Table 1.
Assemblage information of four MTA MAGs and reference genomes
| Completeness | Contamination | Strain heterogeneity | Size (Mbp) | Contigs | GC (%) | Sequencing coverages | Sampling spot (and depth) | Note | |
|---|---|---|---|---|---|---|---|---|---|
| Metagenomic assembled “bins” | |||||||||
| MTA1 | 100 | 0 | 0 | 1.28 | 7 | 33.2 | 97 × | Mariana Trench 4000–10,500 m (predominantly 8000 m) | Predominant phylotype in hadal zone, alpha AOA |
| MTA4 | 24.84 | 0.49 | 0 | 0.42 | 159 | 34.6 | – | Mariana Trench 2000–10,500 m (predominantly 2000 m) | Member of the gamma AOA |
| MTA5 | 82.94 | 1.94 | 0 | 1.59 | 380 | 34.9 | 10 × | Mariana Trench 2000 m | amoA gene phylogenetically clustered with thermophilic Thaumarchaeota |
| MTA6 | 98.22 | 0 | 0 | 1.07 | 39 | 33.4 | 5 × | Mariana Trench 2000 m | Nearly identical to CN25 |
| Merged bin of DMGI | – | ~ 400 | – | – | – | 32.1 | 400 × | Mariana Trench 2000–10,500 m (predominantly 2000 m) | Highly merged bin of gamma AOA |
| Other representative SAGs (partial) | |||||||||
| PRT-SC01 | 32.69 | 1.94 | 33.33 | 0.61 | 140 | 33.1 | – | Puerto Rico Trench, Atlantic 8000 m | Predominant phylotype in hadal zone; alpha AOA |
| AAA282-K18 | 77.99 | 0 | 0 | 1.04 | 40 | 33.4 | – | Dark ocean depth > 200 m | Similar to MTA1 and PRT-SC01 alpha AOA |
| AB-629-I23 | 95.87 | 9.47 | 0 | 1.31 | 133 | 35.7 | – | Dark ocean depth > 200 m | Member of the gamma AOA |
| AAA007-O23 | 96.84 | 0 | 0 | 1.09 | 4 | 35.6 | – | Mesopelagic zone (200–1000 m) | Member of the gamma AOA |
| AAA799-D07 | 41.18 | 1.46 | 0 | 0.44 | – | Red sea brine pool 2000 m | Member of the gamma AOA | ||
| AAA799-E16 | 85.11 | 2.59 | 75.00 | 1.45 | – | Red sea brine pool 2000 m | Closed related to Nitrosopumilus maritimus SCM1 | ||
| AAA799-N04 | 84.47 | 0.24 | 0 | 1.33 | – | Red sea brine pool 2000 m | Closed related to Nitrosopumilus maritimus SCM1 | ||
| Pure culture strains | |||||||||
| SCM1 | 100 | 1.94 | 0 | 1.65 | 1 | 34.2 | – | Seawater aquarium | Type strain |
| Enrichment strains | |||||||||
| CN25 | 100 | 2.91 | 0 | 1.23 | 1 | 33.2 | – | Open ocean 25 m | Streamlined, similar size to MTA1 |
| SPOT01 | 100 | 0.97 | 0 | 1.36 | 1 | 31.4 | – | San Pedro Ocean Time-Series site 75 m | Streamlined, similar size to MTA1 |
| D3C | 99.51 | 0 | 0 | 1.71 | 1 | 33.8 | – | Northern Adriatic seawater off Piran depth 0.5 m | |
| NF5 | 100 | 0 | 0 | 1.8 | 1 | 33.4 | – | Northern Adriatic Seawater off Piran depth 0.5 m | |
| BG20 | 99.03 | 5.83 | 83.33 | 1.85 | 343 | 32.5 | – | Low-salinity sediments of the San Francisco Bay estuary | |
| SFB1 | 98.06 | 0 | 0 | 1.77 | 1 | 32.6 | – | Low-salinity sediments of the San Francisco Bay estuary | |
| AR2 | 97.09 | 0 | 0 | 1.69 | 1 | 33.6 | – | Sediments from Svalbard in the Arctic Circle | |
| AR1 | 94.66 | 0 | 0 | 1.64 | 1 | 34.2 | – | Sediments from Svalbard in the Arctic Circle | |
| BD31 | 92.39 | 1.94 | 0 | 1.57 | 171 | 33.8 | – | Coastal/estuarine sediments in San Francisco Bay 1 cm sediments | |
Qualities of these assemblies were examined by CheckM based on 145 single-copy markers for Thaumarchaeota. For SAGs and MAGs completeness > 90%, contamination < 5%, containing all the rRNA and tRNA genes are considered to be high quality [32]. Currently in deep-sea AOA only MTA1 meet these standards (several SAGs or MAGs lack rRNA or tRNA genes, although their completeness is high enough)