Table 1. Characteristics of the five metatranscriptomes generated from the suboxic zone of Gotland Deep station 271 (2008). Samples for the free-flow and the PUMP-CTD approach were taken 15 August, UTC 11.09 and UTC 15.46, respectively.
| Metatranscriptome parameter |
Free-flow approach |
PUMP-CTD approach |
|||
|---|---|---|---|---|---|
| Unfixed reference | In situ fixed by stop solution | In situ fixed by Carnoy fixative | Reference collected by free-flow | Sample collected by PUMP-CTD | |
| Total no. of readsa | 18 157 | 29 666 | 32 914 | 72 512 | 37 013 |
| rRNA reads (%)b | 70 | 76 | 74 | 49 | 53 |
| Total mRNA readsc | 5447 | 7120 | 8558 | 36981 | 17396 |
| Total size of potential mRNA reads (Mbp)a | 1.6 | 2.2 | 2.5 | 11.7 | 5.40 |
| Average length of potential mRNA reads (bp)a | 279 | 304 | 307 | 317 | 314 |
| NH4+ transporter transcripts (%)d (no. of reads) | 0.83 (45) | 2.32 (165) | 2.15 (184) | 2.89 (1067) | 1.28 (222) |
| amoA transcripts (%)e (no. of reads) | 0.18 (10) | 0.46 (33) | 0.23 (20) | 1.00 (371) | 0.20 (36) |
| amoB transcripts (%)d (no. of reads) | 0.02 (1) | 0.07 (5) | 0.02 (2) | 0.06 (24) | 0.07 (12) |
| amoC transcripts (%)d (no. of reads) | 0.04 (2) | 0.34 (24) | 0.13 (11) | 0.44 (161) | 0.33 (57) |
| recA transcripts (%)f (no. of reads) | 0.02 (1) | 0.01 (1) | 0.07 (6) | 0.30 (126) | 1.96 (341) |
Based on GS-FLX titanium pyrosequencing.
Identification of sequences using the Ribosomal Database Project II (RDP-II) and the SILVA project small subunit (SSU) data set.
Sequences with no hits against the RDP-II and the SILVA project SSU and large subunit (LSU) data set.
Based on BLAST similarities (e-value ⩽0.01) against the genome of Candidatus Nitrosopumilus maritimus, analyzed using MG-RAST (Meyer et al., 2008) as described in Supplementary Figure 2, and calculated as the fraction of specific transcripts compared with total mRNA transcripts.
Based on hits against a self-generated thaumarchaeal amoA-consensus sequences database and calculated as the fraction of specific transcripts compared with total mRNA transcripts.
Based on hits against self-generated ‘Sulfurimonas sp. GD1'-based recA-consensus sequences database and calculated as the fraction of specific transcripts compared with total mRNA transcripts.