TABLE 5.2 Characteristics of Archaeal Phylogenetic Groups

Environmental origin Metabolism

Other characteristics



Extreme halophiles


Salt lakes

Swamps, marshes, marine sediments, guts, sewage treatment

Heterotrophic; aerobic;

nonphotosynthetic phosphorylation

Anaerobic;generate methane; fix CO2; electrons from hydrogen

Require salt for growth, cell walls and enzymes stabilized by Na+


metabolizing thermophiles

Crenarchaeota Hypothermophiles

Hydrothermal Anaerobic sulfur Polar flagella vents oxidizers, thermophiles, heterotrophs, methanogens, sulfate reducers

Halobacterium, Natronobacterium




Thermococcus pyrococcus archaeoglobus

Hot sulfur rich environments (hot springs, thermal vents)

Oxidize elemental sulfur, aerobic or anaerobic

Some lack cell wall, Thermoplasma e.g., Thermoplasma; sulfolobus, group includes Acidothermus

Thermus aquaticus pyrodictium occultum

Nonthermophilic Soil, marine One strain crenarchaeotes

Korarchaeota/ Xenarchaeota

Nanoarchaeota cultivated Hot springs None cultivated

Hot vents

Symbiont of Archaea

Coccoid; <400 nm Nanoarchaeum in diameter equitans there was considerable evidence that numbers of organisms appearing on soil isolation plates were several orders of magnitude lower than total cell numbers, determined by microscopy and other methods (Torsvik et al., 1996). This suggested that knowledge of natural communities might be limited. The next revolution in micro-bial taxonomy confirmed this suspicion. It arose through the development of techniques for amplification, using the polymerase chain reaction, of 16S rRNA genes directly from DNA extracted from soil, without any intervening cultivation steps (Pace et al., 1986). Analysis of these sequences led to several major discoveries:

1. the existence of high-level, novel taxonomic groups with very few or no cultivated representatives;

2. high abundance of these groups in many soil environments;

3. tremendous diversity within taxonomic groups established on the basis of cultivated organisms;

4. the existence of novel subgroups within these established groups.

The outcome of molecular studies is illustrated in Fig. 5.2, which shows 40 high-level groups within the bacterial domain. Only ca. 50% of these groups have representatives in laboratory culture and representation is often low. Although not without disadvantages, molecular approaches have now replaced cultivation-based techniques for characterizing soil microbial communities (see Chap. 4). Their value has increased as sequence databases have expanded, which has enabled organisms to be putatively identified and compared between environments. Their use has also introduced new questions and challenges and has influenced our view of the ecology and role of soil microorganisms. For example, organisms that were previously considered to be "typical" soil organisms (bacilli, pseudomonads, actinobacteria) are often found at relatively low abundance, while some of the novel, "yet-to-be-cultured" organisms are ubiquitous and present at high relative abundance (e.g., planctomycetes; Rappe and Giovannoni, 2003). Similarly, Archaea were considered to be extremophiles, adapted to conditions atypical of most soils (high temperature, high salt concentration, acid, or anaerobic). It is now known that members of the Crenarchaeota typically represent 1-2% of temperate soil prokaryote communities, but have not yet been cultivated (Buckley and Schmidt, 2003). The lack of availability of cultivated representatives of these organisms denies us knowledge of their physiological characteristics and potential, and we can therefore only speculate on their role in soil. This has two implications for future studies—the need to develop methods for cultivating these organisms and/or the need to develop additional molecular approaches, or at least cultivation-independent approaches, to establish their ecosystem function in situ.

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