Comparative metagenomics of bathypelagic plankton and bottom sediment from the Sea of Marmara - PubMed (original) (raw)

Comparative metagenomics of bathypelagic plankton and bottom sediment from the Sea of Marmara

Achim Quaiser et al. ISME J. 2011 Feb.

Abstract

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.

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Figures

Figure 1

Relative proportions of different archaeal, bacterial and eukaryotic taxa based on SSU rDNA sequences detected in gene libraries and metagenomic data in deep-sea plankton and bottom sediment of the Marmara Sea. Pyrosequence indicates SSU rDNA percentages in metagenomic pyrosequence data as classified by MEGAN; no eukaryotic SSU rDNA sequences were identified in them.

Figure 2

Relative proportions of different archaeal, bacterial and eukaryotic taxa identified in different metagenomic data sets based on their content of SSU rDNA sequences. The taxonomic assignment was carried out using MEGAN. The total number of SSU rDNA matches in each metagenome is indicated in parentheses.

Figure 3

Best reciprocal TBLASTN high scoring pairs (HSPs) between selected metagenomes.

Figure 4

MUMMER-based identification of shared sequences in metagenomes. (a) Number of shared sequences in Marmara and ALOHA deep-sea plankton and whale carcass metagenomes. (b) Cluster analysis of selected metagenomes based on shared sequences.

Figure 5

Cluster analysis of several metagenomes based on matches to different COG and KEGG categories normalized to the respective number of sequence fragments. For COGs, only functional categories having at least 10 matches in all 7 metagenomes were retained (831 COGs), from which the most frequent 74 are shown (see also Supplementary Figure S19). For KEGGs, only functional categories having at least 1 match in all 7 metagenomes or at least 20 matches in 1 metagenome were retained (148 KEGGs; see also Supplementary Figure S20). The names of particular KEGG categories showing strong differences across metagenomes are shown at the bottom.

Figure 6

Comparison of the relative proportion of key metabolic enzymes in Marmara deep-sea plankton and sediment with other metagenomes.

Figure 7

Percentage of coverage of the most abundantly recruited genomes in Marmara deep-sea plankton (Ma101) and sediment (Ma29) as compared with those most represented in other selected metagenomes. The numbers in parentheses indicate the numbers of matching reads; aa, based on amino acids (promer); nt based on nucleotides (nucmer).

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Comparative metagenomics of bathypelagic plankton and bottom sediment from the Sea of Marmara - PubMed (original) (raw)