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

Abstract

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.

Taxogenomic status of phylogenetically distant Frankia clusters warrants their elevation to the rank of genus: A description of Protofrankia gen. nov., Parafrankia gen. nov., and Pseudofrankia gen. nov. as three novel genera within the family Frankiaceae

“…Cluster 1 contains as-yet-uncultured Frankia microsymbionts, which are characterised by profuse sporulation within nodules tissues (Sp + types; Schwintzer, 1990 ), and a very higher proportion of cluster 2 strains are as-yet-uncultured. The Candidatus status has been used to accommodate some of these uncultured Frankia which were defined based on genome sequences ( Persson et al, 2011 , 2015 ; Nguyen et al, 2016 , 2019 ; Normand et al, 2017 ; Herrera-Belaroussi et al, 2020 ; Pozzi et al, 2020 ; Berckx et al, 2022 ). Two strains from cluster 2 have been successfully cultivated following a dual approach consisting of comparative genomics and direct physiological assay on nodule tissues ( Gtari et al, 2015 ; Gueddou et al, 2019 ).…”

“…Cluster 4 includes Frankia asymbiotica ( Nouioui et al, 2017c ), Frankia inefficax ( Nouioui et al, 2017a ), and Frankia saprophytica ( Nouioui et al, 2018a ). Additionally, four candidate species are also defined to accommodate uncultured taxa: Candidatus Frankia datiscae ( Persson et al, 2011 ) and Candidatus Frankia californiensis ( Normand et al, 2017 ) from cluster 2, as well as Candidatus Frankia alpina ( Pozzi et al, 2020 ) and Candidatus Frankia nodulisporulans ( Herrera-Belaroussi et al, 2020 ) from cluster 1.…”

Gene losses resulting in specialized metabolism in the earliest divergent symbiotic Frankia clade can be linked to its low saprotrophic capabilities

“…This means that the production of isocitrate will inevitably lead to the synthesis of 2-oxoglutarate (2-OG). Intriguingly, the icl gene also seemed to be missing in cluster-1 strains that could never be cultured, such as Candidatus Frankia nodulisporulans or Candidatus Frankia alpina (Pozzi et al , 2020; Herrera-Belaroussi et al , 2020). Thus, the lack of icl could be a common feature for those Frankia strains which only have a short phase of saprotrophic growth, and mostly rely on a host plant to support their growth.…”

Draft Genomes of Symbiotic Frankia Strains AgB32 and AgKG'84/4 from Root Nodules of Alnus Glutinosa growing under Contrasted Environmental Conditions

“…Cluster 1c with Casuarina-infective strains remains at the root of this cluster with several distinguishing features such as the lack of vesicles in nodules, a host-derived hemoglobin protection against oxygen and a distinct host range [6]. Alnus-infective symbiotic strains have been described initially on the basis of DNA/DNA homology as quite close to one another [14] but the full extent of diversity has slowly emerged with studies targeting new cultured strains and uncultured frankiae from specific environments [38,[42][43][44][45][46][47].…”