Distribution of Frankia genotypes occupying Alnus nepalensis nodules with respect to altitude and soil characteristics in the Sikkim Himalayas

Abstract

doi: 10.1111/j.1399-3054.2006.00872.x We investigated the distribution of Frankia genotypes with respect to three altitudinal zones in the Sikkim Himalayas. The study was carried out for 90 Alnus nepalensis trees at nine different locations from three altitudes from the east and north districts of Sikkim, India. We used a PCR-based technique to amplify the internally transcribed spacer (ITS) region of the rrn operon using two primers specific for the distal part of 16S ribosomal RNA (rRNA), ITS and proximal part of 23S rRNA genes of Frankia. The PCR products were digested with the restriction enzyme RsaI to generate amplified recombinant DNA restriction analysis (ARDRA) patterns. Frankia genotypes were categorized on the basis of 17 different ARDRA patterns. Nucleotide sequences of some representative amplicons were also obtained. Rhizosphere soil samples associated with the 90 trees were collected and analysed for eight different soil properties. In general, soil properties did not differ by site or altitude, and did not correlate with Frankia genotypes. Frankia community composition was strongly affected by altitude and to a lesser extent by site

Molecular diversity of Frankia from root nodules of Hippophae salicifolia D.Don found in Sikkim

“…This diversity was confi rmed by the nucleotide sequencing. In a similar study we found two different ARPs for ten Alnus nepalensis root nodule samples collected from North Sikkim [14]. This is indicative of a larger diversity for Frankia nodulating Hippophae salicifolia compared to that nodulating alder.…”

“…The gel was then scanned and photographed using BioRad GelDoc1000 and the profi les were analyzed using the Multi Analyst ® software. These patterns were compared with patterns of similar digestion carried out on alder compatible Frankia [14]. NT-SYS (version 2.1) was used for cluster analysis of the banding patterns.…”

“…Each cycle comprised 1 min denaturation at 94°C, 1 minute annealing at 49°C and 1 min of elongation at 72°C. A hot start was given for 5 min at 94°C and at the end of the run an additional 7 min extension time at 72°C was added to allow complete extension of all DNA double strands [14]. The annealing temperature was standardized for securing amplifi cation of Hippophae compatible Frankia DNA.…”

“…Extraction of total genomic DNA from individual nodule lobes was carried out following the methodology given by Rouvier et al [12] with minor modifi cations [13,14].…”

Diversity of Frankia Populations in Root Nodules of Geographically Isolated Arizona Alder Trees in Central Arizona (United States)

“…At a threshold of 5%, all Frankia populations in nodules of A. oblongifolia were placed in one group, suggesting no differentiation by mountaintop and a limited overall level of diversity, with one cluster present, compared to the potential presence of at least six clusters of frankiae within the Alnus host infection group described in previous studies (34,49). Low overall diversity has also been described to occur in other studies of natural Frankia diversity in root nodules of various alder species (11,23,27,29).…”