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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
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Microbiome

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