PCR-restriction fragment length polymorphism identification and host range of single-spore isolates of the flexible Frankia sp. strain UFI 132715

The δ15N value of N2 fixing actinorhizal plants and legumes grown with N2 as the only nitrogen source

The aim of this study was to investigate the effects of different plant parts and the age of plants at harvest as well as N2 fixing bacterial strains on the N concentration in symbiotic plant parts, especially on the δ15N signature of the actinorhizal plants and legumes. The 15N natural abundance method was used. Two actinorhizal plants were studied: Alnus incana (L.) infected with the Frankia strains ArI3 or “lsF” (local source of Frankia) and Hippophaë rhamnoides (L.) infected with the Frankia strains T1 or E15b. Two legume species were studied: Hedysarum coronarium (L.), infected with a soil suspension, and Robinia pseudoacacia (L.), infected with a crushed nodule suspension. It was particularly interesting that in A. incana, the two Frankia strains affected not only N concentration and δ15N signature of leaves and roots, but also had an impact on plant growth at first harvest. In Hippophaë rhamnoides plants inoculated with the Frankia strains T1 and E15b, N concentrations and δ15N values did not differ at any harvest time. However, plants nodulated by the Frankia strain T1 showed a higher nitrogen fixation rate and higher plant dry matter at all harvesting times. Based on our results for the quantification of N2 fixation with the “B” value, that is the δ15N value of the N2 fixing plants relying only on N2 fixation, plant parts, ages and strains should be carefully considered.

Proposal of a type strain for Frankia alni (Woronin 1866) Von Tubeuf 1895, emended description of Frankia alni, and recognition of Frankia casuarinae sp. nov. and Frankia elaeagni sp. nov

Before the establishment of pure cultures, the species Frankia alni, 'Frankia casuarinae' and 'Frankia elaeagni' were proposed to encompass all causal agents of the nitrogen-fixing root nodules of dicotyledonous plants from the genera Alnus, Casuarina or Elaeagnus. The sole Frankia species with a validly published name, the type species F. alni, was described by Woronin (1866) as present in the root of alder. Until now no type strain has been designated for F. alni, even though the absence of a type strain has seriously inhibited the application of modern taxonomic methods to the genus Frankia. Thus, we propose that strain ACN14aT, isolated in pure culture from Alnus viridis ssp. crispa with morphological properties matching the original description of F. alni, be recognized as the type strain of this species according to Rule 18f of the International Code of Nomenclature of Bacteria. We compared ACN14aT to two strains, CcI3T and BMG5.12T, isolated from Casuarina cunninghamiana and Elaeagnus angustifolia, respectively, based on chemotaxonomy, phenotype microarray data and molecular data retrieved from genome sequences. All three tested strains grew as branched hyphae, produced vesicles and multilocular sporangia containing non-motile spores and metabolized short fatty acids, TCA-cycle intermediates and carbohydrates. Chemotaxonomically, the three strains were indistinguishable with respect to phospholipids (phosphatidylinositol, diphosphatidylglycerol, glycophospholipids and phosphatidylglycerol) and cell-sugar composition (glucose, mannose, ribose, rhamnose, galactose and xylose, with the latter two being diagnostic for the genus). The major fatty acids identified in all three strains were iso-C16 : 0, C17 : 1ω8c, C15 : 0, C17 : 0 and C16 : 0. ACN14aT and BMG5.12T also shared C15 : 1ω6c, while C18 : 1ω9c was found to be unique to BMG5.12T. The major menaquinones identified in all three novel type strains were MK-9(H8), MK-9(H6) and MK-9(H4). MK-9(H2) was shared by ACN14aT and BMG5.12T, while MK-10(H4) and MK-8(H4) were only found in BMG5.12T. Analysis of 16S rRNA gene sequences showed 98.1-98.9 % identity between strains ACN14aT, CcI3T and BMG5.12T. Digital DNA-DNA hybridization values between the three type strains were well below 70 %. These results confirm the separation of the strains into three distinct species, Frankia alni, Frankia casuarinae sp. nov. and Frankia elaeagni sp. nov. Thus, we propose ACN14aT (=DSM 45986T=CECT 9034T), CcI3T (=DSM 45818T=CECT 9043T) and BMG5.12T (=DSM 46783T=CECT 9031T) as the respective type strains.

Permanent Draft Genome Sequence for Frankia sp. Strain EI5c, a Single-Spore Isolate of a Nitrogen-Fixing Actinobacterium, Isolated from the Root Nodules of Elaeagnus angustifolia

Frankia sp. strain EI5c is a member of Frankia lineage III, which is able to reinfect plants of the Eleagnaceae, Rhamnaceae, Myricaceae, and Gymnostoma, as well as the genus Alnus. Here, we report the 6.6-Mbp draft genome sequence of Frankia sp. strain EI5c with a G+C content of 72.14 % and 5,458 candidate protein-encoding genes.

Heavy metal resistance patterns of Frankia strains

The sensitivity of 12 Frankia strains to heavy metals was determined by a growth inhibition assay. In general, all of the strains were sensitive to low concentrations (<0.5 mM) of Ag(1+), AsO(2)(1-), Cd(2+), SbO(2)(1-), and Ni(2+), but most of the strains were less sensitive to Pb(2+) (6 to 8 mM), CrO(4)(2-) (1.0 to 1.75 mM), AsO(4)(3-) (>50 mM), and SeO(2)(2-) (1.5 to 3.5 mM). While most strains were sensitive to 0.1 mM Cu(2+), four strains were resistant to elevated levels of Cu(2+) (2 to 5 mM and concentrations as high as 20 mM). The mechanism of SeO(2)(2-) resistance seems to involve reduction of the selenite oxyanion to insoluble elemental selenium, whereas Pb(2+) resistance and Cu(2+) resistance may involve sequestration or binding mechanisms. Indications of the resistance mechanisms for the other heavy metals were not as clear.

Polymerase chain reaction - restriction fragment length polymorphisms for assessing and increasing biodiversity ofFrankiaculture collections

During the last few years, some Frankia culture collections that maintained a large number of unidentified and uncharacterized Frankia strains were closed because of funding shortages. To reduce the costs of maintenance, we evaluated the biodiversity of half of the Frankia strains from our collection, by polymerase chain reaction - restriction fragment length polymorphisms (PCR-RFLPs) of nifD-nifK intergenic spacer and 16S-23S rDNA intergenic spacer regions. In this way we were able to reduce the number of strains without reducing the biodiversity of the whole collection. In general the nifD-nifK target proved to be more polymorphic than the rrn target. From 51 isolates of Elaeagnus frankiae, PCR-RFLP results allowed us to detect 13 identical strains, and to predict that the genomic species P8 of Akimov and Dobritsa (1992) very likely agrees with genomic species 5 of Fernandez et al. (1989). Moreover, we revealed genomic groups not yet described, as well as intraspecific variability. For Alnus frankiae, the polymorphisms shown by both the nif and the rrn PCR-RFLPs revealed three host plant species-specific subgroups inside Frankia alni. An expandable data base was created to serve as reference for future biodiversity evaluations on both culture collections and unisolated Frankia populations. It will be accessible by Internet at the International Frankia Website (http://www.unifi.it/unifi/distam/frankia/international.html).Key words: Frankia, PCR-RFLP, nifD-nifK intergenic spacer, rrn 16S-23S intergenic spacer, biodiversity, culture collections.

Antibiotic resistance patterns ofFrankiastrains

A major hurdle in the development of a genetic system for Frankia is the lack of genetic markers. To identify potential genetic markers, 12 strains of Frankia were screened for resistance to antibiotics by the use of a growth inhibition assay. All of the strains demonstrated sensitivity to tested antibiotics. Several strains had distinctive patterns of antibiotic resistance that are potentially useful as genetic markers. Novobiocin was the antibiotic to which the most strains were resistant.Key words: genetics, genetic markers, Frankia, actinorhizal, nitrogen fixation, vesicles.

A novel technique for isolation ofFrankiaand generation of single-spore cultures

The conventional isolation techniques for Frankia strains are likely to yield mixed cultures of genetically different strains. This makes genetic studies difficult. We report the development of a method based on calcium alginate beads for the isolation and genetic purification of Frankia strains.Key words: Frankia, alginate beads, isolation, single-spore cultures.

Actinorhizal symbioses and their N2 fixation

More than 200 angiosperms, distributed in 25 genera, develop root nodule symbioses (actinorhizas) with soil bacteria of the actinomycetous genus Frankia. Although most soils studied contain infective Frankia, cultured strains are available only after isolation from root nodules. Frankia infects roots via root hairs in some hosts or via intercellular penetration in others. The nodule originates in the pericycle. The number of nodules in Alnus is determined by the plant in an autoregulated process that, in turn, is modulated by nutrients such as nitrogen and phosphate. Except in the genera Allocausarina and Casuarina, Frankia in nodules develops so-called vesicles where nitrogenase is localized. Sporulation of Frankia occurs in some symbioses. As a group, actinorhizal plants show a large range of anatomical and biochemical adaptations in order to balance the oxygen tension near nitrogenase. In symbioses with well aerated nodule tissue like Alnus, the vesicles have a multilayered envelope composed mainly of lipids, bacterio-hopanetetrol and their derivatives. This envelope is assumed to retard the diffusion of oxygen into the nitrogenase-containing vesicle. In symbioses like Casuarina, the infected plant cells themselves, rather than Frankia, appear to retard oxygen diffusion, and high concentrations of haemoglobin indicate an infected region with a low oxygen tension. At least in Alnus spp., ammonia resulting from N₂ fixation is assimilated by glutamine synthetase in the plant. The carbon compound(s) used by Frankia in nodules is not yet known. Nitrogenase activity decreases in response to a number of environmental factors but recovers upon return to normal conditions. This dynamism in nitrogenase activity is often explained by loss and recovery of active nitrogenase and has been traced to loss and recovery of the nitrogenase proteins themselves. Recovery is partly due to growth of Frankia and to development of new vesicles in the Alnus nodules. In the field, varying conditions continuously affect the plants and the measured rate of N₂ fixation is a result not only of the conditions prevailing at the moment but also of the conditions experienced over preceding days. N₂ fixed by actinorhizal plants is substantial and actinorhizal plants have great potential in soil reclamation and in various types of forestry. Several species are also useful in horticulture. CONTENTS Summary 375 I. Introduction 376 II. The partners of actinorhizal symbioses 377 III. Root nodules 380 IV. Nitrogen fixation and related processes 385 V. Environmental effects on nitrogen fixation 389 VI. Ecological role 397 VII. Concluding remarks 398 Acknowledgements 398 References 398.