The nodular microsymbionts of Gymnostoma spp. are Elaeagnus-infective Frankia strains

Diversity and regulation of symbiotic nitrogen fixation in plants

Plants associate with nitrogen-fixing bacteria to secure nitrogen, which is generally the most limiting nutrient for plant growth. Endosymbiotic nitrogen-fixing associations are widespread among diverse plant lineages, ranging from microalgae to angiosperms, and are primarily one of three types: cyanobacterial, actinorhizal or rhizobial. The large overlap in the signaling pathways and infection components of arbuscular mycorrhizal, actinorhizal and rhizobial symbioses reflects their evolutionary relatedness. These beneficial associations are influenced by environmental factors and other microorganisms in the rhizosphere. In this review, we summarize the diversity of nitrogen-fixing symbioses, key signal transduction pathways and colonization mechanisms relevant to such interactions, and compare and contrast these interactions with arbuscular mycorrhizal associations from an evolutionary standpoint. Additionally, we highlight recent studies on environmental factors regulating nitrogen-fixing symbioses to provide insights into the adaptation of symbiotic plants to complex environments.

Sequence analysis ofrpoBandrpoDgene fragments reveals the phylogenetic diversity of actinobacteria of genus Frankia

Partial rpoD, rpoB, and 16S rRNA gene sequences were obtained from databases and (or) amplified from 12 strains of Frankia . These strains belonged to either Cluster 1 (Alnus-, Myrica-, Comptonia-, and Casuarina-infective strains) or Cluster 3 (Elaeagnus-infective strain). An rpoD gene-based PCR approach was designed to allow the detection of frankiae in complex samples. Additionally, partial gene sequences obtained using 2 rpoB gene primer sets (named rpoB-1 and rpoB-2) were used to generate phylogenetic eurograms to find a molecular tool able to assess biodiversity among Frankia strains. The rpoB-2 primer set allowed separation of closely related strains and groupings representative of host plant compatibility groups. One exception to this was for strains ACN10a and ACN14a, isolated from the same geographical location. Results obtained showed that rpoB-2 is a tool of great interest to evaluate relatedness of Frankia strains, and assess biodiversity in this genus. Additionally, since rpoB-2 phylogenetic profiles of the Frankia strains studied reflected the species of host plants they were isolated from, the study of rpoB (a house-keeping gene) shows promise for future ecological studies on these symbioses.

Typing of nitrogen-fixing Frankia strains by matrix-assisted laser desorption ionization-time-of-flight (MALDI-TOF) mass spectrometry

Matrix-assisted laser desorption ionization-time-of-flight (MALDI-TOF) mass spectrometry (MS) was evaluated as a technique to characterize strains of the nitrogen-fixing actinomycete Frankia. MALDI-TOF MS reliably distinguished 37 isolates within the genus Frankia and assigned them to their respective host infection groups, i.e., the Alnus/Casuarina and the Elaeagnus host infection groups. The assignment of individual strains to sub-groups within the respective host infection groups was consistent with classification based on comparative sequence analysis of nifH gene fragments, confirming the usefulness of MALDI-TOF MS as a rapid and reliable tool for the characterization of Frankia strains.

Assessment of the genetic diversity ofFrankiamicrosymbionts ofElaeagnus angustifoliaL. plants growing in a Tunisian date-palm oasis by analysis of PCR amplifiednifD-Kintergenic spacer

Diversity of Frankia microsymbionts of non-native Elaeagnus angustifolia L. plants spontaneously growing in a Tunisian desertic retreat area, the date-palm oasis of Tozeur, was investigated by polymerase chain reaction – restriction fragment length polymorphism (PCR–RFLP) and PCR-sequencing techniques targeting the nifD-K intergenic spacer. Three PCR–RFLP haplotypes (I, II, and III) were detected among collected nodules. Haplotype I was detected at all five sampling sites and dominated the other haplotypes present at these sites. This haplotype was also exhibited by strain BMG5.10, which was isolated by a plant-capturing assay in 1998 from soil collected in the same locality, qualifying it to be the most competitive haplotype in the edapho-climatic condition of the studied desertic date-palm oasis. nifD-K sequences of the three haplotypes formed a closely related phylogenetic subgroup. These results suggest that Frankia variability is constrained by severe edapho-climatic conditions of retreated desert in Tunisian area.

Nickel mine spoils revegetation attempts: effect of pioneer plants on two functional bacterial communities involved in the N-cycle

Nickel mine spoils in New Caledonia represent an extreme environment, rich in nickel and strongly deficient in elementary elements such as carbon and nitrogen. To rehabilitate these sites, revegetation attempts are performed with endemic plant species establishing dinitrogen-fixation symbiosis (Gymnostoma webbianum and Serianthes calycina). As this biological fixation process provides the major source of available nitrogen in this extreme environment, it could be expected that nitrogen cycling would be stimulated. To study the revegetation effect on mine spoils, the effect of the two pioneer plants on the structure and activity of two functional bacterial communities involved in the N-cycle was investigated. nifH and narG genes were used as molecular markers for dinitrogen-fixers and dissimilatory nitrate reducers respectively. In order to assess the influence of the plants on both communities, nine clone libraries were constructed for each targeted gene. Libraries containing 602 and 513 nifH and narG clones, respectively, were screened by restriction fragment length polymorphism (RFLP) analysis. One hundred and forty-one and 78 representative clones from at least all RFLP families containing more than one clone were sequenced from nifH and narG clone libraries respectively. Both pioneer plants modified the diversity and activity of the two functional communities. However, distinct effects were observed depending on the plant species and the community considered. Serianthes calycina strongly selected a diazotroph phylotype and restored the potential activity of both communities. In contrast, G. webbianum selected no particular phylotype and only restored a fixing activity.

Genetic diversity of Frankia microsymbionts from the relict species Myrica faya (Ait.) and Myrica rivas-martinezii (S.) in Canary Islands and Hawaii

In the Western Canary Islands, Myrica faya and Myrica rivas-martinezii (Myricaceae) are phylogenetically close, endemic, actinorhizal species presumed to be remnants either of the European or the African Tertiary floras. Unisolated Frankia strains from field-collected nodules on Tenerife, Gomera, and La Palma Islands were compared by their rrs gene and 16S-23S intergenic spacer (IGS) restriction patterns. To compare the genetic diversity of Frankia strains from within and outside the host's native range, nodules of M. faya field plants were collected both in Canary Islands and in Hawaii, where this species is an exotic invasive. Myrica rivas-martinezii, endemic to the Canary Islands, was sparsely nodulated in the field. Frankia strains harbored in field-collected nodules of M. faya and M. rivas-martinezii belonged to the Elaeagnaceae strains' genetic cluster and exhibited a high degree of diversity. Frankia genotypes were specific to each host species. In the Canary archipelago, we found no relationship between site of collection and Frankia genotype for M. faya. The only exceptions were strains from site 2 in Tenerife, a location with a geological history different from the other sites sampled. Hawaiian and Canarian M. faya strains had no genotypes in common, raising questions concerning the origin of M. faya-infective Frankia in Hawaii. Nodular strains of M. rivas-martinezii from nursery plants were genetically characterized and shown to be divergent from the strains of field-collected nodules and belong to the Alnus-Casuarina strains cluster. This suggests Myrica may have the potential to nodulate with a broader range of Frankia genotypes under artificial conditions than has been detected in field-collected nodules.

Molecular phylogeny of Myricaceae: a reexamination of host-symbiont specificity

The phylogeny of 13 species of Myricaceae, the most ancient actinorhizal family involved in a nitrogen-fixing symbiosis with the actinomycete Frankia, was established by the analysis of their rbcL gene and 18S-26S ITS. The phylogenetic position of those species was then compared to their specificity of association with Frankia in their natural habitat and to their nodulation potential determined on greenhouse-grown seedlings. The results showed that Genus Myrica, including M. gale and M. hartwegii, and Genus Comptonia, including C. peregrina, belong to a phylogenetic cluster distinct from the other Myrica species transferred in a new genus, Morella. This grouping parallels the natural specificity of each cluster with Comptonia-Myrica and Morella being nodulated by two phylogenetically divergent clusters of Frankia strains, the Alnus and Elaeagnaceae-infective strains clusters, respectively. Under laboratory conditions, Comptonia and Morella had a nodulation potential larger than under natural conditions. From this study it appears that the Myricaceae are split into two different specificity groups. It can be hypothesized that the early divergence of the genera led to the selection of genetically diverse Frankia strains which is contradictory to the earlier proposal that evolution has proceeded toward narrower promiscuity within the family.

Assessing the phylogeny of Frankia-actinorhizal plant nitrogen-fixing root nodule symbioses with Frankia 16S rRNA and glutamine synthetase gene sequences

Actinomycetes from the genus Frankia induce nitrogen-fixing root nodules on actinorhizal plants in the "core rosid" clade of eudicots. Reported here are nine partial Frankia 16S rRNA gene sequences including the first from host plants of the rosaceous genera Cercocarpus and Chamaebatia, 24 partial glutamine synthetase (GSI; glnA) sequences from Frankia in nodules of 17 of the 23 actinorhizal genera, and the partial glnA sequence of Acidothermus cellulolyticus. Phylogenetic analyses of combined Frankia 16S rDNA and glnA sequences indicate that infective strains belong to three major clades (I-III) and that Clade I strains consisting of unisolated symbionts from the Coriariaceae, Datiscaceae, Rosaceae, and Ceanothus of the Rhamnaceae are basal to the other clades. Clock-like mutation rates in glnA sequence alignments indicate that all three major Frankia clades diverged early during the emergence of eudicots in the Cretaceous period, and suggest that present-day symbioses are the result of an ancestral symbiosis that emerged before the divergence of extant actinorhizal plants.

High hopanoid/total lipids ratio in Frankia mycelia is not related to the nitrogen status

Vesicles are specific Frankia structures which are produced under nitrogen-limiting culture conditions. Hopanoids are the most abundant lipids in these vesicles and are believed to protect the nitrogenase against oxygen. The amounts and quality of each hopanoid were estimated in different Frankia strains cultivated under nitrogen-depleted and nitrogen-replete conditions in order to detect a possible variation. Studied Frankia strains nodulating Eleagnus were phylogenetically characterized by analysis of the nifD-K intergenic region as closely related to genomic species 4 and 5. Phylogenetically different strains belonging to three infectivity groups were cultivated in the same medium with and without nitrogen source for 10 d before hopanoid content analysis by HPLC. Four hopanoids together accounted for 23-87% and 15-87% of the total lipids under nitrogen-replete and nitrogen-depleted culture conditions, respectively. Two of the hopanoids found, bacteriohopanetetrols and their phenylacetic acid esters, have previously been described in Frankia Two new hopanoids, moretan-29-ol and a bacteriohopanetetrol propionate, have also been identified. The moretan-29-ol and bacteriohopanetetrols were found to be the most abundant hopanoids whereas the bacteriohopanetetrol propionate and phenylacetates were present at a concentration close to the limit of detection. The ratio of (bacteriohopanetetrols + moretan-29-ol)/(total lipids) varied in most of the strains between nitrogen-depleted and nitrogen-replete culture conditions. In most of the strains, the hopanoid content was found to be slightly higher under nitrogen-replete conditions than under nitrogen-depleted conditions. These results suggest that remobilization, rather than neosynthesis of hopanoids, is implicated in vesicle formation in Frankia under nitrogen-depleted conditions.

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.

Genomic fingerprinting ofFrankiamicrosymbionts fromCeanothuscopopulations using repetitive sequences and polymerase chain reactions

Specificity between Ceanothus species and their microsymbionts, Frankia, were investigated with nodules collected from three geographically separated copopulations of Ceanothus species. Nodules were analyzed using DNA sequencing and repetitive sequence polymerase chain reaction (rep-PCR) techniques. DNA sequencing of the intergenic spacer region between 16S and 23S rRNA genes suggested that Ceanothus-microsymbiotic Frankia are closely related at the intraspecific level. Diversity of the microsymbionts was further analyzed by genomic fingerprinting using repetitive sequences and PCR. A newly designed direct repeat (DR) sequence and a BOX sequence were used as PCR primers after justification that these primers can generate Frankia-specific fingerprints from nodule DNA. Analysis of the nodules using BOX- and DR-PCR showed that Ceanothus-microsymbiotic Frankia exhibited less diversity within each copopulation than among copopulations. These data suggested that geographic separation plays a more important role for divergence of Ceanothus-microsymbiotic Frankia than host plant.Key words: Frankia, Ceanothus, rep-PCR, diversity.

Co-evolution between Frankia populations and host plants in the family Casuarinaceae and consequent patterns of global dispersal

Symbioses between the root nodule-forming, nitrogen-fixing actinomycete Frankia and its angiospermous host plants are important in the nitrogen economies of numerous terrestrial ecosystems. Molecular characterization of Frankia strains using polymerase chain reaction/restriction fragment length polymorphism (PCR/RFLP) analyses of the 16S rRNA-ITS gene and of the nifD-nifK spacer was conducted directly on root nodules collected worldwide from Casuarina and Allocasuarina trees. In their native habitats in Australia, host species contained seven distinctive sets of Frankia in seven different molecular phylogenetic groups. Where Casuarina and Allocasuarina trees are newly planted outside Australia, they do not normally nodulate unless Frankia is introduced with the host seedling. Nodules from Casuarina trees introduced outside Australia over the last two centuries were found to contain Frankia from only one of the seven phylogenetic groups associated with the host genus Casuarina in Australia. The phylogenetic group of Frankia found in Casuarina and Allocasuarina trees introduced outside Australia is the only group that has yielded isolates in pure culture, suggesting a greater ability to survive independently of a host. Furthermore, the Frankia species in this group are able to nodulate a wider range of host species than those in the other six groups. In baiting studies, Casuarina spp. are compatible with more Frankia microsymbiont groups than Allocasuarina host spp. adapted to drier soil conditions, and C. equisetifolia has broader microsymbiont compatibility than other Casuarina spp. Some Frankia associated with the nodular rhizosphere and rhizoplan, but not with the nodular tissue, of Australian hosts were able to nodulate cosmopolitan Myrica plants that have broad microsymbiont compatibility and, hence, are a potential host of Casuarinaceae-infective Frankia outside the hosts' native range. The results are consistent with the idea that Frankia symbiotic promiscuity and ease of isolation on organic substrates, suggesting saprophytic potential, are associated with increased microsymbiont ability to disperse and adapt to diverse new environments, and that both genetics and environment determine a host's nodular microsymbiont.

Molecular phylogenies of plants and Frankia support multiple origins of actinorhizal symbioses

Molecular phylogenetic trees were reconstructed from nucleotide sequences of nifH and 16S rDNA for Frankia and of rbcL for actinorhizal plants. Comparison of Frankia phylogenetic trees reconstructed using nifH and 16S rDNA sequences indicated that subgroupings of both trees correspond with each other in terms of plant origins of Frankia strains. The results suggested that 16S rDNAs can be utilized for coevolution analysis of actinorhizal symbioses. Frankia and plant phylogenetic trees reconstructed using 16S rDNA and rbcL sequences were compared. The comparison by tree matching and likelihood ratio tests indicated that although branching orders of both trees do not strictly correspond with each other, subgroupings of Frankia and their host plants correspond with each other in terms of symbiotic partnership. Estimated divergence times among Frankia and plant clades indicated that Frankia clades diverged more recently than plant clades. Taken together, actinorhizal symbioses originated more than three times after the four plant clades diverged.

Distribution of gymnostoma spp. microsymbiotic frankia strains in new caledonia is related to soil type and to host-plant species

The diversity of the Frankia strains that are naturally in symbiosis with plants belonging to the Gymnostoma genus in New Caledonia was investigated. A direct molecular characterization of DNA extracted from nodules was performed, followed by characterization by restriction fragment length polymorphism (RFLP) of the ribosomal rrs-rrl (16S-23S) intergenic spacer (IGS) polymerase chain reaction (PCR)-amplified region. Seventeen different patterns were identified among the 358 microsymbiotic strains studied in the eight species of host plant present in New Caledonia. This genotypical approach permitted us to show that a large diversity existed among the patterns and that these did not exhibit a strict specificity to any host-plant species comparable with that previously found in the Casuarina and Allocasuarina symbioses in Australia. Despite this lack of specificity, a correspondence analysis nevertheless showed that the distribution of these patterns was related to soil type and to host-plant species. Furthermore, several Frankia strains were exclusively associated with the ultramafic soils.

Natural diversity of Frankia strains in actinorhizal root nodules from promiscuous hosts in the family Myricaceae

Actinorhizal plants invade nitrogen-poor soils because of their ability to form root nodule symbioses with N(2)-fixing actinomycetes known as Frankia. Frankia strains are difficult to isolate, so the diversity of strains inhabiting nodules in nature is not known. To address this problem, we have used the variability in bacterial 16S rRNA gene sequences amplified from root nodules as a means to estimate molecular diversity. Nodules were collected from 96 sites primarily in northeastern North America; each site contained one of three species of the family Myricaceae. Plants in this family are considered to be promiscuous hosts because several species are effectively nodulated by most isolated strains of Frankia in the greenhouse. We found that strain evenness varies greatly between the plant species so that estimating total strain richness of Frankia within myricaceous nodules with the sample size used was problematical. Nevertheless, Myrica pensylvanica, the common bayberry, was found to have sufficient diversity to serve as a reservoir host for Frankia strains that infect plants from other actinorhizal families. Myrica gale, sweet gale, yielded a few dominant sequences, indicating either symbiont specialization or niche selection of particular ecotypes. Strains in Comptonia peregrina nodules had an intermediate level of diversity and were all from a single major group of Frankia.

Diversity of frankia strains in root nodules of plants from the families elaeagnaceae and rhamnaceae

Partial 16S ribosomal DNAs (rDNAs) were PCR amplified and sequenced from Frankia strains living in root nodules of plants belonging to the families Elaeagnaceae and Rhamnaceae, including Colletia hystrix, Elaeagnus angustifolia, an unidentified Elaeagnus sp., Talguenea quinquenervia, and Trevoa trinervis. Nearly full-length 16S rDNAs were sequenced from strains of Frankia living in nodules of Ceanothus americanus, C. hystrix, Coriaria arborea, and Trevoa trinervis. Partial sequences also were obtained from Frankia strains isolated and cultured from the nodules of C. hystrix, Discaria serratifolia, D. trinervis, Retanilla ephedra, T. quinquenervia, and T. trinervis (Rhamnaceae). Comparison of these sequences and other published sequences of Frankia 16S rDNA reveals that the microsymbionts and isolated strains from the two plant families form a distinct phylogenetic clade, except for those from C. americanus. All sequences in the clade have a common 2-base deletion compared with other Frankia strains. Sequences from C. americanus nodules lack the deletion and cluster with Frankia strains infecting plants of the family Rosaceae. Published plant phylogenies (based on chloroplast rbcL sequences) group the members of the families Elaeagnaceae and Rhamnaceae together in the same clade. Thus, with the exception of C. americanus, actinorhizal plants of these families and their Frankia microsymbionts share a common symbiotic origin.