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To extend comparative metagenomic analyses of the deep-sea, we produced metagenomic data by direct 454 pyrosequencing from bathypelagic plankton (1000 m depth) and bottom sediment of the Sea of Marmara, the gateway between the Eastern Mediterranean and the Black Seas. Data from small subunit ribosomal RNA (SSU rRNA) gene libraries and direct pyrosequencing of the same samples indicated that Gamma- and Alpha-proteobacteria, followed by Bacteroidetes, dominated the bacterial fraction in Marmara deep-sea plankton, whereas Planctomycetes, Delta- and Gamma-proteobacteria were the most abundant groups in high bacterial-diversity sediment. Group I Crenarchaeota/Thaumarchaeota dominated the archaeal plankton fraction, although group II and III Euryarchaeota were also present. Eukaryotes were highly diverse in SSU rRNA gene libraries, with group I (Duboscquellida) and II (Syndiniales) alveolates and Radiozoa dominating plankton, and Opisthokonta and Alveolates, sediment. However, eukaryotic sequences were scarce in pyrosequence data. Archaeal amo genes were abundant in plankton, suggesting that Marmara planktonic Thaumarchaeota are ammonia oxidizers. Genes involved in sulfate reduction, carbon monoxide oxidation, anammox and sulfatases were over-represented in sediment. Genome recruitment analyses showed that Alteromonas macleodii 'surface ecotype', Pelagibacter ubique and Nitrosopumilus maritimus were highly represented in 1000 m-deep plankton. A comparative analysis of Marmara metagenomes with ALOHA deep-sea and surface plankton, whale carcasses, Peru subsurface sediment and soil metagenomes clustered deep-sea Marmara plankton with deep-ALOHA plankton and whale carcasses, likely because of the suboxic conditions in the deep Marmara water column. The Marmara sediment clustered with the soil metagenome, highlighting the common ecological role of both types of microbial communities in the degradation of organic matter and the completion of biogeochemical cycles. [ABSTRACT FROM AUTHOR]

Lake Van harbors the largest known microbialites on Earth. The surface of these huge carbonate pinnacles is covered by coccoid cyanobacteria whereas their central axis is occupied by a channel through which neutral, relatively Ca-enriched, groundwater flows into highly alkaline (pH ~9.7) Ca-poor lake water. Previous microscopy observations showed the presence of aragonite globules composed by rounded nanostructures of uncertain origin that resemble similar bodies found in some meteorites. Here, we have carried out fine-scale mineralogical and microbial diversity analyses from surface and internal microbialite samples. Electron transmission microscopy revealed that the nanostructures correspond to rounded aragonite nanoprecipitates. A progressive mineralization of cells by the deposition of nanoprecipitates on their surface was observed from external towards internal microbialite areas. Molecular diversity studies based on 16S rDNA amplification revealed the presence of bacterial lineages affiliated to the Alpha-, Beta- and Gammaproteobacteria, the Cyanobacteria, the Cytophaga-Flexibacter-Bacteroides (CFB) group, the Actinobacteria and the Firmicutes. Cyanobacteria and CFB members were only detected in surface layers. The most abundant and diverse lineages were the Firmicutes (low GC Gram positives). To the exclusion of cyanobacteria, the closest cultivated members to the Lake Van phylotypes were most frequently alkaliphilic and/or heterotrophic bacteria able to degrade complex organics. These heterotrophic bacteria may play a crucial role in the formation of Lake Van microbialites by locally promoting carbonate precipitation. [ABSTRACT FROM AUTHOR]