Nealson and D A Stahl Crenarchaeota in Lake Michigan sediment

Introduction. Marine and freshwater sediments are major sinks of both natural and anthropogenic materials (5). Although microbial activity is recognized to control the transformation of these materials and influence processes in the overlaying water, relatively little is known about the contributing populations. This is mostly a consequence of the well-recognized limitations of pure-culture methodology. A more complete understanding of sediment processes and anthropogenic influence will require methods independent of prior growth in culture. For example, the direct recovery of rRNA sequences from the environment allows uncultured forms to be cataloged within a phylogenetic framework (28). With increasing use of this and other direct methods, the pure-culture collection is now recognized to comprise a very small fraction of the natural diversity in most environments (4, 16, 27). Sediments are no exception (9, 10, 20, 23). We are employing a combination of molecular, microbiolog-ical, and chemical techniques to evaluate the contribution of different microbial groups to sediment processes at a site in Lake Michigan near Fox Point, Wis. For example, group-specific hybridization probes for the three domains (archaea, bacteria , and eucarya) are being used to measure temporal and vertical changes in abundance of the corresponding populations (18, 20). We anticipated that most of the archaea in this environment would be anaerobic methanogens. However, there were characteristically two major peaks of archaeal 16S rRNA hybrid-ization: one near the sediment surface in the oxic zone and one in the zone immediately below it. This unexpected distribution, and earlier studies showing that methanogen-specific probe hybridization could account for only a fraction of archaeal probe hybridization (1a), suggested the presence of novel ar-chaea. We evaluated this hypothesis, using selective PCR amplification of archaeal 16S rDNA. We report here that four of the archaeal sequences recovered are closely related to the recently discovered pelagic marine crenarchaeota (7, 13, 14) but that these crenarchaeota accounted for only ϳ10% of the