CHAPTER 19

Archaeal Diversity

19.1 Archaeal Traits and Phylogeny

19.2 Crenarchaeota across the Temperature Range

19.3 Thaumarchaeota: Symbionts and Ammonia Oxidizers

19.4 Methanogenic Euryarchaeota

19.5 Halophilic Euryarchaeota

19.6 Extremophilic Euryarchaeota and Deeply Branching Divisions

Archaea are found in all soil and water habitats, in symbiosis with animals and plants, and in extreme environments that exclude bacteria and eukaryotes. Archaea include hyperthermophiles inhabiting Earth’s hottest habitats, as well as Arctic and Antarctic psychrophiles. Methanogens inhabit the digestive tracts of humans and other animals, as well as anaerobic soil and water, with consequences for global climate. Many archaea collaborate with bacteria in multispecies biofilms. No archaeon is yet known to cause disease, but archaea do interact with our innate immune system.

In 1977, Carl Woese revealed the existence of a third kind of life—the Archaea, a domain of life-forms very different from the plants, animals, and bacteria that had long been known. Today, the Archaea continue to yield surprises. An example is the candidate species Altiarchaeum hamiconexum, first known as the SM1 euryarchaeon discovered in 2004 by Rudolph Huber and his students at the University of Regensburg, Germany. The marsh-dwelling microbe is an archaeon related to methanogens, and it appears to fix CO2, but its precise metabolism remains unknown. Christine Moissl-Eichinger (see the Current Research Highlight) showed how this organism forms netlike biofilms by use of grappling-hook appendages, called hami (singular, hamus) (Fig. 19.1). Each grappling hook contains paired barbs along an extended protein filament many times the length of the cell. The filament ends with a triple fishhook that enables filaments to clasp each other. No other kind of cell is known to make this type of appendage.

FIGURE 19.1 Grappling hooks (hami) of Altiarchaeum species. A. Hooked appendages extending from a cell (TEM). B. Cryo-EM tomography model of a grappling hook (hamus).

Archaea are known for extremophiles, such as hyperthermophiles growing above 100°C and hyperacidophiles at below pH 1. Extremophiles are of interest to biotechnology because their enzymes may catalyze reactions under industrially useful conditions, such as high salt or acidity. But we also find archaea throughout mesophilic soil and water, and within the digestive tracts of humans and other animals. Moissl-Eichinger even discovered archaea on human skin, comprising more than 4% of the skin’s prokaryotic microbiome. She argues that archaea exist everywhere, in every livable habitat; we just need the right methods to find them.

How do archaea in “moderate” habitats interact with bacteria and eukaryotes? Many archaea join bacteria within biofilms in soil and on marine particles. For example, Altiarchaeum envelops sulfide-oxidizing bacteria in its grappling appendages to form thick biofilms like pearls on a string. Other archaea cooperate with eukaryotes, for example, by colonizing the surface of plant roots. Even in these shared habitats, archaea show unique traits, such as energy-yielding methanogenesis and cyclic diether membranes. Perhaps the most compelling unique feature of archaea, from the human point of view, is that no archaea are known to cause disease. Recent reports find gut methanogens associated with the inflammatory response, but no causal relationship has yet been demonstrated.

In Chapter 19 we explore the diversity of archaea. We emphasize the unique structures and metabolic pathways of archaeal cells. While surveying their major taxonomic categories, we introduce research techniques used to study organisms in extreme environments and those with unique forms of metabolism, such as methanogenesis.