Further cultivation efforts are Selleck CDK inhibitor needed to determine their physiology. The
archaeal phylotypes detected in the hot water sample were similar between the libraries, i.e. HO78W9 vs. HO78W21, amplified with the primer sets Arc9F–Uni1046R and Arch21F–Arch958R (Fig. 2a and b), respectively. The coverage values were 99–100% (Table 1) and the rarefaction curves leveled off (Fig. S2). These results indicate that almost all of the archaeal phylotypes in the hot water were recoverable by the primer sets used. However, we are not able to exclude the possibility that there are novel Archaea that could not be recovered with either primer set, such as the ARMAN group (Baker et al., 2006). Archaeal diversity in the hot water (78 °C) is likely to be lower than that in the solfataric mud (28 °C), which is supported by the Chao1 species richness estimates, Shannon diversity index (Table 1) and rarefaction curves (Fig. S2) for both clone libraries HO78W9 and HO78W21. Differences in the community structures of the mud sample determined using Arc9F–Uni1406R and Arch21F–Arch958R, i.e. HO28S9 vs. HO28S21, were observed (Fig. 2c and d). The detection frequency of the TRG-I to -IV
clones (57.0% of the total clone number) was higher in the HO28S9 library than in the HO28S21 library (12.8%) (Fig. 2c and d), although both libraries were derived from the same DNA extract. In contrast, the detection frequencies of Vulcanisaeta, Thermocladium and UTRCG were relatively unless higher in HO28S21 (23.4%, 9.6% and 9.6%, respectively, Fig. 2d) than in HO28S9 (1.1%, 2.2% and 1.1%, respectively, Fig. 2c). The differences most likely resulted see more from the efficient annealing of the forward primer Arch9F used with the 16S rRNA gene of the phylotypes in the TRGs (Fig. 5). In fact, the 16S rRNA gene sequences of most phylotypes in the TRGs have C at position 21 of the 16S rRNA gene sequence (rrnB) of M. jannaschii (L77117) (Fig. S3). Arch21F has A at its 3′ final end (the M. jannaschii position is
21), which could cause a low amplification efficiency of the 16S rRNA gene of the TRGs. Actually, the phylotypes of the TRGs represented over half of the total clone number of the HO28S9 library (Fig. 2c). Such phylotypes were also detected in the HO28S21 library (<10% of the total number of clones, Fig. 2d) despite the mismatch. This is probably because of the non-Watson–Crick base pairing of A–G and/or loss of the 3′ end of A during storage of the primer. A larger number of unique phylotypes in the TRGs was detected in the HO28S9 library than in the HO28S21 library (Fig. S4). This may also reflect the differences in the sequences of the primer sets used. The phylotypes related to Vulcanisaeta and Thermocladium accounted for higher percentages of the HO28S21 library (23.4% and 9.6%, respectively, Fig. 2d) than the HO28S9 library (both 1.1%, Fig. 2c).