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Microbial Domains in the Ocean: a Lesson from the Archaea

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Microbial Domains in the Ocean: a Lesson from the Archaea or collective redistirbution of any portion of this article by photocopy machine, reposting, or other means is permitted only with the approval of The approval Oceanography portionthe ofwith any permitted articleonly photocopy by is of machine, reposting, this means or collective or other redistirbution This article has This been published in A S ea of M I C R obe S > SeCTIon V. EX amPleS of DIveRSITY > CHAPTER 10. MICRobIal CommUNITIES Oceanography > A . WaTER ColUmn Microbial Domains in the Ocean: journal of The 20, NumberOceanography 2, a quarterly , Volume A Lesson from the Archaea BY EDWARD F. DELonG NEW VIEWS of Sea MICRobeS (Bacteria, Archaea, and Eukarya), it is “fishing expeditions” pioneered by Norm Microbial life thrives in virtually every only recently that a clear picture of “who Pace and Stephen Giovannoni, and later habitat imaginable in the ocean, from the lives where” in the ocean has emerged. others, in the early 1990s, proved to be scalding temperatures found at hydro- From the standpoint of oceanogra- reasonably productive enterprises. A S ociety. ociety. thermal vents, to frigid environments in phy, why should we care about microbial strong motivation for these microbial C and under polar sea ice, to high-pressure The 2007 by opyright Oceanography habitats in the ocean’s deepest trenches. Our understanding of microbial life in many of these ocean habitats, especially in plankton, has advanced remarkably Our understanding of microbial life in over the past 30 years or so. The recogni- many of these ocean habitats, especially S tion of the ubiquity and distribution of in plankton, has advanced remarkably rights All reserved.ociety. S photoautotrophic cyanobacteria such ociety. as Synechococcus and Prochlorococcus over the past 30 years or so. S end all correspondence to: [email protected] or Th e [email protected] Oceanography to: correspondence all end (Johnson and Sieburth, 1979; Waterbury et al., 1979; Chisholm et al., 1988), the P isolation of pressure-requiring piezo- article use for research. and this copy in teaching to granted is ermission philic bacteria (Yayanos et al., 1979), the diversity or microbial taxonomic dis- surveys was the general recognition that discovery of Pelagibacter (Giovannoni tributions and abundance? As a fledg- microbial activities drive most of the et al., 1990), and recognition of the high ling Assistant Scientist at the Woods major biogeochemical cycles in the sea. abundance of marine phage (Bergh et Hole Oceanographic Institution in Furthermore, it was suspected that many al., 1989) represent just a few recent the late 1980s, I remember my chagrin dominant planktonic microbial groups milestones in microbial oceanography. while pondering critical reviewer com- might be undetected because of their Even at a level as fundamental as the dis- ments on my (failed) grant proposals recalcitrance to cultivation. Given the S tribution of life’s three major domains that aimed to survey marine microbial “great plate count anomaly” (e.g., the ociety, diversity, which read something like this: observation that cultivable planktonic P O Box 1931, EDWARD F. DELonG (delong@ “DeLong is out on a fishing expedition, microbes accounted for only a small mit.edu) is Professor, Department of without any hypothesis.” At the time, percentage of total direct epifluores- R ockville, MD 20849-1931, R Biological Engineering and Department some of us wondered: If you don’t really cence microscopic counts [Staley and reproduction, systemmatic epublication, of Civil and Environmental Engineering, know what lives in the ocean, might Konopka, 1985]), it seemed quite pos- Massachusetts Institute of Technology, not a little fishing be a good idea? As it sible that dominant planktonic micro- Cambridge, MA, USA. turned out, the early oceanic microbial bial groups, some responsible for critical US A. 124 Oceanography Vol. 20, No. 2 biogeochemical cycling processes, likely of marine microbial life and led to the to most other life forms. The existence remained unknown. This presumption discovery of a new microbial taxo- of novel archaeal types was first hinted turned out to be more or less correct. nomic group in the sea, the planktonic at during cultivation-independent A fundamental advance that acceler- Crenarchaea. The pattern of initial ribosomal RNA surveys in open-ocean ated relatively unbiased microbial cen- discovery using these techniques, and and coastal marine waters. Initial work sus taking was the invention by Norm subsequent in-depth biological and eco- used the polymerase chain reaction Pace and collaborators of cultivation- logical characterization, is now a recur- (PCR) to amplify ribosomal RNA genes independent, molecular-phylogenetic survey approaches (Olsen et al., 1986). This strategy uses common molecular sequences found in every cell (e.g., ribo- ...it is only recently that a clear picture of somal RNA sequence) that can serve “who lives where” in the ocean has emerged. as a sort barcode to identify and track microbes by “reading” DNA sequences extracted directly from the environ- ment, without the need for cultivation. ring theme in marine microbial ecology. from mixed microbial populations. In Such cultivation-independent surveys While this story represents only one 1992, Jed Fuhrman of the University taught us that large amounts of micro- example, it illustrates how characteriza- of Southern California first reported bial diversity found in natural habitats tion of dominant microbial inhabitants the existence of a new type of archaeal had totally slipped beneath the radar of in the sea can lead to new insights into ribosomal RNA sequence from deep- cultivation-based approaches. Indeed, global biogeochemical processes. As water planktonic microbes in the Pacific some of the most abundant microbial well, the important interplay and syn- Ocean (Fuhrman et al., 1992). At about groups on our planet have been discov- ergy between cultivation-dependent and the same time, I independently discov- ered using such molecular-based surveys, cultivation-independent approaches for ered and reported on the distribution and had not been evident from cul- characterizing marine microbes in the and abundance of two different coastal ture-based studies. Characterizing these wild is quite evident (see also the article archaeal groups, one related to the deep- microorganisms is critical for gaining a by Giovannoni et al., this issue). water archaea (planktonic Crenarchaea) deeper and truer understanding of native and another, new group (planktonic microbial inhabitants and their funda- OCeanIC ARCHaea? Euryarchaea) that were phylogenetic mental environmental activities (see The Archaea are a curious phyloge- neighbors to halophiles and methano- below). Together, both cultivation-based netic domain (formerly kingdom) gens (DeLong, 1992). I was also able to and cultivation-independent approaches, comprised of an odd assortment of demonstrate quantitatively that marine which now extend to environmental cultured microbes that fall into three archaea contribute significantly to genomic sequencing surveys, are yielding major groupings: extreme halophiles, marine microbial plankton biomass. significant contributions to our under- methanogens, and extreme thermo- The surprise then was that any standing of microbial taxa and activities philes and thermoacidophiles (Woese, archaea could be found in cold, aero- in the deep blue sea. 1987). Why such an odd assortment of bic habitats of coastal and open-ocean The impact of cultivation- salt-loving, or anaerobic, or heat-lov- waters—and, to top it off, they were independent surveys of microbes in the ing microbes should form such a coher- abundant. No cultivated, character- environment has been well reviewed ent phylogenetic grouping is still not ized archaea were known to grow at the (Rappé and Giovannoni, 2003). The that well understood. The dogma until combined salinity, temperature, and following story is one tale of how this 1992 was that archaea inhabit mainly oxygen concentration found in tem- approach altered our understanding “extreme” environments, inhospitable perate oceanic waters, shallow or deep. Oceanography June 2007 125 of the total picoplankton cell counts from water depths of 80–3000 m. At the Hawaii Ocean Time-series (HOT) sta- tion ALOHA, Dave Karl and collabora- tors showed that Crenarchaea comprised as much as 30% of the total microbial counts in deep waters below the euphotic zone (Karner et al., 2001). In aggregate, these and other data suggest that pelagic Crenarchaea comprise a significant pro- portion of overall planktonic microbial biomass throughout the world’s ocean. BIoloGY and EColoGY of PlanKTonIC MARIne CRenaRCHaea Creative application of biochemical, geochemical, and genomic techniques have provided considerable data on the planktonic Crenarchaea. These stud- Figure 1. Epifluorescence micrograph ofCenarchaeum symbiosum, a symbiotic marine crenarchaeon (green cells) closely related to planktonic archaea. The green fluorescence is derived from fluorescein- ies, combined with isolation in pure labeled, rRNA-targeted probes used for in situ nucleic acid hybridization to identify archaeal cells. culture of a marine crenarchaeon (see below), now provide some specific clues regarding the biogeochemical and eco- logical importance of this abundant Following on the heels of these first oce- planktonic Crenarchaea were found to marine microbial group. anic sightings, archaeal groups began contribute as much as 20% to the total Lipid analyses of cold
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