Frankia saprophytica sp. nov., an atypical, non-infective (Nod–) and non-nitrogen fixing (Fix–) actinobacterium isolated from Coriaria nepalensis root nodules

Abstract

Strain CN3, a Coriaria nepalensis isolate, appears to form hyphae and sporangia typical of members fo the genus Frankia. However, it failed to form vesicles, to reduce acetylene and to induce nodules on its original host plant. A polyphasic approach was used here to determine the taxonomic status of strain CN3. The 16S rRNA gene sequence of strain CN3 showed the highest sequence identity with Frankia asymbiotica type strain M16386 (99.4 %). Digital DNA-DNA hybridization between strains CN3 and M16386 was 25.7 %, which is clearly below the accepted cut-off point of 70 %. The G+C content of DNA was 71.8 mol%. Whole-cell hydrolysates of strain CN3 were rich in meso-diaminopimelic acid. Cell-wall sugars were composed of galactose, glucose, mannose, rhamnose and traces of ribose. The polar lipid profile contained phosphatidylinositol, phosphatidylglycerol, diphosphatidylglycerol, phosphoglycolipids, phospholipid, six uncharacterized glycolipids and two uncharacterized lipids. The predominant menaquinone (>25 %) was MK-9(H6). Major fatty acids (>15 %) of strain CN3 consisted of iso-C16 : 0, C17 : 1ω8c and C15 : 0. Based on 16S rRNA gene phylogeny, genome sequence analysis and phenotypic results, strain CN3 (=DSM 105290=CECT 9314) is proposed to represent the type strain of a novel species, Frankia saprophytica sp. nov.

Draft genomes of non-nitrogen-fixing Frankia strains

“…Both genospecies CN and Ag lack genes essential for nitrogen-fixation, as observed for cluster 4 species F. inefficax EUI1c T 23 and F. saprophytica CN3 T 25 , but not for F. asymbiotica M16386 T 24 . While F. inefficax EUI1c T was observed to form ineffective nodules, none of the other species were able to form nodules on their original host plant.…”

“…Frankia coriariae BMG5.1 T 16 , Candidatus Frankia datiscae Dg1 17 , Candidatus Frankia californiensis Dg2 18 and Candidatus Frankia meridionalis Cppng1 19 represent species in cluster 2, while Frankia elaeagni BMG5.12 T 12 , Frankia discariae BCU110501 T 20 , Frankia soli NRRL B-16219 T 21 and Frankia irregularis G2 T 22 are species in cluster 3. Cluster 4 frankiae are represented by three species, Frankia inefficax EuI1c T 23 , Frankia asymbiotica M16386 T 24 and Frankia saprophytica CN3 T 25 .…”

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

“…In addition, four species can be reclassified as members of the genus. Frankia discariae (Nouioui et al, 2018b), F. irregularis (Nouioui et al, 2018a), F. soli (Gtari et al, 2020), and F. colletiae (Nouioui et al, 2022) Basonym: Frankia elaeagni (Nouioui et al, 2016). The description of Parafrankia elaeagni is the same as that given by Nouioui et al (2016) for F. elaeagni.…”

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

“…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].…”