1. ¹Institute for Coastal Marine Environment (IAMC), CNR, Messina, Italy
2. ²Environmental Microbiology Laboratory, HZI-Helmholtz Centre for Infection Research, Braunschweig, Germany
3. ³School of Biological Sciences, University of Bangor, Wales, UK
4. ⁴Mediterranean Science Commission, CIESM, Monte-Carlo, Monaco

Correspondence: MM Yakimov, Institute for Coastal Marine Environment (IAMC), CNR, Spianata S. Raineri, 86, Messina 98122, Italy. E-mail: michail.yakimov@iamc.cnr.it

⁵These authors contributed equally to this work

Received 9 July 2007; Revised 11 September 2007; Accepted 11 September 2007; Published online 4 October 2007.

Abstract

Meso- and bathypelagic ecosystems represent the most common marine ecological niche on Earth and contain complex communities of microorganisms that are for the most part ecophysiologically poorly characterized. Gradients of physico-chemical factors (for example, depth-related gradients of light, temperature, salinity, nutrients and pressure) constitute major forces shaping ecosystems at activity 'hot spots' on the ocean floor, such as hydrothermal vents, cold seepages and mud volcanoes and hypersaline lakes, though the relationships between community composition, activities and environmental parameters remain largely elusive. We report here results of a detailed study of primary producing microbial communities in the deep Eastern Mediterranean Sea. The brine column of the deep anoxic hypersaline brine lake, L'Atalante, the overlying water column and the brine-seawater interface, were characterized physico- and geochemically, and microbiologically, in terms of their microbial community compositions, functional gene distributions and [¹⁴C]bicarbonate assimilation activities. The depth distribution of genes encoding the crenarchaeal ammonia monooxygenase subunit (amoA), and the bacterial ribulose-1,5-biphosphate carboxylase/oxygenase large subunit (RuBisCO), was found to coincide with two different types of chemoautotrophy. Meso- and bathypelagic microbial communities were enriched in ammonia-oxidizing Crenarchaeota, whereas the autotrophic community at the oxic/anoxic interface of L'Atalante lake was dominated by Epsilonproteobacteria and sulfur-oxidizing Gammaproteobacteria. These autotrophic microbes are thus the basis of the food webs populating these deep-sea ecosystems.