Frankia canadensis sp. nov., isolated from root nodules of Alnus incana subspecies rugosa

Frankia strains induce the formation of nitrogen-fixing nodules on roots of actinorhizal plants. Phylogenetically, Frankia strains can be grouped in four clusters. The earliest divergent cluster, cluster-2, has a particularly wide host range. The analysis of cluster-2 strains has been hampered by the fact that with two exceptions, they could never be cultured. In this study, 12 Frankia-enriched metagenomes of Frankia cluster-2 strains or strain assemblages were sequenced based on seven inoculum sources. Sequences obtained via DNA isolated from whole nodules were compared with those of DNA isolated from fractionated preparations enhanced in the Frankia symbiotic structures. The results show that cluster-2 inocula represent groups of strains, and that strains not represented in symbiotic structures, that is, unable to perform symbiotic nitrogen fixation, may still be able to colonize nodules. Transposase gene abundance was compared in the different Frankia-enriched metagenomes with the result that North American strains contain more transposase genes than Eurasian strains. An analysis of the evolution and distribution of the host plants indicated that bursts of transposition may have coincided with niche competition with other cluster-2 Frankia strains. The first genome of an inoculum from the Southern Hemisphere, obtained from nodules of Coriaria papuana in Papua New Guinea, represents a novel species, postulated as Candidatus Frankia meridionalis. All Frankia-enriched metagenomes obtained in this study contained homologs of the canonical nod genes nodABC; the North American genomes also contained the sulfotransferase gene nodH, while the genome from the Southern Hemisphere only contained nodC and a truncated copy of nodB.

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“…(2015) for ACN1ag, Nouioui et al. (2019) for CpI1-S, Normand et al. (2018) for ARgP5, Mansour et al.…”

Section: Introductionmentioning

confidence: 99%

Frankia-Enriched Metagenomes from the Earliest Diverging Symbiotic Frankia Cluster: They Come in Teams

Nguyen

Wibberg

Vigil-Stenman

et al. 2019

Genome Biology and Evolution

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“…The standard approach based on DNA–DNA hybridization [11] has identified several genomospecies but since these had few distinguishing physiological features, species were not named, except for Frankia alni . One had to wait for genomes to become available [12] and on a concerted international effort to see first species Frankia alni emended[13] , and later, several others proposed: Frankia casuarinae , Frankia elaeagni [13], Frankia asymbiotica [14], Frankia canadensis [15] , Frankia coriariae [16], Frankia discariae [17], Frankia inefficax [18] , Frankia irregularis [19], Frankia saprophytica [20], Frankia soli [21] , Frankia torreyi [8], and even three unisolated species: ' Candidatus Fankia californiensis' [22], ' Candidatus Frankia datiscae' [23] and ' Candidatus Frankia meridionalis' [24].…”

Section: Introductionmentioning

confidence: 99%

Proposal of 'Candidatus Frankia alpina', the uncultured symbiont of Alnus alnobetula and A. incana that forms spore-containing nitrogen-fixing root nodules

Pozzi

Herrera-Belaroussi

Schwob

et al. 2020

International Journal of Systematic and Evolutionary Microbiology

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The members of the genus Frankia are, with a few exceptions, a group of nitrogen-fixing symbiotic actinobacteria that nodulate mostly woody dicotyledonous plants belonging to three orders, eight families and 23 genera of pioneer dicots. These bacteria have been characterized phylogenetically and grouped into four molecular clusters. One of the clusters, cluster 1 contains strains that induce nodules on Alnus spp. (Betulaceae), Myrica spp., Morella spp. and Comptonia spp. (Myricaceae) that have global distributions. Some of these strains produce not only hyphae and vesicles, as other cluster 1 strains do, but also numerous sporangia in their host symbiotic tissues, hence their phenotype being described as spore-positive (Sp+). While Sp+ strains have resisted repeated attempts at cultivation, their genomes have recently been characterized and found to be different from those of all described species, being markedly smaller than their phylogenetic neighbours. We thus hereby propose to create a 'Candidatus Frankia alpina' species for some strains present in nodules of Alnus alnobetula and A. incana that grow in alpine environments at high altitudes or in subarctic environments at high latitudes.

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“…These obstacles have been addressed by the application of better methods for cultivating Frankia strains and by marked improvements in their systematics, mainly due to the application of genome sequence-based taxonomic procedures (Nouioui et al, 2016). The genus currently encompasses 11 validly named species: Frankia alni (Nouioui et al, 2016), the type species, Frankia asymbiotica (Nouioui et al, 2017c), Frankia canadensis (Normand et al, 2018), Frankia casuarinae (Nouioui et al, 2016), Frankia coriariae (Gtari et al, 2015; Nouioui et al, 2017a), Frankia discariae (Nouioui et al, 2017d), Frankia elaeagni (Gtari et al, 2004; Nouioui et al, 2016), Frankia inefficax (Nouioui et al, 2017a), Frankia irregularis (Nouioui et al, 2018b), Frankia saprophytica (Nouioui et al, 2018a), and Frankia torreyi (Nouioui et al, 2019), with the prospect of more to come in the near future (Tisa et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

“…Frankia type strains can be assigned to four clusters with distinct host ranges (Normand et al, 2007; Tisa et al, 2013). Cluster 1 strains nodulate host plants classified in the families Betulaceae , Casuarinaceae (apart from Gymnostoma ), and Myricaceae and can be further divided into three subgroups; those assigned to subcluster 1a infect Alnus – Myrica species, subcluster 1b strains, such as strain ARgP5 (Normand et al, 2018), infect Alnus and Myricaceae species while subcluster 1c includes Frankia strains that infect Allocasuarina and Casuarina species (Normand et al, 1996). In turn, cluster 2 strains are associated with plants classified in the families Coriariaceae , Datiscaceae , and Rosaceae and the type genus Ceanothus of the family Rhamnaceae while those in cluster 3 infect host plants belonging to the families Elaeagnaceae , Myricaceae , and Rhamnaceae (except Ceanothus ); the genus Gymnostoma and occasionally Alnus species.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2019

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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 ( trp D), anthranilate synthases, and aminases ( trp A 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.

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Frankia canadensis sp. nov., isolated from root nodules of Alnus incana subspecies rugosa

Cited by 33 publications

References 69 publications

Frankia-Enriched Metagenomes from the Earliest Diverging Symbiotic Frankia Cluster: They Come in Teams

Frankia-Enriched Metagenomes from the Earliest Diverging Symbiotic Frankia Cluster: They Come in Teams

Proposal of 'Candidatus Frankia alpina', the uncultured symbiont of Alnus alnobetula and A. incana that forms spore-containing nitrogen-fixing root nodules

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

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