Research Article: Complete Genome Sequence of Thermus aquaticus Y51MC23

Date Published: October 14, 2015

Publisher: Public Library of Science

Author(s): Phillip J. Brumm, Scott Monsma, Brendan Keough, Svetlana Jasinovica, Erin Ferguson, Thomas Schoenfeld, Michael Lodes, David A. Mead, Hodaka Fujii.


Thermus aquaticus Y51MC23 was isolated from a boiling spring in the Lower Geyser Basin of Yellowstone National Park. Remarkably, this T. aquaticus strain is able to grow anaerobically and produces multiple morphological forms. Y51MC23 is a Gram-negative, rod-shaped organism that grows well between 50°C and 80°C with maximum growth rate at 65°C to 70°C. Growth studies suggest that Y51MC23 primarily scavenges protein from the environment, supported by the high number of secreted and intracellular proteases and peptidases as well as transporter systems for amino acids and peptides. The genome was assembled de novo using a 350 bp fragment library (paired end sequencing) and an 8 kb long span mate pair library. A closed and finished genome was obtained consisting of a single chromosome of 2.15 Mb and four plasmids of 11, 14, 70, and 79 kb. Unlike other Thermus species, functions usually found on megaplasmids were identified on the chromosome. The Y51MC23 genome contains two full and two partial prophage as well as numerous CRISPR loci. The high identity and synteny between Y51MC23 prophage 2 and that of Thermus sp. 2.9 is interesting, given the 8,800 km separation of the two hot springs from which they were isolated. The anaerobic lifestyle of Y51MC23 is complex, with multiple morphologies present in cultures. The use of fluorescence microscopy reveals new details about these unusual morphological features, including the presence of multiple types of large and small spheres, often forming a confluent layer of spheres. Many of the spheres appear to be formed not from cell envelope or outer membrane components as previously believed, but from a remodeled peptidoglycan cell wall. These complex morphological forms may serve multiple functions in the survival of the organism, including food and nucleic acid storage as well as colony attachment and organization.

Partial Text

Thermus aquaticus YT-1 holds a special place in the history of microbiology. The thermophile was first isolated and cultured from a hot spring in Yellowstone National Park in 1969 [1]. The discovery of life at high temperatures was controversial at that time, but later shown to be quite prevalent as demonstrated by the isolation of Thermus strains from hot water heaters and other sources [2]. The subsequent discovery and characterization of Thermus aquaticus DNA polymerase resulted in the development of amplification and sequencing tools that have revolutionized nearly every field of biology and medicine [3].

Thermus aquaticus Y51MC23 is one of a number of novel thermophilic species isolated from 88°C water in the northern outflow channel of Bath hot spring in the Lower Geyser Basin of Yellowstone National Park [41]. The general features of the organism are summarized in Table 1. The temperature of Bath hot spring is 93.5°C at the source, which is the boiling point at the spring’s elevation. The pH of the spring is 8.9 with SiO2 (244.8 mg/l) and Cl- (297.1 mg/l) the dominant dissolved minerals [42]. Y51MC23 is a gram-negative, rod-shaped organism that grows well between 50°C and 80°C with maximum growth rate at 65°C to 70°C (optimum pH for growth is 7.6). The organism forms yellow colonies on YTP-2 agar, and cells isolated from liquid cultures are yellow. Colonies are catalase positive, forming bubbles when tested with aqueous hydrogen peroxide. Like most Thermus species, Y51MC23 grows well on media containing low concentrations of salts (2 to 4 g/l), yeast extract and protein hydrolysates such as tryptone or peptone and it does not grow in standard laboratory media such as Luria broth. Unlike the type strain T. aquaticus YT-1 [1], Y51MC23 is unable to grow on a minimal medium containing salts and glucose. Y51MC23 is able to grow under both aerobic and anaerobic conditions, in sharp contrast to YT-1, which was reported to be an obligate aerobe [1]. Cellular morphology in liquid culture is complicated and will be discussed in a later section.

Thermus aquaticus, the first thermophilic bacterium shown to grow at temperatures well over 55°C, started a revolution in thermal biology with its initial description in 1969 [1]. The ubiquitous presence of Thermus species [2] suggests the genus has remarkable survival adaptations not present in other organisms, resulting in extensive research to understand its role as a model organism for life at high temperatures [87].