Genetic diversity of rhizobia isolated from nodules of the relic species Vavilovia formosa (Stev.) Fed.

Abstract

Sixteen bacterial strains were isolated from root nodules of Vavilovia formosa plants originated from the North Ossetian State Natural Reserve (Caucasus, Russia). Phylogenetic analysis of these strains was performed using partial 16S rRNA gene and internally transcribed spacer (ITS) sequences. The results showed that the isolates belong to three families of root nodule bacteria. Twelve of them were related to the genus Rhizobium (family Rhizobiaceae) but four strains can be most probably identified as Phyllobacterium-related (family Phyllobacteriaceae), Bosea- and Rhodopseudomonas-related (family Bradyrhizobiaceae). Amplified fragment length polymorphism clustering was congruent with ITS phylogeny but displayed more variability for Rhizobium isolates, which formed a single group at the level of 30 % similarity. We expect that the isolates obtained can belong to new taxa at genus, species or subspecies levels. The results of PCR amplification of the nodulation genes nodC and nodX showed their presence in all Rhizobium isolates and one Rhodopseudomonas-related isolate. The nodC gene sequences of V. formosa isolates were closely related to those of the species Rhizobium leguminosarum bv. viciae but formed separate clusters and did not intermingle with any reference strains. The presence of the nodX gene, which is necessary for nodulation of Afghan peas (Pisum sativum L.) originated from the Middle East, allows the speculation that these wild-type pea cultivars may be the closest existing relatives of V. formosa. Thus, the studies of genetic diversity and symbiotic genes of V. formosa microsymbionts provide the primary information about their phylogeny and contribute to the conservation of this relict leguminous species.

Ribosomal protein biomarkers provide root nodule bacterial identification by MALDI-TOF MS

“…This makes MALDI-TOF MS and the rhizobia-specific module an ideal replacement for the demanding and expensive sequencing of partial 16S rRNA or AFLP/RFLP analyses that have been performed to identify and determine the diversity of microsymbionts of wild legumes in recent large-scale studies (Aserse et al 2013;Safronova et al 2014;Yang et al 2013;Zhao et al 2014). In the economically important field of symbiotic nitrogen fixation in agricultural systems, knowledge of the biodiversity of rhizobia and of local populations is important for the design of successful inoculation strategies (Lindström et al 2010).…”

Extra-slow-growing Tardiphaga strains isolated from nodules of Vavilovia formosa (Stev.) Fed.

“…Type species are indicated by the letter "T" (Ding et al 2012). Despite the previously published information about the amplification of nodC gene in the isolate Vaf-27 (Safronova et al 2014), homologues of this gene as well as of two other canonical nodA and nodB genes were not detected during the whole-genome sequence analysis of the strain Vaf-27.…”

“…One of the reasons for the failure of V. formosa cultivation ex situ may be a lack of its nitrogen-fixing rhizobial microsymbionts which play an important role for growth and productivity of plants, their adaptation to the habitat and competition for environmental space (Tikhonovich and Provorov 2007). However, because of the very rare occurrence of Vavilovia, the first rhizobial isolates from nodules of this plant species were described only in 2014 (Safronova et al 2014). Contrary to common perception that the tribe Fabeae forms symbiosis only with strains of subspecies Rhizobium leguminosarum bv.…”

“…Contrary to common perception that the tribe Fabeae forms symbiosis only with strains of subspecies Rhizobium leguminosarum bv. viciae, the isolates from V. formosa belonged to three different families of root nodule bacteria: Rhizobiaceae, Phyllobacteriaceae and Bradyrhizobiaceae (Safronova et al 2014(Safronova et al , 2015.…”

ALFP-FINGERPRINTING FOR PASPORTIZATION OF Aspergillus nige L-4, THE CITRIC ACID COMMERCIAL PRODUCER

“…AFLP (amplified fragments length polymorphism) fingerprinting is a common technique in molecular genetics of microorganism. Using AFLP-fingerprinting, the differences have been successfully found between close related strains in different taxonomic groups including rhizobia [8][9][10][11][12], lactobacteria [13][14][15][16], and myceliar fungi Trichoderma and Aspergillus [17][18][19][20]. AFLP-fingerprinting is high reproducible, so it may be considered promising to authenticate microorganisms [21].…”