Thaumarchaeota may be the most abundant cells in the deep ocean.

Another surprise of environmental sequencing has been the discovery that the immense volumes of ocean beneath the surface waters contain vast numbers of archaeons that have not yet been cultured in the lab. In the deep ocean, these organisms may be nearly as abundant as the combined number of all bacteria on and below the surface. Recently segregated as the Thaumarchaeota, these archaeons are chemoautotrophs, deriving energy from the oxidation of ammonia (Fig. 26.19). Thus, like the discovery of SAR11, the discovery of marine thaumarchaeotes makes it clear that before the still-emerging age of environmental genetics and genomics, we simply didn’t have a very good idea of which microorganisms lived where and did what in the oceans. Fortunately, that situation is changing rapidly.

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HOW DO WE KNOW?

FIG. 26.19

How abundant are archaeons in the oceans?

BACKGROUND Early exploration of microbial diversity in the oceans revealed that archaeons are tremendously abundant. Just how abundant are they, and what metabolisms do they employ to obtain energy and carbon?

METHOD Scientists sampled seawater throughout the depth of the ocean at a test site in the northern Pacific Ocean. To the samples, they added molecular tags bound to fluorescent molecules that are visible under the microscope. The tags were RNA sequences that bind to small-subunit ribosomal RNA genes known to be useful in identifying different types of bacteria and archaeons. In this way, separate fluorescent markers were attached to thaumarchaeote archaeons, euryarchaeote archaeons, and bacteria.

RESULTS By counting the cells marked by different fluorescent tags in seawater samples, the biologists showed that bacteria dominate microbial communities in near-surface seawater, but that thaumarchaeotes are as numerous as bacteria in deeper waters (Fig. 26.19a).

image
Surveys of cell abundance through a depth profile of the Pacific Ocean show that bacteria dominate cell numbers near the surface, but thaumarchaeotes make up about 40% of all cells in deeper waters.
FIG. 26.19

CONCLUSION Marine thaumarchaeota, unknown in 1990, are now known to be among the most abundant organisms in the oceans.

FOLLOW-UP WORK Archaea are among the most abundant of all cells in the world’s oceans. How do these cells live? Microbial samples from water known to be sites of nitrification (that is, the conversion of ammonia to nitrite or nitrate) contained an abundance of thaumarchaeote cells. The high numbers of thaumarchaeotes from these communities supported the hypothesis that they are nitrifiers—the higher the abundance of thaumarchaeote cells (Fig. 26.19b, dark blue line), the higher the amount of nitrite produced (Fig. 26.19b, light blue line). Thaumarchaeotes were grown in pure culture and shown to grow by consuming ammonia (Fig. 26.19b, red line). In other words, these organisms oxidize ammonia to provide the ATP and reducing power needed to incorporate CO2 into organic molecules. Therefore, they play a major role in the marine nitrogen cycle, thriving where sources of carbon and energy for other types of metabolism are scarce.

image
Growth of a marine thaumarchaeote in a medium containing ammonium chloride and bicarbonate as the only sources of energy and carbon, respectively. As cell number increased, ammonia (the ammonium ion NH4+) was increasingly converted to nitrite (NO2–), supporting the hypothesis that these cells are ammonia-oxidizing chemoautotrophs.

SOURCES Karner, M. B., E. F. DeLong, and D. M. Karl. 2001. “Archaeal Dominance in the Mesopelagic Zone of the Pacific Ocean.” Nature 409:507–510 (The figure has been modified to reflect more recent nomenclature.); Könneke, K., et al. 2005. “Isolation of an Autotrophic Ammonia-Oxidizing Marine Archaeon.” Nature 437:543–546.