DNA microarray technology allows for a quick and easy comparison of complete transcriptomes, resulting in improved molecular insight in fluctuations of gene expression. After emergence of the microarray technology about a decade ago, the technique has now matured and has become routine in many molecular biology laboratories. Numerous studies have been performed that have provided global transcription patterns of many organisms under a wide range of conditions. Initially, implementation of this high-throughput technology has lead to high expectations for ground breaking discoveries. Here an evaluation is performed of the insight that transcriptome analysis has brought about in the field of hyperthermophilic archaea. The examples that will be discussed have been selected on the basis of their impact, in terms of either biological insight or technological progress. 1. Thermophiles Forty years ago it was generally accepted that life was not possible at temperatures higher than 60°C. In 1969, however, Brock and Freeze discovered that the upper temperature limit goes as high as 75°C when microorganisms were isolated from thermal springs in Yellowstone National Park [1, 2]. The pioneering work of Brock set the stage for further exploration of a wide range of thermal ecosystems. Numerous microorganisms defined as thermophiles have since been found to thrive optimally between 50 and 80°C, but also many appeared to have their optimal temperature for growth from 80°C to well above 100°C, the hyperthermophiles. Recently it has been shown that some archaea can endure temperatures as high as 122°C and even proliferate in such conditions. Although there are several bacterial representatives in the group as well, most of the known hyperthermophiles belong to the archaea. Thermophilic organisms can be found in water-containing geothermally heated environments. These volcanic ecosystems are mainly situated along terrestrial and submarine fracture zones where tectonic plates are converging or diverging. The terrestrial biotopes of (hyper)thermophiles are mainly aerobic, sulfur containing solfataric fields with temperature as high as 100°C (depending on the altitude) and the pH in a dual range: either acidic (values from below zero to 4.0 [3]) or neutral to slightly alkali (7.0–9.0) [4]. The marine biotopes for (hyper)thermophiles consist of different hydrothermal systems ranging from shallow to abyssal depths. Temperatures in those anaerobic environments can range up to 400°C and the pH is usually in the range of 5.0 to 8.5. Progress in culturing thermophilic archaea and
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