TABLE 1.
Ribotype diversity for habitats sampled multiple times by GOSa
| Classification | Coastal habitat
|
Estuary habitat
|
Open-ocean habitat
|
Entire GOS metagenome
|
||||
|---|---|---|---|---|---|---|---|---|
| No. of hits | % of hits | No. of hits | % of hits | No. of hits | % of hits | No. of hits | % of hits | |
| Archaea | 14 | 0.4 | 0 | 0.0 | 8 | 0.2 | 32 | 0.3 |
| Bacteria | ||||||||
| Actinobacteria | 230 | 7.3 | 92 | 23.8 | 188 | 5.0 | 824 | 8.2 |
| CFB | 252 | 8.0 | 28 | 7.3 | 126 | 3.3 | 603 | 6.0 |
| Chlamydiae/Verrucomicrobia | 12 | 0.4 | 4 | 1.0 | 9 | 0.2 | 41 | 0.4 |
| Chloroflexi | 0.1 | 0.8 | 0.1 | 0.2 | ||||
| Unclassified | 2 | 0.1 | 3 | 0.8 | 1 | 0.0 | 15 | 0.1 |
| SAR202 | 0 | 0.0 | 0 | 0.0 | 1 | 0.0 | 1 | 0.0 |
| Cyanobacteria | 167 | 5.3 | 0 | 0.0 | 255 | 6.7 | 532 | 5.3 |
| Deinococcus/Thermus | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 4 | 0.0 |
| Fibrobacteres/Acidobacteria | 6 | 0.2 | 0 | 0.0 | 3 | 0.1 | 33 | 0.3 |
| Firmicutes | 4 | 0.1 | 1 | 0.3 | 5 | 0.1 | 22 | 0.2 |
| OP11 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 |
| OD1 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 2 | 0.0 |
| SR1 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 |
| Planctomycetales | 1 | 0.0 | 2 | 0.5 | 4 | 0.1 | 19 | 0.2 |
| Alphaproteobacteria | 51.3 | 36.8 | 40.8 | 43.1 | ||||
| Unclassified | 128 | 4.1 | 8 | 2.1 | 162 | 4.3 | 410 | 4.1 |
| Caulobacterales | 2 | 0.1 | 0 | 0.0 | 2 | 0.1 | 7 | 0.1 |
| Rhizobiales | 26 | 0.8 | 2 | 0.5 | 13 | 0.3 | 91 | 0.9 |
| Rhodobacterales | 39 | 1.2 | 0 | 0.0 | 35 | 0.9 | 122 | 1.2 |
| Rhodobacterales, Roseobacter clade | 118 | 3.8 | 1 | 0.3 | 40 | 1.1 | 258 | 2.6 |
| Rhodospirillales | 13 | 0.4 | 1 | 0.3 | 27 | 0.7 | 54 | 0.5 |
| Rickettsiales | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 1 | 0.0 |
| Rickettsiales, SAR11 cluster | 1,149 | 36.7 | 127 | 32.9 | 1,178 | 31.0 | 3,093 | 30.9 |
| SAR116 cluster | 130 | 4.1 | 3 | 0.8 | 89 | 2.3 | 275 | 2.7 |
| Sphingomonadales | 3 | 0.1 | 0 | 0.0 | 3 | 0.1 | 10 | 0.1 |
| Betaproteobacteria | 0.9 | 11.1 | 5.2 | 2.8 | ||||
| Unclassified | 8 | 0.3 | 9 | 2.3 | 1 | 0.0 | 23 | 0.2 |
| Burkholderiales | 20 | 0.6 | 34 | 8.8 | 195 | 5.1 | 260 | 2.6 |
| Deltaproteobacteria | 0.2 | 0.0 | 0.8 | 0.4 | ||||
| Unclassified | 0 | 0.0 | 0 | 0.0 | 1 | 0.0 | 2 | 0.0 |
| Bdellovibrionales | 0 | 0.0 | 0 | 0.0 | 1 | 0.0 | 2 | 0.0 |
| Desulfobacterales | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 |
| Desulfovibrionales | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 1 | 0.0 |
| Desulfuromonadales | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 1 | 0.0 |
| Myxococcales | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 |
| SAR324 | 5 | 0.2 | 0 | 0.0 | 27 | 0.7 | 38 | 0.4 |
| Syntrophobacterales | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 |
| Epsilonproteobacteria | 0.0 | 0.0 | 0.0 | 0.1 | ||||
| Unclassified | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 |
| Campylobacterales | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 4 | 0.1 |
| Sulfurovum | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 2 | 0.0 |
| Gammaproteobacteria | 14.0 | 4.9 | 21.2 | 17.3 | ||||
| Unclassified | 140 | 4.5 | 2 | 0.5 | 196 | 5.2 | 562 | 5.6 |
| Aeromonadales | 3 | 0.1 | 0 | 0.0 | 16 | 0.4 | 19 | 0.2 |
| Alteromonadales | 17 | 0.5 | 1 | 0.3 | 249 | 6.6 | 290 | 2.9 |
| Chromatiales | 1 | 0.0 | 0 | 0.0 | 3 | 0.1 | 5 | 0.0 |
| Enterobacteriales | 2 | 0.1 | 0 | 0.0 | 4 | 0.1 | 6 | 0.1 |
| Methylococcales | 5 | 0.2 | 1 | 0.3 | 7 | 0.2 | 15 | 0.1 |
| Nitrincola | 6 | 0.2 | 0 | 0.0 | 11 | 0.3 | 38 | 0.4 |
| Oceanospirillales | 9 | 0.3 | 0 | 0.0 | 15 | 0.4 | 47 | 0.5 |
| Pasteurellales | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 |
| Pseudomonadales | 18 | 0.6 | 2 | 0.5 | 27 | 0.7 | 67 | 0.7 |
| SAR86 cluster | 231 | 7.4 | 12 | 3.1 | 269 | 7.1 | 636 | 6.3 |
| Thiotrichales | 0 | 0.0 | 1 | 0.3 | 0 | 0.0 | 8 | 0.1 |
| Vibrionales | 7 | 0.2 | 0 | 0.0 | 7 | 0.2 | 40 | 0.4 |
| Xanthomonadales | 1 | 0.0 | 0 | 0.0 | 0 | 0.0 | 5 | 0.0 |
| SAR406 | 32 | 1.0 | 0 | 0.0 | 66 | 1.7 | 106 | 1.1 |
| Spirochaetes | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 |
| Unclassified | 20 | 0.6 | 0 | 0.0 | 43 | 1.1 | 67 | 0.7 |
| Eukaryotes | 9 | 0.3 | 0 | 0.0 | 15 | 0.4 | 28 | 0.3 |
| Unclassified at >90% | 303 | 9.7 | 52 | 13.5 | 494 | 13.0 | 1,304 | 13.0 |
| Total | 3,133 | 386 | 3,794 | 10,025 | ||||
a
Coastal habitats were sampled 18 times, estuary habitats 3 times, and open-ocean habitats 14 times. Ribotype diversity for individual samples is provided in Table S3 in the supplemental material. The number of hits listed for each taxonomic bin is the raw, unnormalized count after duplicate reads (paired-end reads) were removed. Numbers in bold are total percentages of hits that were binned into the indicated domain/phylum/clade.