Abyssal marine sediments cover a large proportion of the ocean floor, but linkages between their microbial community structure and redox stratification have remained poorly constrained. This study compares the downcore gradients in microbial community composition to porewater oxygen and nitrate concentration profiles in an abyssal marine sediment column in the South Pacific Ocean. Archaeal 16S rRNA clone libraries showed a stratified archaeal community that changed from Marine Group I Archaea in the aerobic and nitrate-reducing upper sediment column towards deeply branching, uncultured crenarchaeotal and euryarchaeotal lineages in nitrate-depleted, anaerobic sediment horizons. Bacterial 16S rRNA clone libraries revealed a similar shift on the phylum and subphylum level within the bacteria, from a complex community of Alpha-, Gamma- and Deltaproteobacteria, Actinobacteria and Gemmatimonadetes in oxic surface sediments towards uncultured Chloroflexi and Planctomycetes in the anaerobic sediment column. The distinct stratification of largely uncultured bacterial and archaeal groups within the oxic and nitrate-reducing marine sediment column provides initial constraints for their microbial habitat preferences.

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 (...

Heterotrophic microbial communities in seawater and sediments metabolize much of the organic carbon produced in the ocean. Although carbon cycling and preservation depend critically on the capabilities of these microbial communities, their compositions and capabilities have seldom been examined simultaneously at the same site. To compare the abilities of seawater and sedimentary microbial communities to initiate organic matter degradation, we measured the extracellular enzymatic hydrolysis rates of 10 substrates (polysaccharides and algal extracts) in surface seawater and bottom water as well as in surface and anoxic sediments of an Arctic fjord. Patterns of enzyme activities differed between seawater and sediments, not just quantitatively, in accordance with higher cell numbers in sediments, but also in their more diversified enzyme spectrum. Sedimentary microbial communities hydrolyzed all of the fluorescently labeled polysaccharide and algal extracts, in most cases at higher rates in subsurface than surface sediments. In seawater, in contrast, only 5 of the 7 polysaccharides and 2 of the 3 algal extracts were hydrolyzed, and hydrolysis rates in surface and deepwater were virtually identical. To compare bacterial communities, 16S rRNA gene clone libraries were constructed from the same seawater and sediment samples; they diverged strongly in composition. Thus, the broader enzymatic capabilities of the sedimentary microbial communities may result from the compositional differences between seawater and sedimentary microbial communities, rather than from gene expression differences among compositionally similar communities. The greater number of phylum-and subphylum-level lineages and operational taxonomic units in sediments than in seawater samples may reflect the necessity of a wider range of enzymatic capabilities and strategies to access organic matter that has already been degraded during passage through the water column. When transformations of marine organic matter are considered, differences in community composition and their different abilities to access organic matter should be taken into account.The degradation of marine organic matter in the ocean is due in large part to the concerted effects of microbial communities in the water column and in the sediments, which collectively reprocess and ultimately remineralize most of the organic matter initially produced in the surface ocean (18, 39). These communities rely on extracellular enzymes to hydrolyze high-molecularweight organic matter to sizes sufficiently small for cellular uptake. They then respire a fraction of the organic carbon and excrete transformation products as dissolved organic carbon (DOC) that may in turn be used by other members of the microbial community. The composition and capabilities of heterotrophic microbial communities in seawater and sediments thus play a critical role in the global carbon cycle. Although numerous geochemical investigations of carbon cycling have followed the transformations of particulate organic matter as it s...

Examining the patterns of archaeal diversity in little-explored organic-lean marine subsurface sediments presents an opportunity to study the association of phylogenetic affiliation and habitat preference in uncultured marine Archaea. Here we have compiled and re-analyzed published archaeal 16S rRNA clone library datasets across a spectrum of sediment trophic states characterized by a wide range of terminal electron-accepting processes. Our results show that organic-lean marine sediments in deep marine basins and oligotrophic open ocean locations are inhabited by distinct lineages of archaea that are not found in the more frequently studied, organic-rich continental margin sediments. We hypothesize that different combinations of electron donor and acceptor concentrations along the organic-rich/organic-lean spectrum result in distinct archaeal communities, and propose an integrated classification of habitat characteristics and archaeal community structure.

Although oligotrophic, abyssal marine sediments cover most of the sea bottom, previous investigations of microbial diversity have primarily focused on organic-rich, anoxic sediments of continental margins. In contrast, abyssal open-ocean sediments are oxidized and contain limiting organic substrate concentrations. This study examines the archaeal diversity of oligotrophic, oxic and nitrate-reducing marine sediments and oxic bottom water in the South Pacific Gyre. 16S rDNA clone library analysis identified phylogenetically distinct lineages of the Marine Group I (MG-I) Crenarchaeota in oxidized sediment that are different from those in bottom water. Thus, the sediment habitat selects for different MG-I lineages, within short vertical distances of a few centimetres.