Open Access Research article

Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities

Thorsten Stoeck1, Anke Behnke1, Richard Christen2, Linda Amaral-Zettler3, Maria J Rodriguez-Mora4, Andrei Chistoserdov4, William Orsi5 and Virginia P Edgcomb6*

Author Affiliations

1 Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany

2 Université de Nice et CNRS UMR 6543, Laboratoire de Biologie Virtuelle, Centre de Biochimie, Parc Valose. F 06108 Nice, France

3 Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, USA

4 University of Louisiana at Lafayette, Lafayette, LA, USA

5 Northeastern University, Boston, MA, USA

6 Woods Hole Oceanographic Institution, Woods Hole, MA, USA

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BMC Biology 2009, 7:72  doi:10.1186/1741-7007-7-72

Published: 3 November 2009

Additional files

Additional file 1:

Scanning electron micrograph of an unidentified ciliate isolated from anoxic, sulfidic waters of the Cariaco Basin. Figure S1. The ciliate in the picture, isolated from anoxic waters of the Cariaco basin, is covered with bacterial ectosymbionts. Protists with bacterial ectosymbionts are frequently recovered from sulfidic waters of both, the Cariaco Basin as well as the Framvaren Fjord. It is not unlikely that these as yet unidentified bacteria may play a role as an adaptive mechanisms for some protists to thrive in anoxic sulfidic environments. This picture is courtesy of Orsi W., Edgcomb V., Hohemann T. and Epstein S.S. as part of a study on bacterial ectosymbionts on protists from the Cariaco Basin (Orsi et al., in preparation for publication).

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Additional file 2:

Taxonomy and proportion of abundant metazoan operational taxonomic units. Table S1. Taxonomy and proportion of abundant metazoan operational taxonomic units (OTUs) accounting for at least 1% of all metazoan OTUs of a specific amplicon library from four anoxic water samples from the Caribbean Cariaco deep-sea basin (CAR1-4) and four anoxic water samples of the Norwegian Framvaren Fjord (FV1-4). OTUs were established based on identical best GenBank hit. For each OTU the best GenBank match is given (accession no., organism description, and taxonomy), as well as the number of total and unique tags. Unique tags are tags clustered at 0 differences.

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Additional file 3:

Numbers of unique metazoan operational taxonomic units. Figure S2. Number of unique metazoan operational taxonomic units (OTUs) obtained from four samples of the Caribbean Cariaco Basin (CAR1-4, Figure S2-A) and four samples of the Norwegian Framvaren Fjord (FV1-4, Figure S2-B) at different levels of nucleotide differences. Tags were clustered at nt differences zero to five differences as described in pipeline 2 of the sequence data processing paragraph in the methods section. A difference can be an insertion or a mutation necessary to align the two sequences. At k differences, two tags having k or fewer differences are placed in the same cluster; if they have more than k differences, they are in two different clusters.

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Additional file 4:

Relative contribution of metazoan operational taxonomic units to total eukaryote operational taxonomic units. Table S2. Relative contribution of metazoan operational taxonomic units (OTUs) to total eukaryote OTUs when clustered at 5 nt differences (OTUs5 nt) in the Franvaren Fjord (FV1-FV4) and the Cariaco Basin (CAR1-CAR4) amplicon libraries.

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Additional file 5:

Relative taxonomic distribution of unique protistan and fungal V9 tags. Table S3. Accompanying data to Figure 4. Relative taxonomic distribution of unique protistan and fungal V9 tags generated from four anoxic water samples of the Caribbean Cariaco deep-sea basin (CAR1-4) and from four anoxic water samples of the Norwegian Framvaren Fjord (FV1-4). Phylum-based assignment; phyla that were represented by a proportion ≥1% of all unique tags in at least one of the eight libraries used for 454 sequencing is shown. The category "others" denotes tags that could not be assigned to a taxonomic entity based on an 80% BLASTn similarity threshold and tags which fell into other phyla or taxon groups but were represented by <1% of the unique tags in all of the eight PCR amplicon libraries used for 454 sequencing. Table S4. Accompanying data to Figure 5. Relative taxonomic distribution of unique protistan and fungal V9 tags generated from four anoxic water samples of the Caribbean Cariaco deep-sea basin (CAR1-4) and from four anoxic water samples of the Norwegian Framvaren Fjord (FV1-4) within the Dinozoa. Table S5. Accompanying data to Figure 6. Relative taxonomic distribution of unique protistan and fungal V9 tags generated from four anoxic water samples of the Caribbean Cariaco deep-sea basin (CAR1-4) and from four anoxic water samples of the Norwegian Framvaren Fjord (FV1-4) within the Ciliophora. Table S6. Accompanying data to Figure 7. Relative taxonomic distribution of unique protistan and fungal V9 tags generated from four anoxic water samples of the Caribbean Cariaco deep-sea basin (CAR1-4) and from four anoxic water samples of the Norwegian Framvaren Fjord (FV1-4) within the Bacillariophyta. Table S7. Accompanying data to Figure 8. Relative taxonomic distribution of unique protistan and fungal V9 tags generated from four anoxic water samples of the Caribbean Cariaco deep-sea basin (CAR1-4) and from four anoxic water samples of the Norwegian Framvaren Fjord (FV1-4) within the Chlorophyta. Table S8. Accompanying data to Figure 9. Relative taxonomic distribution of unique protistan and fungal V9 tags generated from four anoxic water samples of the Caribbean Cariaco deep-sea basin (CAR1-4) and from four anoxic water samples of the Norwegian Framvaren Fjord (FV1-4) within the Heterokontophyta.

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