Final Activity Report Summary - ILVIROMAB (Impact of Lysogenic Viruses on Marine Bacterioplankton) The open and deep ocean belongs to the largest and least studied ecosystems on this planet. Processes in the deep ocean are driven by microorganisms, such as viruses, bacteria and archaea. Because of its large size, the deep ocean is anticipated to play a critical role in climate change. Viruses are the most numerous microorganisms in the ocean and show the largest unknown sequence diversity. Nevertheless, almost no viruses infecting bacteria in the deep ocean have been isolated and no viruses infecting archaea. The latter is due to the fact that only a single archaeon has been isolated from the deep ocean water column, although archaea contribute significantly to the total cell numbers in this depth layers and are responsible for chemoautotrophic production. The Marie Curie intra-European fellowship ILVIROMAB took advantage of the fact that the 'Laboratoire d' Océanographie de Villefranche' (LOV) in France is situated at a place in the Mediterranean, which basically lacks a shelf. Therefore, deep marine water was close by and led to the establishment of a permanent sampling station, DYFAMED (now MOOSE), 30 nautical miles off Nice, which was visited once per month and sampled up to 2 000 m depth. At this station, the first study on the seasonal variability of viral parameters and the seasonal co-variation of viral and prokaryotic diversity was performed to gain deep insight into the dark ocean. Viral and prokaryotic diversity decreased with depth and, even though this decrease was stronger for viruses than for prokaryotes, viral abundance was still 10 times higher than prokaryotic abundance in the deep layer, i.e. from 1 000 to 2 000 m. Viral and prokaryotic abundance varied several folds in deep marine waters during the seasonal study, suggesting that the deep sea was more dynamic than previously thought. It could be shown that this variation was strongly linked to the development of water stratification, i.e. that the surface waters warmed up and built up a so-called mixed layer, which was to some extent physically separated from the deeper water. This water stratification allowed for the development of a spring phytoplankton bloom, which was possibly the reason for the seasonal signal we obtained. Nevertheless, evidence could be presented for episodic events leading to variation viruses and prokaryotes in the deep sea. Via identification of different groups of prokaryotes by a cell-specific approach (FISH), we found that bacteria typically dominated in all water layers; however, the crenarchaeota showed very high relative abundances in deep water and particularly in the twilight zone, i.e. in the mesopelagic, ranging from circa 200 to 800 m depth. This supported findings from other oceans. In addition, using 16S ribosomal Ribonucleic acid (rRNA) gene based fingerprints, it could be shown that surface water, the twilight zone and the dark ocean were characterised by specific bacterial and eury- and crenarchaeal communities. In addition, community composition changed with the water stratification even in the dark ocean, thus corroborating the idea that there was a considerable variability of diversity in the deep ocean. Nevertheless, specific bands were found for the surface and deep water when there was no stratification, showing that there were factors in addition to water stratification that altered the seasonal changes of microbial communities. Finally, a fingerprinting method for viruses was developed, which was based on the total, i.e. community, Deoxyribonucleic acid (DNA). The so far performed analysis indicated that there was a strong covariation between host and virus diversity. This fingerprint method could be used in the future to identify specific types of viruses and determine whether there were free in the environment or dormant in the genome of their hosts. Moreover, the bands in the fingerprints were sequenced, along with a similar approach for prokaryotes, and this would yield first information on the sequence diversity of viruses and dynamics of viruses and prokaryotes in the deep ocean.