Table 3.
Summary statistics of each OGC and their comparison between freshwater and marine metagenomes
| Wilcoxon test | Permanova | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Median besta (allb) | Besta | Allb | Besta | Allb | |||||||||
| Fresh | Ocean | W | P value | W | P value | F | R2 | P value | F | R2 | P value | ||
| Translation, ribosomal structure and biogenesis | J | 9.4% | 10.4% | 70 | 0.098 | 118 | 0.030 | 4.7 | 0.21 | 0.002 | 6.1 | 0.21 | 0.001 |
| RNA processing and modification | A | 0.0% | 0.0% | 38 | 0.473 | 57 | 0.270 | 8.1 | 0.31 | 0.001 | 10.3 | 0.31 | 0.001 |
| Transcription | K | 3.3% | 3.1% | 9 | 0.002 | 11 | 0.000 | 13.0 | 0.42 | 0.001 | 17.1 | 0.43 | 0.001 |
| Replication, recombination and repair | L | 8.4% (8.6%) | 6.4% | 4 | 0.000 | 6 | 0.000 | 10.2 | 0.36 | 0.001 | 13.8 | 0.38 | 0.001 |
| Chromatin structure and dynamics | B | 0.0% | 0.0% | 54 | 0.678 | 75 | 0.894 | 3.7 | 0.17 | 0.003 | 3.9 | 0.14 | 0.003 |
| Cell cycle control, cell division, chromosome partitioning | D | 1.4% (1.3%) | 1.5% | 66 | 0.181 | 107 | 0.123 | 11.4 | 0.39 | 0.002 | 15.1 | 0.40 | 0.001 |
| Nuclear structure | Y | 0.0% | 0.0% | 40 | 0.447 | 71 | 0.655 | NA | NA | NA | NA | NA | NA |
| Defence mechanisms | V | 2.0% | 1.7% | 20 | 0.031 | 25 | 0.003 | 5.7 | 0.24 | 0.005 | 7.9 | 0.26 | 0.001 |
| Signal transduction mechanisms | T | 1.9% | 1.2% | 1 | 0.000 | 1 | 0.000 | 12.3 | 0.41 | 0.001 | 16.9 | 0.42 | 0.001 |
| Cell wall/membrane/envelope biogenesis | M | 6.3% | 5.3% | 12 | 0.004 | 17 | 0.000 | 10.0 | 0.36 | 0.001 | 14.2 | 0.38 | 0.001 |
| Cell motility | N | 0.2% | 0.2% | 29 | 0.157 | 57 | 0.270 | 2.2 | 0.11 | 0.075 | 2.5 | 0.10 | 0.047 |
| Cytoskeleton | Z | 0.1% | 0.3% | 81 | 0.010 | 127 | 0.007 | 3.6 | 0.17 | 0.023 | 3.2 | 0.12 | 0.021 |
| Extracellular structures | W | 0.0% | 0.0% | 48 | NA | 78 | NA | NA | NA | NA | NA | NA | NA |
| Intracellular trafficking, secretion and vesicular transport | U | 1.3% | 1.4% | 73 | 0.057 | 114 | 0.052 | 5.3 | 0.23 | 0.002 | 7.6 | 0.25 | 0.001 |
| Posttranslational modification, protein turnover, chaperones | O | 5.0% | 5.6% | 82 | 0.007 | 137 | 0.001 | 10.4 | 0.37 | 0.001 | 13.0 | 0.36 | 0.001 |
| Energy production and conversion | C | 9.5% | 11.2% (11.1%) | 89 | 0.001 | 148 | 0.000 | 6.6 | 0.27 | 0.001 | 9.2 | 0.29 | 0.001 |
| Carbohydrate transport and metabolism | G | 5.5% | 5.3% | 22 | 0.047 | 48 | 0.110 | 7.2 | 0.28 | 0.001 | 8.8 | 0.28 | 0.001 |
| Amino acid transport and metabolism | E | 11.7% | 13.7% | 89 | 0.001 | 146 | 0.000 | 11.9 | 0.40 | 0.001 | 14.6 | 0.39 | 0.001 |
| Nucleotide transport and metabolism | F | 3.8% | 4.2% | 65 | 0.208 | 101 | 0.225 | 6.9 | 0.28 | 0.001 | 8.0 | 0.26 | 0.001 |
| Coenzyme transport and metabolism | H | 4.1% | 4.9% | 96 | 0.000 | 156 | 0.000 | 7.9 | 0.31 | 0.002 | 10.0 | 0.30 | 0.001 |
| Lipid transport and metabolism | I | 4.2% | 4.4% (4.3%) | 69 | 0.115 | 106 | 0.137 | 8.6 | 0.32 | 0.001 | 11.3 | 0.33 | 0.001 |
| Inorganic ion transport and metabolism | P | 4.2% (4.1%) | 4.3% | 58 | 0.473 | 101 | 0.225 | 13.0 | 0.42 | 0.001 | 16.8 | 0.42 | 0.001 |
| Secondary metabolites biosynthesis, transport and catabolism | Q | 1.8% (1.7%) | 1.5% | 27 | 0.115 | 51 | 0.152 | 10.5 | 0.37 | 0.001 | 13.8 | 0.38 | 0.001 |
| General function prediction only | R | 10.0% | 9.2% (9.1%) | 26 | 0.098 | 38 | 0.030 | 8.8 | 0.33 | 0.001 | 11.7 | 0.34 | 0.001 |
| Function unknown | S | 5.5% | 3.9% | 6 | 0.000 | 7 | 0.000 | 12.2 | 0.40 | 0.001 | 16.0 | 0.41 | 0.001 |
a
Smaller data set of eight lake and 12 ocean samples, excluding worst quality samples (see Table S1).
b
Full data set of 12 lake and 13 ocean samples (see Table S1).
Average and standard deviation are derived from the relative fraction of OCGs averaged over all marine and freshwater metagenomes, respectively. P-values and W statistics from Wilcoxon test on the contribution of ORFs to each OGC as well as results from PERMANOVA to test for differences in functional composition between marine and freshwaters using normalized COGs from each OGC.
NA, Not Assessed.