Frankia umida sp. nov., isolated from root nodules of Alnus glutinosa L.

Frankia strain Ag45/Mut15(T) was isolated from a root nodule of Alnus glutinosa growing in a swamp at lake Grossensee, Germany. The strain forms root nodules on A. glutinosa , in which it produces hyphae and clusters of N-2-fixing vesicles. N-2-fixing vesicles are also produced in nitrogen- free growth medium, in addition to hyphae and sporangia. The whole- cell hydrolysates of strain Ag45/Mut15(T )contained meso-diaminopimelic acid in the peptidoglycan and ribose, xylose, mannose, glucose, galactose and a trace of rhamnose as cell - wall sugars. The major polar lipids were phosphatidylglycerol, phosphatidylinositol, diphosphati- dylglycerol and glyco- phospholipid. The predominant (>20 %) menaquinones were MK- 9(H-6) and MK- 9(H-4). The major fatty acid profile (>10 %) consisted of iso- C-16:0, C-17: 1 omega 8c and C-17:0. Pairwise 16S rRNA gene distances showed that strain Ag45/Mut15(T) was most closely related to Frankia torreyi CpI1(T) and Candidatus Frankia nodulisporulans with 16S rRNA gene similarity values of 0.001335 substitutions per site. An multilocus sequence analysis phylogeny based on atpD , dnaA , ftsZ , pgk and rpoB amino acid sequences positioned the strain within cluster 1 of Alnus-and Myrica-nodulating species, close to Candidatus F. nodulisporu- lans AgTrST and F. canadensis ARgP5(T). The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between the studied strain Ag45/Mut15(T) and all validly named Frankia species were below the defined threshold for prokaryotic species demarcation. Candidatus F. nodulisporulans AgTrST, which cannot be cultivated in vitro , was found to be the closest phy- logenetic neighbour to strain strain Ag45/Mut15(T) with dDDH and ANI values of 61.8 and 97 %, respectively. Strain Ag45/Mut15(T) was not able to sporulate in nodule tissues like strain AgTrST.Phenotypic, physiological and phylogenomic analyses confirmed the assignment of strain Ag45/Mut15(T) (=DSM 114737(T)=LMG 326O1(T)) to a novel species, withAg45/Mut15(T) as type strain, for which the name Frankia umida sp. nov. is proposed.

Automated summary

A new Frankia strain, named Frankia umida sp. nov., was isolated, which has the ability to produce hyphae and N-2-fixing vesicles on the root nodules of Alnus glutinosa.