Marine Crenarchaeota are the most abundant single group of prokaryotes in the ocean, but their physiology and role in marine biogeochemical cycles are unknown. Recently, a member of this clade was isolated from a sea aquarium and shown to be capable of nitrification, tentatively suggesting that Crenarchaeota may play a role in the oceanic nitrogen cycle. We enriched a crenarchaeote from North Sea water and showed that its abundance, and not that of bacteria, correlates with ammonium oxidation to nitrite. A time series study in the North Sea revealed that the abundance of the gene encoding for the archaeal ammonia monooxygenase alfa subunit ( amoA ) is correlated with a decline in ammonium concentrations and with the abundance of Crenarchaeota. Remarkably, the archaeal amoA abundance was 1–2 orders of magnitude higher than those of bacterial nitrifiers, which are commonly thought to mediate the oxidation of ammonium to nitrite in marine environments. Analysis of Atlantic waters of the upper 1,000 m, where most of the ammonium regeneration and oxidation takes place, showed that crenarchaeotal amoA copy numbers are also 1–3 orders of magnitude higher than those of bacterial amoA . Our data thus suggest a major role for Archaea in oceanic nitrification.

Nitrospira are barely studied and mostly uncultured nitrite-oxidizing bacteria, which are, according to molecular data, among the most diverse and widespread nitrifiers in natural ecosystems and biological wastewater treatment. Here, environmental genomics was used to reconstruct the complete genome of "Candidatus Nitrospira defluvii" from an activated sludge enrichment culture. On the basis of this first-deciphered Nitrospira genome and of experimental data, we show that Ca. N. defluvii differs dramatically from other known nitrite oxidizers in the key enzyme nitrite oxidoreductase (NXR), in the composition of the respiratory chain, and in the pathway used for autotrophic carbon fixation, suggesting multiple independent evolution of chemolithoautotrophic nitrite oxidation. Adaptations of Ca. N. defluvii to substrate-limited conditions include an unusual periplasmic NXR, which is constitutively expressed, and pathways for the transport, oxidation, and assimilation of simple organic compounds that allow a mixotrophic lifestyle. The reverse tricarboxylic acid cycle as the pathway for CO2 fixation and the lack of most classical defense mechanisms against oxidative stress suggest that Nitrospira evolved from microaerophilic or even anaerobic ancestors. Unexpectedly, comparative genomic analyses indicate functionally significant lateral gene-transfer events between the genus Nitrospira and anaerobic ammonium-oxidizing planctomycetes, which share highly similar forms of NXR and other proteins reflecting that two key processes of the nitrogen cycle are evolutionarily connected.

Diatoms are one of the most important organisms contributing to aquatic primary productivity and their sterols are frequently used as markers for their presence and abundance. In this study, the sterol composition of .100 diatom cultures was analyzed and its distribution was compared to the diatom phylogeny to identify typical diatom biomarkers. Forty-four sterols were detected, 11 of them being commonly present as major sterols (contributing .10% to the total sterols). 24-Methylcholesta-5,24(28)-dien-3b-ol is the most common sterol in diatoms, being present in 67% of all cultures analyzed, followed by the D 5 sterols, cholest-5-en-3b-ol (cholesterol), 24-methylcholest-5-en-3b-ol, and 24-ethylcholest-5-en-3b-ol. 24-Methylcholesta-5,22E-dien-3b-ol, previously suggested to be specific for diatoms, was only the fifth most common sterol; this sterol was absent in some of the major diatom groups, and high relative concentrations seem to be restricted to pennate diatoms. No sterols are restricted to specific phylogenetic groups of diatoms. Cluster analyses, however, do reveal distinct sterol distributions: Thalassiosirales typically contain high relative abundances of 24-methylcholesta-5,24(28)-dien-3b-ol, high relative abundances of cholesta-5,22E-dien-3b-ol are typical for Cymatosirales, high relative abundances of 24-ethylcholesta-5,22E-dien-3b-ol are characteristic for related Amphora, Amphiprora, and Entomoneis species, and a combination of high relative abundances of 24-methylcholest-5-en-3b-ol, 24-methylcholesta-5,24(28)-dien3b-ol, and 24-ethylcholest-5-en-3b-ol is typical for Attheya species. High contributions of 24-methylcholesta-5,22E-dien-3b-ol (.50% of all sterols) seem to be restricted to pennate diatoms. None of the major sterols found in diatoms can be used as an unambiguous diatom biomarker because all of them have been reported as common sterols in other algal groups.

[1] Holocene sea surface temperatures (SST) of the Black Sea have been reconstructed using sedimentary C 37 unsaturated alkenones assumed to be derived from the coccolithophorid haptophyte Emiliania huxleyi, whose fossil coccoliths are an important constituent of the unit I sediments. However, alkenones can also be biosynthesized by haptophyte species that do not produce microscopic recognizable coccoliths. A speciesspecific identification of haptophytes is important in such U 37 K 0 -based past SST reconstructions since different species have different alkenone-SST calibrations. We showed that 18S rDNA of E. huxleyi made up only a very small percentage (less than 0.8%) of the total eukaryotic 18S rDNA within the up to 3600-year-old fossil record obtained from the depocenter (>2000 m) of the Black Sea. The predominant fossil 18S rDNA was derived from dinoflagellates (Gymnodinium spp.), which are predominant members of the summer phytoplankton bloom in the modern Black Sea. Using a polymerase chain reaction/denaturing gradient gel electrophoresis method selective for haptophytes, we recovered substantial numbers of a preserved 458-base-pair (bp)-long 18S rDNA fragment of E. huxleyi from the Holocene Black Sea sediments. Additional fossil haptophyte sequences were not detected, indicating that the E. huxleyi alkenone-SST calibration can be applied for at least the last $3600 years. The ancient E. huxleyi DNA was well protected against degradation since the DNA/alkenone ratio did not significantly decrease throughout the whole sediment core and 20% of $2700-year-old fossil E. huxleyi DNA was still up to 23,000 base pairs long. We showed that fossil DNA offers great potential to study the Holocene paleoecology and paleoenvironment of anoxic deep-sea settings in unprecedented detail.

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