Skip to main content

Table 2 Gene and transcript inventories for the ten reference genome bins recruiting the highest number of metagenome reads

From: Metagenomic and metatranscriptomic inventories of the lower Amazon River, May 2011

Reference genome Phylum Mean transcripts L−1 Mean genes L−1 Mean % of transcripts Mean % of genes Genome sizea PA genome equivalents L−1 FL genome equivalents L−1 Total genome equivalents L−1
Actinobacterium SCGC AAA027-L06 Actinobacteria 4.84 × 109 4.97 × 1011 11.2 7.1 1244 1.92 × 108 2.08 × 108 4.00 × 108
Schlesneria paludicola Planctomycetes 1.30 × 109 1.51 × 1011 1.7 2.5 7033 1.71 × 107 4.41 × 106 2.15 × 107
Polynucleobacter necessarius asym. Betaproteobacteria 1.55 × 109 1.49 × 1011 1.1 1.3 2077 4.19 × 107 2.73 × 107 6.91 × 107
Candidatus Solibacter usitatus Ellin6076 Acidobacteria 1.16 × 109 1.44 × 1011 1.4 0.9 7998 1.31 × 107 5.53 × 106 1.86 × 107
Pedosphaera parvula Verrucomicrobia 2.00 × 109 1.16 × 1011 1.0 1.2 6510 1.25 × 107 5.36 × 106 1.79 × 107
Niastella koreensis GR20-10 Bacteriodetes 1.04 × 109 1.12 × 1011 2.7 1.4 7136 9.54 × 106 6.09 × 106 1.56 × 107
Ilumatobacter coccineum YM16-304 Actinobacteria 4.44 × 108 1.10 × 1011 0.2 1.2 4233 1.56 × 107 1.04 × 107 2.60 × 107
Candidatus Nitrospira defluvii Nitrospirae 1.44 × 109 7.42 × 1010 0.7 0.3 3938 1.45 × 107 4.34 × 106 1.88 × 107
Betaproteobacterium CB Betaproteobacteria 5.38 × 108 7.27 × 1010 0.5 0.4 2034 2.11 × 107 1.46 × 107 3.57 × 107
Opitutus terrae PB90-1 Verrucomicrobia 6.94 × 108 6.75 × 1010 0.4 0.5 4612 7.61 × 106 7.04 × 106 1.46 × 107
Sum   1.50 × 1010 1.49 × 1012 20.8 16.8     6.38 × 108b
  1. Data were averaged across five locations (Fig. 1a) sampled in the lower Amazon River in May 2011
  2. aNumber of protein-encoding genes in the reference genome
  3. bThe top ten taxa averaged 16.8 % of the genes in Amazon River water. Applying this same proportion to the number of genome equivalents contributed by the top ten taxa (6.38 × 108), the total genome equivalent is estimated at 3.80 × 109 genomes L−1. By comparison, direct epifluorescence microscopy counts indicate 3.46 × 109 cells L−1