, 1990) and the mallard program (Ashelford et al., 2006). The nucleotide sequences of the clones without chimeric sequences were aligned using muscle (Edgar, 2004). Putative introns observed in the sequences of clones were removed by judging from the alignments. Clones having 97% sequence similarity or higher were treated as a phylotype using dotur (Schloss & Handelsman, 2005). The exon sequences of the phylotypes were realigned with other published sequences including the closest one determined by blast searches (Altschul et al.,
1990). The construction of phylogenetic selleck inhibitor trees and the diversity analysis were performed as described previously (Kato et al., 2009a). The nucleotide sequences of the phylotypes reported in this paper have been deposited in the DDBJ database under accession numbers AB600328–AB600387. The phylotypes detected in the hot water sample were related to cultured (hyper)thermophilic members of Crenarchaeota (Figs 2a, b and 3), i.e. Vulcanisaeta, Caldivirga, Thermoproteus, Acidilobus and Stygiolobus (Zillig et al., 1981; Segerer et al., 1991; Itoh et al., 1999, 2002; Prokofeva et al., 2000) with 97–99% similarity. These members have been isolated from terrestrial hot springs and include thermoacidophiles for which the optimum growth temperatures and pH are 80–90 °C and 2.5–6.8, respectively, as summarized in the previous report (Itoh, 2003). The detection of phylotypes
related to these thermoacidophiles in the Megestrol Acetate hot water sample is consistent with the high-temperature (78 °C) and acidic environment (pH 3.5). One clone (HO78W9A61, AB600380) detected SAHA HDAC mw in the hot water was related to the environmental clone OP-9, which is affiliated with the Nanoarchaeota (Hohn et al., 2002) (94% similarity). We excluded this clone in the construction of the phylogenetic tree and the statistical analysis because of the short length of the sequence (190 bp). Phylotypes affiliated with
Nanoarchaeota have been detected in other hot spring fields (Hohn et al., 2002; Casanueva et al., 2008). All euryarchaeotic phylotypes detected in the mud sample were related to members of the Thermoplasmata, a thermoacidophilic group. In this study, these phylotypes were clustered in four groups: Thermoplasma-related groups I to IV (TRG-I to IV) (Fig. 4). Cultured species related to Thermoplasma and other acidic environmental clones were included in the TRG-I (Fig. 4). The phylotypes in TRG-I, except HO28S9A75, were closely related to a thermoacidophilic archaeon, Thermogymnomonas acidicola, which belongs to a recently reported Thermoplasma-related genus (Itoh et al., 2007) (90–93% similarity). This archaeon, which grows in the range 38–68 °C and at pH 1.8–4.0, was isolated from a solfataric soil in Hakone, Japan (Itoh et al., 2007). In contrast, TRG-II, III and IV include no cultured species (Fig. 4).