A hypersaline, endoevaporitic microbial community in Eilat, Israel, was studied by microscopy and by PCR amplification of genes for 16S rRNA from different layers. In terms of biomass, the oxygenic layers of the community were dominated by Cyanobacteria of the Halothece, Spirulina, and Phormidium types, but cell counts (based on 4,6-diamidino-2-phenylindole staining) and molecular surveys (clone libraries of PCR-amplified genes for 16S rRNA) showed that oxygenic phototrophs were outnumbered by the other constituents of the community, including chemotrophs and anoxygenic phototrophs. Bacterial clone libraries were dominated by phylotypes affiliated with the Bacteroidetes group and both photo-and chemotrophic groups of ␣-proteobacteria. Green filaments related to the Chloroflexi were less abundant than reported from hypersaline microbial mats growing at lower salinities and were only detected in the deepest part of the anoxygenic phototrophic zone. Also detected were nonphototrophic ␥-and ␦-proteobacteria, Planctomycetes, the TM6 group, Firmicutes, and Spirochetes. Several of the phylotypes showed a distinct vertical distribution in the crust, suggesting specific adaptations to the presence or absence of oxygen and light. Archaea were less abundant than Bacteria, their diversity was lower, and the community was less stratified. Detected archaeal groups included organisms affiliated with the Methanosarcinales, the Halobacteriales, and uncultured groups of Euryarchaeota.

A diffusely venting chimney spire from the East Pacific Rise (9 degrees N) was analysed by petrographic thin sectioning and 16S rRNA gene cloning and sequencing in parallel, to correlate microbial community composition with mineralogy and inferred in situ conditions within the chimney mineral matrix. Both approaches indicated a zonation of the chimney spire into distinct microhabitats for different bacteria and archaea. The thermal gradient inferred from the mineral composition and porosity of the chimney was consistent with the distribution of bacterial and archaeal phylotypes in the chimney matrix. A novel phylogenetic lineage of euryarchaeota was found that co-occurred with clones related to cultured hyperthermophilic archaea. A few phylotypes related to mesophilic bacteria were found in the hot core of the chimney, indicating that seawater influx during retrieval and cooling of these highly porous structures can entrain microorganisms into chimney layers that are not their native habitat.

In Arctic marine bacterial communities, members of the phylum Verrucomicrobia are consistently detected, although not typically abundant, in 16S rRNA gene clone libraries and pyrotag surveys of the marine water column and in sediments. In an Arctic fjord (Smeerenburgfjord) of Svalbard, members of the Verrucomicrobia, together with Flavobacteria and smaller proportions of Alpha-and Gammaproteobacteria, constituted the most frequently detected bacterioplankton community members in 16S rRNA gene-based clone library analyses of the water column. Parallel measurements in the water column of the activities of six endo-acting polysaccharide hydrolases showed that chondroitin sulfate, laminarin, and xylan hydrolysis accounted for most of the activity. Several Verrucomicrobia water column phylotypes were affiliated with previously sequenced, glycoside hydrolaserich genomes of individual Verrucomicrobia cells that bound fluorescently labeled laminarin and xylan and therefore constituted candidates for laminarin and xylan hydrolysis. In sediments, the bacterial community was dominated by different lineages of Verrucomicrobia, Bacteroidetes, and Proteobacteria but also included members of multiple phylum-level lineages not observed in the water column. This community hydrolyzed laminarin, xylan, chondroitin sulfate, and three additional polysaccharide substrates at high rates. Comparisons with data from the same fjord in the previous summer showed that the bacterial community in Smeerenburgfjord changed in composition, most conspicuously in the changing detection frequency of Verrucomicrobia in the water column. Nonetheless, in both years the community hydrolyzed the same polysaccharide substrates.A major fraction of heterotrophic activity in the ocean is carried out by marine microbial communities (1). These communities use substrates such as high-molecular-weight carbohydrates (polysaccharides), which constitute a large percentage of phytoplankton biomass, particulate organic matter, and dissolved organic matter (DOM) in the ocean (2-5) and therefore fuel a considerable proportion of heterotrophic activity. To initiate the degradation of complex organic matter, bacteria must initially hydrolyze high-molecular-weight substrates by using extracellular enzymes in order to yield substrates sufficiently small to be taken into the microbial cell for further processing (6).The substrate spectrum and the rates of polysaccharide-hydrolyzing extracellular enzymes produced by microbial communities vary by location and depth in the ocean (7-9, 83) and can change through processes such as aggregate formation (10). Bacterial groups differ in their enzymatic spectra, as shown through field studies (11, 12), as well as genomic and microbiological investigation (13-16). Microbial communities involved in polysaccharide degradation in the water column include heterotrophic Gammaproteobacteria, fast-growing opportunists that can adapt quickly to changing substrate availability (17) and that include isolates that grow on rich standard media (...

and IPOD Expedition 301 ScientistsPerfluorocarbon tracers (PFTs) are used during cruises of the Ocean Drilling Program (ODP) and Integrated Ocean Program (IODP) to measure sample contamination with drilling fluid. Drilling fluid is supplied with a constant PFT concentration that can then be detected and quantified in sediment and basalt core samples. During IODP Expedition 301, we used washing (2×) and flaming to effectively remove PFT from the exterior of basalt rocks. Near-complete removal from the exterior allowed us to demonstrate that the interior of basalts was only minutely, if at all, contaminated with drilling fluid. We examined horizontal and vertical trends in sediment core contamination. Contamination decreased greatly between the core exterior to halfway along the core radius, and slightly from halfway to the center of cores, and was generally very low in halfway and center portions. Clay cores were, on average, more contaminated than cores with fine sand. Contamination was typically highest in the two uppermost sections (sections 1 and 2) and lower below (sections 3-5). There was no relationship between depth of core origin and contamination. To determine mechanisms of contamination in halfway and interior parts of cores, we estimated the diffusive flux of PFT from the core liner towards the core center. Based on conservative estimates, we concluded that diffusion did not account for any of the PFT measured in halfway and interior parts of cores in this study. Any measurable PFT concentrations in halfway and center parts of cores were caused by advection.

In the ongoing debates about eukaryogenesis—the series of evolutionary events leading to the emergence of the eukaryotic cell from prokaryotic ancestors—members of the Asgard archaea play a key part as the closest archaeal relatives of eukaryotes1. However, the nature and phylogenetic identity of the last common ancestor of Asgard archaea and eukaryotes remain unresolved2–4. Here we analyse distinct phylogenetic marker datasets of an expanded genomic sampling of Asgard archaea and evaluate competing evolutionary scenarios using state-of-the-art phylogenomic approaches. We find that eukaryotes are placed, with high confidence, as a well-nested clade within Asgard archaea and as a sister lineage to Hodarchaeales, a newly proposed order within Heimdallarchaeia. Using sophisticated gene tree and species tree reconciliation approaches, we show that analogous to the evolution of eukaryotic genomes, genome evolution in Asgard archaea involved significantly more gene duplication and fewer gene loss events compared with other archaea. Finally, we infer that the last common ancestor of Asgard archaea was probably a thermophilic chemolithotroph and that the lineage from which eukaryotes evolved adapted to mesophilic conditions and acquired the genetic potential to support a heterotrophic lifestyle. Our work provides key insights into the prokaryote-to-eukaryote transition and a platform for better understanding the emergence of cellular complexity in eukaryotic cells.