Culture-Independent Estimation of Optimal and Maximum Growth Temperatures of Archaea in Subsurface Habitats Based on the G+C Content in 16S rRNA Gene Sequences

Abstract

The temperature ranges of growth of archaea are strongly correlated with the guanine-plus-cytosine (G+C) contents of their 16S rRNA sequences (P GC ). In order to estimate minimum (T min ), optimal (T opt ), and maximum (T max ) growth temperatures of uncultured archaea based on P GC , the 16S rRNA gene sequences of 207 archaeal species were collected from public databases, and their T min , T opt and T max were extracted from description papers and reviews. These values of growth temperatures were plotted againstP GC , and then the regression lines for estimating T min , T opt and T max were calculated. We PCR-amplified the archaeal 16S rRNA gene fragments from the hot water samples, cloned the fragments, and determined the sequences. Growth temperatures of environmental archaea were inferred from G+C content of the 16S rRNA gene sequences by the regression lines. In the terrestrial hot springs (74 • C and 85 • C), both estimated growth temperatures of archaea were higher than in situ temperatures of hot spring waters. Even from tepid hydrothermal fluid (40 • C) we obtained a significant number of archaeal genes indicating high growth temperatures. These results suggested that hot subsurface environments exist under those hydrothermal and geothermal regions. In this study, growth temperatures of uncultured archaea and in situ subsurface temperatures were roughly inferred from 16S rRNA gene sequences of archaea that were transported from the subsurface biosphere. This new method based on microbial molecular information may be applicable to temperature estimation of subsurface environments for We are grateful to the captains and crews of the R/V Yokosuka and Natsushima and to the operation teams of the Shinkai 6500 and Hyper-Dolphin for helping us to collect the deep-sea hydrothermal fluid samples. We thank Dr. Julia Maresca for comments on the manuscript.which it has been difficult to measure the actual temperature with appropriate instrumentation.

Archaeal Community Structures in the Solfataric Acidic Hot Springs with Different Temperatures and Elemental Compositions

“…According to Kimura et al, the growth temperature of archaea are strongly correlated with the G + C content, while the phylotypes containing this amount of G + C were grouped as the moderately thermophilic and hyperthermophilic archaea [37]. Therefore, all phylotypes detected in this study could possibly be related to moderately thermophilic and hyperthermophilic archaea.…”

“…This phylotype showed 95-96% sequence similarity with published environmental clones, NAKO74-07 and HS3wa_52 detected from Nakabusa hot spring, Japan (DNA database Accession no. AB366602) [37] and Tatung Volcano hot spring, Taiwan (DNA database Accession no. FJ797311).…”

Defining boundaries for the distribution of microbial communities beneath the sediment-buried, hydrothermally active seafloor

“…In the 16S rRNA gene clone libraries obtained from the deepest sediments of the microbially habitable terrain in the subseafloor environment, putative thermophilic phylotypes, such as members of HWCGIV, thermophilic ANME-1, OP1 and Thermotogae, were found (Figure 3; Supplementary Data S1). According to the molecular thermometer calculation based on the GC content of the 16S rRNA gene sequences (Kimura et al, 2010), the potential growth temperature range was estimated to be the highest (50 -76°C) for members of HWCGIV among the putative thermophilic populations.…”

Expression and Function of Different Guanine-Plus-Cytosine Content 16S rRNA Genes in Haloarcula hispanica at Different Temperatures

“…Because thermophilic and hyperthermophilic archaea have greater P GC values for 16S rRNA genes compared with psychrophilic and mesophilic archaea (Galtier and Lobry, 1997; Khachane et al, 2005; Kimura et al, 2006, 2007, 2010), Kimura et al (2013) proposed linear regression equations to infer T min , T opt , and T max of cultured and not-yet cultured archaea based on P GC of 16S rRNA genes. We therefore used these equations to estimate growth temperatures of H. hispanica based on P GC value of each 16S rRNA gene.…”

“…Previous studies have reported that 16S rRNA gene sequences are naturally inscribed with the thermal features of their prokaryotic hosts (Galtier and Lobry, 1997; Khachane et al, 2005; Kimura et al, 2007, 2010, 2013). The observation was based on a high correlation between the growth temperatures of the prokaryotes and the P GC of their 16S rRNA sequences: 16S rRNA genes of hyperthermophiles and thermophiles tend to have high P GC , whereas 16S rRNA genes of mesophiles and psychrophiles have relatively low P GC .…”