixation, nitrate respiration, and ureolysis in A. glutinosa root nodules are higher than those in the other two alders. Redundancy analysis revealed that the total nitrogen content mostly affects the Frankia community. Overall, there are significant differences in the community composition and structure of potential nitrogen-fixing microorganism in the root nodules and rhizosphere soils between the three alders. A. glutinosa showed a relatively stronger nitrogen fixation capacity than A. formosana and A. cremastogyne. The results help elucidates how the community structure and nitrogen-fixing ability of potential nitrogen-fixing microorganism differ between alder species and serve as a reference for applying Frankia to alder plantations.

Contrasting response of soil microbiomes to long-term fertilization in various highland cropping systems

Soil microbiomes play important roles in supporting agricultural ecosystems. However, it is still not well-known how soil microbiomes and their functionality respond to fertilization in various cropping systems. Here we examined the effects of 36 years of phosphorus, nitrogen, and manure application on soil bacterial communities, functionality and crop productivity in three contrasting cropping systems (i.e., continuous leguminous alfalfa (AC), continuous winter wheat (WC), and grain-legume rotation of winter wheat + millet - pea - winter wheat (GLR)) in a highland region of China's Loess Plateau. We showed that long-term fertilization significantly affected soil bacterial communities and that the effects varied with cropping system. Compared with the unfertilized control, fertilization increased soil bacterial richness and diversity in the leguminous AC system, whereas it decreased those in the GLR system. Fertilization, particularly manure application, enlarged the differences in soil bacterial communities among cropping systems. Soil bacterial communities were mostly affected by the soil organic carbon and nitrogen contents in the WC and GLR systems, but by the soil available phosphorous content in the AC system. Crop productivity was closely associated with the abundance of fertilization-responsive taxa in the three cropping systems. Our study highlights that legume and non-legume cropping systems should be disentangled when assessing the responses of soil microbial communities to long-term fertilizer application.

Significance of nitrogen-fixing actinorhizal symbioses for restoration of depleted, degraded, and contaminated soil

Atmospheric nitrogen (N2)-fixing legume trees are frequently used for the restoration of depleted, degraded, and contaminated soils. However, biological N2 fixation (BNF) can also be performed by so-called actinorhizal plants. Actinorhizal plants include a high diversity of woody species and therefore can be applied in a broad spectrum of environments. In contrast to N2-fixing legumes, the potential of actinorhizal plants for soil restoration remains largely unexplored. In this Opinion, we propose related basic research requirements for the characterization of environmental stress responses that determine the restoration potential of actinorhizal plants for depleted, degraded, and contaminated soils. We identify advantages and unexplored processes of actinorhizal plants and describe a mainly uncharted avenue of future research for this important group of plant species.

Plant-Environment Response Pathway Regulation Uncovered by Investigating Non-Typical Legume Symbiosis and Nodulation

Nitrogen is an essential element needed for plants to survive, and legumes are well known to recruit rhizobia to fix atmospheric nitrogen. In this widely studied symbiosis, legumes develop specific structures on the roots to host specific symbionts. This review explores alternate nodule structures and their functions outside of the more widely studied legume-rhizobial symbiosis, as well as discussing other unusual aspects of nodulation. This includes actinorhizal-Frankia, cycad-cyanobacteria, and the non-legume Parasponia andersonii-rhizobia symbioses. Nodules are also not restricted to the roots, either, with examples found within stems and leaves. Recent research has shown that legume-rhizobia nodulation brings a great many other benefits, some direct and some indirect. Rhizobial symbiosis can lead to modifications in other pathways, including the priming of defence responses, and to modulated or enhanced resistance to biotic and abiotic stress. With so many avenues to explore, this review discusses recent discoveries and highlights future directions in the study of nodulation.

Neighbours in nodules: the interactions between Frankia sp. ACN10a and non-Frankia nodular endophytes of alder

In the present study, we report the in vitro interactions between Frankia sp. ACN10a and non-Frankia nodular endophytes (NFNE) isolated from alder. The supernatant of NFNE grown in nitrogen-replete medium had neutral or negative effects on Frankia growth; none had a stimulatory effect. Inhibitory effects were observed for supernatants of some NFNE, notably Micromonospora, Pseudomonas, Serratia and Stenotrophomonas isolates. However, some NFNE-Frankia coculture supernatants could stimulate Frankia growth when used as a culture medium supplement. This was observed for supernatants of Frankia cocultured with Microvirga and Streptomyces isolates. In nitrogen-limited conditions, cocultures of Frankia with some NFNE, including some rhizobia and Cytobacillus, resulted in higher total biomass than Frankia-only cultures, suggesting cooperation, while other NFNE were strongly antagonistic. Microscopic observation of cocultures also revealed compromised Frankia membrane integrity, and some differentiation into stress resistance-associated morphotypes such as sporangia and reproductive torulose hyphae (RTH). Furthermore, the coculture of Frankia with Serratia sp. isolates resulted in higher concentrations of the auxinic plant hormone indole-3-acetic acid and related indolic compounds in the culture supernatant. This study sheds new light on the breadth of microbial interactions that occur amongst bacteria that inhabit the understudied ecological niche of the alder nodule.

Deciphering the role of non-Frankia nodular endophytes in alder through in vitro and genomic characterization

Endophytic bacterial populations are well-positioned to provide benefits to their host plants such as nutrient acquisition and plant hormone level manipulation. Actinorhizal plants such as alders are well known for their microbial symbioses that allow them to colonize harsh environments whether natural or anthropized. Although the nitrogen-fixing actinobacterium Frankia sp. is the main endophyte found in alder root nodules, other bacterial genera, whose roles remain poorly defined, inhabit this niche. In this study, we isolated a diverse panel of non-Frankia nodular endophytes (NFNE). Some NFNE were isolated from alders grown from surface-sterilized seeds and maintained in sterile conditions, suggesting these may have been seed-borne. In vitro testing of 24 NFNE revealed some possessed putative plant growth promotion traits. Their genomes were also sequenced to identify genes related to plant growth promotion traits. This study highlights the complexity of the alder nodular microbial community. It paves the way for further understanding of the biology of nodules and could help improve land reclamation practices that involve alders.

Novel species of Frankia, Frankia gtarii sp. nov. and Frankia tisai sp. nov., isolated from a root nodule of Alnus glutinosa

The status of four Frankia strains isolated from a root nodule of Alnus glutinosa was established in a polyphasic study. Taxogenomics and phenotypic features show that the isolates belong to the genus Frankia. All four strains form extensively branched substrate mycelia, multilocular sporangia, vesicles, lack aerial hyphae, but contain meso-diaminopimelic acid as the diamino acid of the peptidoglycan, galactose, glucose, mannose, ribose, xylose and traces of rhamnose as cell wall sugars, iso-C_16:0 as the predominant fatty acid, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol as the major polar lipids, have comparable genome sizes to other cluster 1, Alnus-infective strains with structural and accessory genes associated with nitrogen fixation. The genome sizes of the isolates range from 7.0 to 7.7 Mbp and the digital DNA G + C contents from 71.3 to 71.5 %. The four sequenced genomes are rich in biosynthetic gene clusters predicted to express for novel specialized metabolites, notably antibiotics. 16S rRNA gene and whole genome sequence analyses show that the isolates fall into two lineages that are closely related to the type strains of Frankia alni and Frankia torreyi. All of these taxa are separated by combinations of phenotypic properties and by digital DNA:DNA hybridization scores which indicate that they belong to different genomic species. Based on these results, it is proposed that isolates Agncl-4^T and Agncl-10, and Agncl-8^T and Agncl-18, be recognised as Frankia gtarii sp. nov. and Frankia tisai sp. nov. respectively, with isolates Agncl-4^T (=DSM 107976^T = CECT 9711^T) and Agncl-8^T (=DSM 107980^T = CECT 9715^T) as the respective type strains.

Salt Stress Tolerance in Casuarina glauca: Insights from the Branchlets Transcriptome

Climate change and the accelerated rate of population growth are imposing a progressive degradation of natural ecosystems worldwide. In this context, the use of pioneer trees represents a powerful approach to reverse the situation. Among others, N₂-fixing actinorhizal trees constitute important elements of plant communities and have been successfully used in land reclamation at a global scale. In this study, we have analyzed the transcriptome of the photosynthetic organs of Casuarina glauca (branchlets) to unravel the molecular mechanisms underlying salt stress tolerance. For that, C. glauca plants supplied either with chemical nitrogen (KNO₃⁺) or nodulated by Frankia (NOD⁺) were exposed to a gradient of salt concentrations (200, 400, and 600 mM NaCl) and RNA-Seq was performed. An average of ca. 25 million clean reads was obtained for each group of plants, corresponding to 86,202 unigenes. The patterns of differentially expressed genes (DEGs) clearly separate two groups: (i) control- and 200 mM NaCl-treated plants, and (ii) 400 and 600 mM NaCl-treated plants. Additionally, although the number of total transcripts was relatively high in both plant groups, the percentage of significant DEGs was very low, ranging from 6 (200 mM NaCl/NOD⁺) to 314 (600 mM NaCl/KNO₃⁺), mostly involving down-regulation. The vast majority of up-regulated genes was related to regulatory processes, reinforcing the hypothesis that some ecotypes of C. glauca have a strong stress-responsive system with an extensive set of constitutive defense mechanisms, complemented by a tight mechanism of transcriptional and post-transcriptional regulation. The results suggest that the robustness of the stress response system in C. glauca is regulated by a limited number of genes that tightly regulate detoxification and protein/enzyme stability, highlighting the complexity of the molecular interactions leading to salinity tolerance in this species.

Cyclopeptide alkaloids from Discaria chacaye (Rhamnaceae) as result of symbiosis with Frankia (Actinomycetales)

Cyclopeptide alkaloids with different biological activities are present in plants of the family Rhamnaceae. Plants of this family grow in a symbiotic relationship with aerobic Gram-positive actinomycetes belonging to the genus Frankia . This goal of this research was a study of the comparative profile of alkaloids present in Discaria chacaye and to establish a connection between the presence or absence of Frankia sp. and the alkaloids. In addition, insecticidal activities of the alkaloidal extract were examined. A total of 24 alkaloids were identified, of which 12 have a benzylisoquinoline skeleton, 9 were cyclopeptides, 2 isoquinolines, and 1 an aporphine. The presence of cyclopeptide alkaloids is associated with Frankia nodules in the plant root. The alkaloid extracts showed insecticidal activity with mortality dose-dependence and LD 50 values between 44 to 71 µg/mL.

Salt Stress in Plants and Mitigation Approaches

Salinization of soils and freshwater resources by natural processes and/or human activities has become an increasing issue that affects environmental services and socioeconomic relations. In addition, salinization jeopardizes agroecosystems, inducing salt stress in most cultivated plants (nutrient deficiency, pH and oxidative stress, biomass reduction), and directly affects the quality and quantity of food production. Depending on the type of salt/stress (alkaline or pH-neutral), specific approaches and solutions should be applied to ameliorate the situation on-site. Various agro-hydrotechnical (soil and water conservation, reduced tillage, mulching, rainwater harvesting, irrigation and drainage, control of seawater intrusion), biological (agroforestry, multi-cropping, cultivation of salt-resistant species, bacterial inoculation, promotion of mycorrhiza, grafting with salt-resistant rootstocks), chemical (application of organic and mineral amendments, phytohormones), bio-ecological (breeding, desalination, application of nano-based products, seed biopriming), and/or institutional solutions (salinity monitoring, integrated national and regional strategies) are very effective against salinity/salt stress and numerous other constraints. Advances in computer science (artificial intelligence, machine learning) provide rapid predictions of salinization processes from the field to the global scale, under numerous scenarios, including climate change. Thus, these results represent a comprehensive outcome and tool for a multidisciplinary approach to protect and control salinization, minimizing damages caused by salt stress.

Metallophores production by bacteria isolated from heavy metal-contaminated soil and sediment at Lerma-Chapala Basin

Environmental pollution as a result of heavy metals (HMs) is a worldwide problem and the implementation of eco-friendly remediation technologies is thus required. Metallophores, low molecular weight compounds, could have important biotechnological applications in the fields of agriculture, medicine, and bioremediation. This study aimed to isolate HM-resistant bacteria from soils and sediments of the Lerma-Chapala Basin and evaluated their abilities to produce metallophores and to promote plant growth. Bacteria from the Lerma-Chapala Basin produced metallophores for all the tested metal ions, presented a greater production of As³⁺ metallophores, and showed high HM resistance especially to Zn²⁺, As⁵⁺, and Ni²⁺. A total of 320 bacteria were isolated with 170 strains showing siderophores synthesis. Members of the Delftia and Pseudomonas genera showed above 92 percent siderophore units (psu) during siderophores production and hydroxamate proved to be the most common functional group among the analyzed siderophores. Our results provided evidence that Lerma-Chapala Basin bacteria and their metallophores could potentially be employed in bioremediation processes or may even have potential for applications in other biotechnological fields.

Optimization of Tissue Culturing and Genetic Transformation Protocol for Casuarina equisetifolia

Casuarina equisetifolia is widely used in agroforestry plantations for soil stabilization, ecosystem rehabilitation, reclamation, and coastal protection. Moreover, C. equisetifolia has remarkable resistance to typhoons, desert, low soil fertility, drought, and salinity, but not cold. Therefore, it is significant to breed high-quality Casuarina varieties to improve the tolerance and adaptability to cold weather by molecular techniques. The establishment of a rapid and efficient callus induction and regeneration system via tissue culture is pre-requisite for the genetic transformation of C. equisetifolia, which is so far lacking. In this study, we reported an efficient and rapid regeneration system using stem segment explants, in which callus induction was found to be optimal in a basal medium supplemented with 0.1 mg⋅L^-1 TDZ and 0.1 mg⋅L^-1 NAA, and proliferation in a basal medium containing 0.1 mg⋅L^-1 TDZ and 0.5 mg⋅L^-1 6-BA. For bud regeneration and rooting, the preferred plant growth regulator (PGR) in basal medium was 0.5 mg⋅L^-1 6-BA, and a combination of 0.02 mg⋅L^-1 IBA and 0.4 mg⋅L^-1 IAA, respectively. We also optimized genetic a transformation protocol using Agrobacterium tumefaciens harboring the binary vector pCAMBIA1301 with β-glucuronidase (GUS) as a reporter gene. Consequently, 5 mg L^-1 hygromycin, 20 mg L^-1 acetosyringone (As), and 2 days of co-cultivation duration were optimized to improve the transformation efficiency. With these optimized parameters, transgenic plants were obtained in about 4 months. Besides that, Agrobacterium rhizogenes-mediated transformation involving adventitious root induction was also optimized. Our findings will not only increase the transformation efficiency but also shorten the time for developing transgenic C. equisetifolia plants. Taken together, this pioneer study on tissue culturing and genetic transformation of C. equisetifolia will pave the way for further genetic manipulation and functional genomics of C. equisetifolia.

Establishment of Ailanthus tryphysa (Dennst.) Alston inoculated with beneficial microbes in barren laterite rocks

Developing countries including India are using laterite bricks extracted from laterite rocks for building construction. Laterite rocks are found barren usually as they are not fit for cultivation. Extraction of laterite bricks from these barren laterite rocks causing land degradation and posing environmental threats in the laterite excavated lands. Hence, planting or establishing of trees on laterite rocks can prevent land degradation and environmental problems. In this study, it was decided to establish Ailanthus tryphysa (Dennst.) Alston a multipurpose native tree species of India on laterite rocks with suitable beneficial microbes as growth promotors. The laterite soils dug out from laterite rocks were tested and found that the soils have lack of beneficial microbes and poor in major nutrients (N, P, K). Therefore the beneficial microbes, arbuscular mycorrhizal fungi and growth promoting bacteria were used for A. tryphysa as they are one of the important soil properties. The laterite soils were also used as potting media for the seedlings of A. tryphysa in nursery and thereafter the cultured beneficial microbes were inoculated in to the seedlings and maintained for three months. After three months the seedlings were planted at laterite rocks and monitored for their growth and survival. The results of the experiment showed that beneficial microbes inoculated seedlings improved the growth, biomass, tissue nutrient content and 95% of survival rate after twelve months in laterite rocks. These results confirmed that the beneficial microbes have successfully established the A. tryphysa seedlings in laterite rocks through transfer of essential nutrients.

Will Casuarina glauca Stress Resilience Be Maintained in the Face of Climate Change?

Actinorhizal plants have been regarded as promising species in the current climate change context due to their high tolerance to a multitude of abiotic stresses. While combined salt-heat stress effects have been studied in crop species, their impact on the model actinorhizal plant, Casuarina glauca, has not yet been fully addressed. The effect of single salt (400 mM NaCl) and heat (control at 26/22 °C, supra optimal temperatures at 35/22 °C and 45/22 °C day/night) conditions on C. glauca branchlets was characterised at the physiological level, and stress-induced metabolite changes were characterised by mass spectrometry-based metabolomics. C. glauca could withstand single salt and heat conditions. However, the harshest stress condition (400 mM NaCl, 45 °C) revealed photosynthetic impairments due to mesophyll and membrane permeability limitations as well as major stress-specific differential responses in C and N metabolism. The increased activity of enzymatic ROS scavengers was, however, revealed to be sufficient to control the plant oxidative status. Although C. glauca could tolerate single salt and heat stresses, their negative interaction enhanced the effects of salt stress. Results demonstrated that C. glauca responses to combined salt-heat stress could be explained as a sum of the responses from each single applied stress.

Frankobactin Metallophores Produced by Nitrogen-Fixing Frankia Actinobacteria Function in Toxic Metal Sequestration

A series of new metallophores, referred to as frankobactins, were extracted from cultures of the symbiotic and nitrogen-fixing actinobacterium Frankia sp. CH37. Structure elucidation revealed a 2-hydroxyphenyl-substituted oxazoline core and a chain composed of five proteinogenic and nonproteinogenic amino acids, suggesting nonribosomal peptide synthesis as the biosynthetic origin. By whole-genome sequencing, bioinformatic analysis, and comparison with other Frankia strains, the genetic locus responsible for the biosynthesis was detected. Spectrophotometric titration of frankobactin with Fe(III) and Cu(II) and mass spectrometry established the 1:1 (metal:frankobactin) coordination. Uptake experiments suggested that frankobactin A₁ (1) did not serve to recruit iron, but to detoxify Cu(II). As frankobactin A₁ prevents the cellular entry of Cu(II), it could play a crucial role in the symbiosis of Frankia sp. and its host in the reclamation of copper-contaminated soil.

Environmental salinization processes: Detection, implications & solutions

A great portion of Earth's freshwater and land resources are salt-affected and thus have restricted use or may become unsuitable for most human activities. Some of the recent scenarios warn that environmental salinization processes will continue to be exacerbated due to global climate change. The most relevant implications and side-effects in ecosystems under excessive salinity are destructive and long lasting (e.g. soil dispersion, water/soil hypersalinity, desertification, ruined biodiversity), often with non-feasible on site remediation, especially at larger scales. Agro-ecosystems are very sensitive to salinization; after a certain threshold is reached, yields and food quality start to deteriorate sharply. Additionally, salinity often coincides with numerous other environmental constrains (drought, waterlogging, pollution, acidity, nutrient deficiency, etc.) that progressively aggravate the threat to food security and general ecosystem resilience. Some well-proven, widely-used and cost-effective traditional ameliorative strategies (e.g. conservation agriculture, application of natural conditioners) help against salinity and other constraints, especially in developing countries. Remotely-sensed and integrated data of salt-affected areas combined with in situ and lab-based observations have never been so easy and rapid to acquire, precise and applicable on huge scales, representing a valuable tool for policy-makers and other stakeholders in implementing targeted measures to control and prevent ecosystem degradation (top-to-bottom approach). Continued progress in biotechnology and ecoengineering offers some of the most advanced and effective solutions against salinity (e.g. nanomaterials, marker-assisted breeding, genome editing, plant-microbial associations), albeit many knowledge gaps and ethical frontiers remain to be overcome before a successful transfer of these potential solutions to the industrial-scale food production can be effective.

Draft Genome Sequences for the Frankia sp. strains CgS1, CcI156 and CgMI4, Nitrogen-Fixing Bacteria Isolated from Casuarina sp. in Egypt

Frankia sp. strains CgS1, CcI156 and CgMI4 were isolated from Casuarina glauca and C. cunninghamiana nodules. Here, we report the 5.26-, 5.33- and 5.20-Mbp draft genome sequences of Frankia sp. strains CgS1, CcI156 and CgMI4, respectively. Analysis of the genome revealed the presence of high numbers of secondary metabolic biosynthetic gene clusters.

Draft Genome Sequences of 10 Bacterial Strains Isolated from Root Nodules of Alnus Trees in New Hampshire

Here, we report the draft genome sequences obtained for 10 bacterial strains isolated from root nodules of Alnus trees. These members of the nodule microbiome were sequenced to determine their potential functional roles in plant health. The selected strains belong to the genera Rhodococcus, Kocuria, Rothia, Herbaspirillum, Streptomyces, and Thiopseudomonas.

Stable Transformation of the Actinobacteria Frankia spp

A stable and efficient plasmid transfer system was developed for nitrogen-fixing symbiotic actinobacteria of the genus Frankia, a key first step in developing a genetic system. Four derivatives of the broad-host-range cloning vector pBBR1MCS were successfully introduced into different Frankia strains by a filter mating with Escherichia coli strain BW29427. Initially, plasmid pHKT1 that expresses green fluorescent protein (GFP) was introduced into Frankia casuarinae strain CcI3 at a frequency of 4.0 × 10^-3, resulting in transformants that were tetracycline resistant and exhibited GFP fluorescence. The presence of the plasmid was confirmed by molecular approaches, including visualization on agarose gel and PCR. Several other pBBR1MCS plasmids were also introduced into F. casuarinae strain CcI3 and other Frankia strains at frequencies ranging from 10^-2 to 10^-4, and the presence of the plasmids was confirmed by PCR. The plasmids were stably maintained for over 2 years and through passage in a plant host. As a proof of concept, a salt tolerance candidate gene from the highly salt-tolerant Frankia sp. strain CcI6 was cloned into pBBR1MCS-3. The resulting construct was introduced into the salt-sensitive F. casuarinae strain CcI3. Endpoint reverse transcriptase PCR (RT-PCR) showed that the gene was expressed in F. casuarinae strain CcI3. The expression provided an increased level of salt tolerance for the transformant. These results represent stable plasmid transfer and exogenous gene expression in Frankia spp., overcoming a major hurdle in the field. This step in the development of genetic tools in Frankia spp. will open up new avenues for research on actinorhizal symbiosis.IMPORTANCE The absence of genetic tools for Frankia research has been a major hindrance to the associated field of actinorhizal symbiosis and the use of the nitrogen-fixing actinobacteria. This study reports on the introduction of plasmids into Frankia spp. and their functional expression of green fluorescent protein and a cloned gene. As the first step in developing genetic tools, this technique opens up the field to a wide array of approaches in an organism with great importance to and potential in the environment.

Genomic Insights Into Plant-Growth-Promoting Potentialities of the Genus Frankia

This study was designed to determine the plant growth promoting (PGP) potential of members of the genus Frankia. To this end, the genomes of 21 representative strains were examined for genes associated directly or indirectly with plant growth. All of the Frankia genomes contained genes that encoded for products associated with the biosynthesis of auxins [indole-3-glycerol phosphate synthases, anthranilate phosphoribosyltransferases (trpD), anthranilate synthases, and aminases (trpA and B)], cytokinins (11 well-conserved genes within the predicted biosynthetic gene cluster), siderophores, and nitrogenases (nif operon except for atypical Frankia) as well as genes that modulate the effects of biotic and abiotic environmental stress (e.g., alkyl hydroperoxide reductases, aquaporin Z, heat shock proteins). In contrast, other genes were associated with strains assigned to one or more of four host-specific clusters. The genes encoding for phosphate solubilization (e.g., low-affinity inorganic phosphate transporters) and lytic enzymes (e.g., cellulases) were found in Frankia cluster 1 genomes, while other genes were found only in cluster 3 genomes (e.g., alkaline phosphatases, extracellular endoglucanases, pectate lyases) or cluster 4 and subcluster 1c genomes (e.g., NAD(P) transhydrogenase genes). Genes encoding for chitinases were found only in the genomes of the type strains of Frankia casuarinae, F. inefficax, F. irregularis, and F. saprophytica. In short, these in silico genome analyses provide an insight into the PGP abilities of Frankia strains of known taxonomic provenance. This is the first study designed to establish the underlying genetic basis of cytokinin production in Frankia strains. Also, the discovery of additional genes in the biosynthetic gene cluster involved in cytokinin production opens up the prospect that Frankia may have novel molecular mechanisms for cytokinin biosynthesis.

Metallophore profiling of nitrogen-fixingFrankiaspp. to understand metal management in the rhizosphere of actinorhizal plants

Frankiaspp. are widespread nitrogen-fixing and metallophore releasing soil bacteria, which often live in symbiosis with a broad spectrum of hosts.

The plant-growth-promoting actinobacteria of the genus Nocardia induces root nodule formation in Casuarina glauca

Actinorhizal plants form a symbiotic association with the nitrogen-fixing actinobacteria Frankia. These plants have important economic and ecological benefits including land reclamation, soil stabilization, and reforestation. Recently, many non-Frankia actinobacteria have been isolated from actinorhizal root nodules suggesting that they might contribute to nodulation. Two Nocardia strains, BMG51109 and BMG111209, were isolated from Casuarina glauca nodules, and they induced root nodule-like structures in original host plant promoting seedling growth. The formed root nodule-like structures lacked a nodular root at the apex, were not capable of reducing nitrogen and had their cortical cells occupied with rod-shaped Nocardiae cells. Both Nocardia strains induced root hair deformation on the host plant. BMG111209 strain induced the expression of the ProCgNin:Gus gene, a plant gene involved in the early steps of the infection process and nodulation development. Nocardia strain BMG51109 produced three types of auxins (Indole-3-acetic acid [IAA], Indole-3-Byturic Acid [IBA] and Phenyl Acetic Acid [PAA]), while Nocardia BMG111209 only produced IAA. Analysis of the Nocardia genomes identified several important predicted biosynthetic gene clusters for plant phytohormones, secondary metabolites, and novel natural products. Co-infection studies showed that Nocardia strain BMG51109 plays a role as a "helper bacteria" promoting an earlier onset of nodulation. This study raises many questions on the ecological significance and functionality of Nocardia bacteria in actinorhizal symbioses.

Simple colony PCR procedure for the filamentous actinobacteria Frankia

Molecular analysis of the filamentous actinobacteria Frankia is laborious because of the slow growth rate and required biomass needed for these techniques. An efficient and simple colony PCR protocol for Frankia was developed that saved time for analysis of any Frankia strains growing on a plate. Previously, it took 5-6 weeks to get the correct size Frankia colonies on plates and then a minimum of 5 weeks of growth in liquid culture for DNA extraction. With this technique, these colonies could be screened after 5-6 weeks of growth by colony PCR. The procedure used a combination of mechanical and heat treatments and required no added buffers or chemicals. Our results demonstrate rapid and efficient PCR.

How Does Salinity Shape Bacterial and Fungal Microbiomes of Alnus glutinosa Roots?

Black alder (Alnus glutinosa Gaertn.) belongs to dual mycorrhizal trees, forming ectomycorrhizal (EM) and arbuscular (AM) root structures, as well as represents actinorrhizal plants that associate with nitrogen-fixing actinomycete Frankia sp. We hypothesized that the unique ternary structure of symbionts can influence community structure of other plant-associated microorganisms (bacterial and fungal endophytes), particularly under seasonally changing salinity in A. glutinosa roots. In our study we analyzed black alder root bacterial and fungal microbiome present at two forest test sites (saline and non-saline) in two different seasons (spring and fall). The dominant type of root microsymbionts of alder were ectomycorrhizal fungi, whose distribution depended on site (salinity): Tomentella, Lactarius, and Phialocephala were more abundant at the saline site. Mortierella and Naucoria (representatives of saprotrophs or endophytes) displayed the opposite tendency. Arbuscular mycorrhizal fungi belonged to Glomeromycota (orders Paraglomales and Glomales), however, they represented less than 1% of all identified fungi. Bacterial community structure depended on test site but not on season. Sequences affiliated with Rhodanobacter, Granulicella, and Sphingomonas dominated at the saline site, while Bradyrhizobium and Rhizobium were more abundant at the non-saline site. Moreover, genus Frankia was observed only at the saline site. In conclusion, bacterial and fungal community structure of alder root microsymbionts and endophytes depends on five soil chemical parameters: salinity, phosphorus, pH, saturation percentage (SP) as well as total organic carbon (TOC), and seasonality does not appear to be an important factor shaping microbial communities. Ectomycorrhizal fungi are the most abundant symbionts of mature alders growing in saline soils. However, specific distribution of nitrogen-fixing Frankia (forming root nodules) and association of arbuscular fungi at early stages of plant development should be taken into account in further studies.

Ectomycorrhizal and endophytic fungi associated with Alnus glutinosa growing in a saline area of central Poland

Alnus glutinosa (black alder) is a mycorrhizal pioneer tree species with tolerance to high concentrations of salt in the soil and can therefore be considered to be an important tree for the regeneration of forests areas devastated by excessive salt. However, there is still a lack of information about the ectomycorrhizal fungi (EMF) associated with mature individuals of A. glutinosa growing in natural saline conditions. The main objective of this study was to test the effect of soil salinity and other physicochemical parameters on root tips colonized by EMF, as well as on the species richness and diversity of an EMF community associated with A. glutinosa growing in natural conditions. We identified a significant effect of soil salinity (expressed as electrical conductivity: EC_e and EC_1:5) on fungal taxa but not on the total level of EM fungal colonization on roots. Increasing soil salinity promoted dark-coloured EMF belonging to the order Thelephorales (Tomentella sp. and Thelephora sp.). These fungi are also commonly found in soils polluted with heavy-metal. The ability of these fungi to grow in contaminated soil may be due to the presence of melanine, a natural dark pigment and common wall component of the Thelephoraceae that is known to act as a protective interface between fungal metabolism and biotic and abiotic environmental stressors. Moreover, increased colonization of fungi belonging to the class of Leotiomycetes and Sordiomycetes, known as endophytic fungal species, was observed at the test sites, that contained a larger content of total phosphorus. This observation confirms the ability of commonly known endophytic fungi to form ectomycorrhizal structures on the roots of A. glutinosa under saline stress conditions.

New Insights on Plant Salt Tolerance Mechanisms and Their Potential Use for Breeding

Soil salinization is a major threat to agriculture in arid and semi-arid regions, where water scarcity and inadequate drainage of irrigated lands severely reduce crop yield. Salt accumulation inhibits plant growth and reduces the ability to uptake water and nutrients, leading to osmotic or water-deficit stress. Salt is also causing injury of the young photosynthetic leaves and acceleration of their senescence, as the Na+ cation is toxic when accumulating in cell cytosol resulting in ionic imbalance and toxicity of transpiring leaves. To cope with salt stress, plants have evolved mainly two types of tolerance mechanisms based on either limiting the entry of salt by the roots, or controlling its concentration and distribution. Understanding the overall control of Na+ accumulation and functional studies of genes involved in transport processes, will provide a new opportunity to improve the salinity tolerance of plants relevant to food security in arid regions. A better understanding of these tolerance mechanisms can be used to breed crops with improved yield performance under salinity stress. Moreover, associations of cultures with nitrogen-fixing bacteria and arbuscular mycorrhizal fungi could serve as an alternative and sustainable strategy to increase crop yields in salt-affected fields.

Inhibition of auxin signaling in Frankia species-infected cells in Casuarina glauca nodules leads to increased nodulation

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 ins and outs of metal homeostasis by the root nodule actinobacterium Frankia

BACKGROUND

Frankia are actinobacteria that form a symbiotic nitrogen-fixing association with actinorhizal plants, and play a significant role in actinorhizal plant colonization of metal contaminated areas. Many Frankia strains are known to be resistant to several toxic metals and metalloids including Pb(2+), Al(+3), SeO2, Cu(2+), AsO4, and Zn(2+). With the availability of eight Frankia genome databases, comparative genomics approaches employing phylogeny, amino acid composition analysis, and synteny were used to identify metal homeostasis mechanisms in eight Frankia strains. Characterized genes from the literature and a meta-analysis of 18 heavy metal gene microarray studies were used for comparison.

RESULTS

Unlike most bacteria, Frankia utilize all of the essential trace elements (Ni, Co, Cu, Se, Mo, B, Zn, Fe, and Mn) and have a comparatively high percentage of metalloproteins, particularly in the more metal resistant strains. Cation diffusion facilitators, being one of the few known metal resistance mechanisms found in the Frankia genomes, were strong candidates for general divalent metal resistance in all of the Frankia strains. Gene duplication and amino acid substitutions that enhanced the metal affinity of CopA and CopCD proteins may be responsible for the copper resistance found in some Frankia strains. CopA and a new potential metal transporter, DUF347, may be involved in the particularly high lead tolerance in Frankia. Selenite resistance involved an alternate sulfur importer (CysPUWA) that prevents sulfur starvation, and reductases to produce elemental selenium. The pattern of arsenate, but not arsenite, resistance was achieved by Frankia using the novel arsenite exporter (AqpS) previously identified in the nitrogen-fixing plant symbiont Sinorhizobium meliloti. Based on the presence of multiple tellurite resistance factors, a new metal resistance (tellurite) was identified and confirmed in Frankia.

CONCLUSIONS

Each strain had a unique combination of metal import, binding, modification, and export genes that explain differences in patterns of metal resistance between strains. Frankia has achieved similar levels of metal and metalloid resistance as bacteria from highly metal-contaminated sites. From a bioremediation standpoint, it is important to understand mechanisms that allow the endosymbiont to survive and infect actinorhizal plants in metal contaminated soils.