03). To determine whether the samples clustered in two dimensional spaces, PCA was applied to UniFrac
metric. The SB203580 manufacturer ordination diagram (Figure 4a) of cbbL clone libraries revealed that strongest variation in the data set was between agricultural soil and saline soils as they were separated on first axis of ordination diagram, which explains high percentage of total variation (55.51%). In case of 16S rRNA gene clone libraries, the first axis HDAC inhibitor separated agricultural and saline soils which explain total community variability (57.78%) among three sample sites (Figure 4b). Figure 4 UniFrac PCA of cbbL and 16S rRNA clone libraries. The ordination plots for the first two dimensions to show the relationship between agricultural and the saline soils for (a) cbbL and (b) 16S rRNA gene assemblages. Agricultural soil (AS) is represented by square and saline soils is represented by diamond (SS1) and circle (SS2). Each axis indicates the fraction of the variance in the data that the axis accounts for. Discussion The study of microbial diversity is crucial for the understanding of structure, function, and evolution of biological communities in order to effectively link
community structure and function. We constructed multiple clone libraries for each gene (cbbL form IC, IA and 16S rRNA) from agricultural and saline soils, which were further analyzed. Form IC was highly diverse in all clone libraries while form IA could only be amplified from the high saline soil (SS2) clone library (Table 3-deazaneplanocin A 3). This is in accordance with the previous work reported by Nanba et al. (2004), Tolli & King (2005) and Selesi et al. (2005) [14, 24, 33]. They also found form IC cbbL sequences almost exclusively dominant in various terrestrial (agroecosystem, pine forest) systems and noted that form IA was less selleck chemical diverse than form IC. Table 3 Oligonucleotide primers used for PCR amplification of
cbbL and 16S rRNA genes Primer Position(nt) Primer sequence(5′-3′) Reference PCR amplification1 AS SS1 SS2 cbbLR1F 634-651 AAGGAYGACGAGAACATC Selesi et al., 2005  + + + cbbLR1R 1435-1454 TCGGTCGGSGTGTAGTTGAA cbbLG1F 397-416 GGCAACGTGTTCGGSTTCAA Selesi et al., 2005  – - – cbbLG1R 1413-1433 TTGATCTCTTTCCACGTTTCC RubIgF 571-590 GAYTTCACCAARGAYGAYGA Spiridonova et al., 2004  – - + RubIgR 1363-1382 TCRAACTTGATYTCYTTCCA 27 F 27-46 AGAGTTTGATCMTGGCTCAG Lane, 1991  + + + 1492 R 1471-1492 TACGGYTACCTTGTTACGACT 1Positive PCR amplification (+), no PCR amplification (−) for the targeted primers in three soil samples. This study targeted functional and phylogenetic markers together in order to reveal the metabolic potentialities of the chemolithoautotrophic bacteria at three different soil habitats. Comparison of microbial populations between different soil habitats includes diversity estimation based on the expected number of OTUs.