Census of the viral metagenome within an activated sludge microbial assemblage

Abstract

The viral metagenome within an activated sludge microbial assemblage was sampled using culture-dependent and culture-independent methods and compared to the diversity of activated sludge bacterial taxa. A total of 70 unique cultured bacterial isolates, 24 cultured bacteriophages, 829 bacterial metagenomic clones of 16S rRNA genes, and 1,161 viral metagenomic clones were subjected to a phylogenetic analysis.

FIG. 1.

Taxonomic breakdown of the significant hits from the AS viral metagenomic libraries based on a BLASTx comparison against the GenBank nr/nt and env databases. Numbers indicate the number of sequences assigned to a particular phylogenetic category based on significant homology with known sequences in GenBank. MGE, mobile genetic element. The viral metagenomic DNA sequences were registered as part of the Wastewater Viral Metagenome project at GenBank (Trace Archives) and are under TI reference numbers 2251203077 to 2251204802.

FIG. 2.

Relative dominance of bacterial divisions represented by sequences from the bacterial culture collection, 16S rRNA gene clone library, cultured bacteriophages, and viral metagenomic library. The percentages of sequences affiliated with each bacterial division are compared among the four phylogenetic surveys. CD, culture dependent; CI, culture independent. Other bacterial divisions with <2% representation include the Chlamydiae (0.1%; bacterial, CI), Nitrospira (0.2%; bacterial, CI), Planctomyces (0.7%; bacterial, CI), Cyanobacteria (1.6%; viral, CI), Spirochetes (0.7%; viral, CI), Chloroflexi (0.5%; viral CI), and Deinococcus (0.5%; viral, CI).

FIG. 3.

Predicted metabolic profiles obtained from SEED analyses of viral metagenomic open reading frames (ORFs).