Table 1.
Predominant MAGsa identified in sulfidic hydrothermal vent streamers (Stevenson Island Deep Hole, Yellowstone Lake, WY) sorted as a function of predicted optimal growth temperature.
| Genome populationa | Phylumb | TOPTc | Len.d | Comp.e | Red.f | G + C %g | Coverageh | Cont.i | N50 (kb)j | Viral cont.k | SNV Dens.l | Trans.m |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Pyrobaculum DHV | A: Crenarchaeota | 91.6 | 1.18 | 75.9 | 3.7 | 56.7 (4.2) | 20.3 (3.2) | 197 | 6.84 | 13 | 40.7 | 1 |
| Thermogladius DHV | A: Crenarchaeota | 85.3 | 1.15 | 95.1 | 3.1 | 52.1 (2.4) | 56.3 (12.6) | 64 | 31.07 | 0 | 71.8 | 0 |
| Acidilobus DHV | A: Crenarchaeota | 82.7 | 1.26 | 95.1 | 3.1 | 59.3 (2.5) | 21.1 (5.9) | 39 | 56.84 | 0 | 9.6 | 2 |
| Thermoproteus DHV | A: Crenarchaeota | 81.9 | 1.44 | 93.8 | 3.7 | 61.2 (3) | 104.1 (24.1) | 87 | 30.03 | 1 | 30.5 | 1 |
| Thermodesulfobacterium DHV | B: Thermodesulfobacteria | 78.8 | 1.73 | 89.9 | 12.9 | 42.6 (2.4) | 47.1 (16.4) | 158 | 18.31 | 1 | 44.1 | 2 |
| Thermofilum DHV | A: Crenarchaeota | 78.7 | 2.16 | 90.7 | 2.5 | 45.1 (4.5) | 41.3 (11.0) | 225 | 16.54 | 37 | 36.3 | 4 |
| Thermocrinis DHV | B: Aquificae | 78.0 | 1.23 | 87.8 | 0.0 | 42.8 (2.9) | 118.4 (353.4) | 177 | 8.57 | 1 | 58.6 | 5 |
| Sulfolobus DHV | A: Crenarchaeota | 76.6 | 1.21 | 99.4 | 2.5 | 52.1 (4.6) | 86.5 (18.0) | 81 | 27.15 | 2 | 71.9 | 1 |
| Desulfurococcaceae DHV | A: Crenarchaeota | 71.8 | 1.46 | 97.5 | 3.1 | 36.4 (1.2) | 16.0 (5.4) | 80 | 30.03 | 0 | 7.8 | 3 |
| Thermoprotei DHV | A: Crenarchaeota | 70.9 | 1.22 | 87.7 | 2.5 | 43.5 (2.6) | 12.3 (4.7) | 138 | 10.97 | 1 | 3.4 | 7 |
| — | ||||||||||||
| Thermoplasmata DHV | A: Thermoplasmata | 67.8 | 1.30 | 97.5 | 6.2 | 35.6 (2.4) | 39.1 (11.3) | 80 | 26.53 | 0 | 17.1 | 4 |
| Archaea DHV | A: Thaum./Aig. | 67.3 | 1.28 | 87.7 | 7.4 | 36.1 (1.3) | 7.4 (3.2) | 176 | 8.56 | 0 | 0.5 | 2 |
| Caldisericum DHV | B: Caldiserica | 66.1 | 1.62 | 97.1 | 0.7 | 36.8 (2) | 42.8 (11.1) | 161 | 19.60 | 4 | 30.8 | 3 |
| Thaumarchaeota DHV | A: Thaumarchaeota | 63.1 | 0.71 | 69.1 | 1.2 | 67.3 (2) | 8.6 (3.8) | 132 | 5.90 | 0 | 1.4 | 4 |
| Sulfurihydrogenibium DHV | B: Aquificae | 59.0 | 2.96 | 94.2 | 54.0** | 31.7 (2.5) | 1414.1 (460.5) | 908 | 4.24 | 35 | 58.5 | 37 |
| Ignisphaera DHV | A: Crenarchaeota | 50.5 | 2.56 | 84.0 | 4.3 | 38.9 (4.1) | 12.7 (4.9) | 405 | 6.64 | 63 | 12.0 | 1 |
| Aminicenantes DHV | B: Aminicenantes | 50.1 | 2.21 | 90.6 | 6.5 | 42.4 (2.1) | 5.5* (1.8) | 134 | 28.98 | 0 | 0.9 | 5 |
| — | ||||||||||||
| Acidobacteria DHV | B: Acidobacteria | 37.7 | 1.91 | 89.2 | 4.3 | 60.1 (1.4) | 11 (4.3) | 275 | 7.66 | 0 | 3.7 | 2 |
| Tibeticola DHV | B: Betaproteobacteria | 36.7 | 2.38 | 96.4 | 0.7 | 66.5 (1.9) | 6.9* (3.3) | 183 | 16.72 | 0 | 1.7 | 12 |
| Campylobacteraceae DHV | B: Epsilonproteobacteria | 34.2 | 1.43 | 95.0 | 2.9 | 42.8 (1.8) | 10.5 (4.2) | 145 | 13.42 | 0 | 3.3 | 3 |
| Sulfuricurvum DHV | B: Epsilonproteobacteria | 29.8 | 1.74 | 95.7 | 7.9 | 44.5 (3.2) | 12.2 (4.7) | 158 | 15.43 | 1 | 5.2 | 8 |
| Nitrosopumilus DHV | A: Thaumarchaeota | 26.4 | 1.61 | 84.0 | 8.0 | 33.2 (1.9) | 4.6* (2.8) | 205 | 8.62 | 2 | 2.2 | 1 |
| Burkholderiales DHV | B: Betaproteobacteria | 25.9 | 4.62 | 94.2 | 7.2 | 65.9 (1.7) | 6.9* (3.3) | 422 | 13.81 | 2 | 2.2 | 35 |
| Thiomicrospiraceae DHV | B: Gammaproteobacteria | 25.3 | 2.25 | 100.0 | 5.8 | 43.8 (2.8) | 53.8 (11.6) | 174 | 28.70 | 15 | 12.0 | 8 |
| Lentimicrobium DHV | B: Bacteriodetes | 22.5 | 2.66 | 92.8 | 3.6 | 34.5 (1.4) | 9.9 (4.1) | 305 | 11.33 | 2 | 2.8 | 10 |
Bold: Sulfurihydrogenibium was the predominant MAG in all four metagenomes and is represented by varying micro-populations that could not be subdivided by tetranucleotide frequency or coverage-based clustering analyses. Empty rows separate groups based on predicted optimal growth temperature, TOPT(upper = hyperthermophiles; middle = thermophiles; lower = mesophiles).
*Co-assembly coverage is mean coverage between both assemblies.
**High redundancy for this MAG was examined carefully and determined to be related to Sulfurihydrogenibium (Supplementary Figure 2; Fig. 4; Supplementary Table 8; Supplementary Table 6).
aMAGs with >1% relative abundance (within their respective metagenome assembly) and greater than ~70% estimated completeness were named by the highest resolution taxonomic rank determined by robust phylogenomic analysis (Supplementary Figure 1), with the suffix “DHV” for Deep Hole Vent. Comprehensive lists of all MAGs recovered are provided in Supplemental Table 2.
bThe corresponding microbial phylum is listed for each MAG, preceded by A for archaea or B for bacteria.
cTOPT = predicted optimal growth temperature based on 2-mer amino acid compositions [41].
dLength (Mb) = cumulative sequence length of all contigs within a MAG.
eComp. = estimated completeness based on single-copy gene detection.
fRed. = estimated redundancy based on single-copy gene detection.
gG + C% = mean percentage of G and C nucleotides determined for each contig within a MAG. Standard deviation from the mean is listed in parentheses.
hCoverage = mean depth of short read recruitment across all contigs within a MAG. For relative abundance see individual assembly information (Supplementary Tables – individual assemblies). Standard deviation from the mean is listed in parentheses. Asterisk indicates average of coverage values between both samples in the co-assembly.
iCont. = the number of contigs within each MAG.
jN50 = minimum contig length required to constitute 50% of the MAG (in kilobase).
kViral contigs listed here identified based on VirSorter and mapping CRISPR variable spacer regions (see “Materials and methods”).
lSNV Dens. = single nucleotide variants per kilobase per genome.
mNumber of transposase sequences detected in each MAG.