|Environment Sampled||Target and Approach||Findings||Reference|
|Wastewater biosolids||Bacterial 16S rRNA genes; PCR, pyrosequencing (454 GS-FLX sequencer)||Most of the pathogenic sequences belonged to the genera Clostridium and Mycobacterium||Bibby et al. 2010|
|Wastewater (activated sludge, influent, and effluent)||Bacterial 16S rRNA gene (hypervariable V4 region); PCR, pyrosequencing (454 GS-FLX sequencer)||Most of the pathogenic sequences belonged to the genera Aeromonas and Clostridium||Ye and Zhang 2011|
|River sediment||Bacterial antibiotic-resistance genes; MDA, pyrosequencing (454 GS-FLX sequencer)||Large amounts of several classes of resistance genes in bacterial communities exposed to antibiotic were identified||Kristiansson et al. 2011|
|Reclaimed and potable water||Viral DNA and RNA; tangential flow filtration, DNase treatment, MDA, pyrosequencing (454 GS-FLX and GS20 sequencer)||Over 50% of the viral sequences had no significant similarity to proteins in GenBank; bacteriophages dominated the DNA viral community; the RNA metagenomes contained sequences related to plant viruses and invertebrate picornaviruses||Rosario et al. 2009|
|Wastewater biosolids||Viral DNA and RNA; DNase and RNase treatment, reverse transcription for RNA, pyrosequencing (454 GS-FLX sequencer), optimal annotation approach specific for viral pathogen identification is described||Parechovirus, coronavirus, adenovirus, aichi virus, and herpesvirus were identified||Bibby et al. 2011|
|Lake water||Viral RNA; tangential flow filtration, DNase and RNase treatment, random amplification (klenow DNA polymerase), pyrosequencing (454GS-FLX sequencer)||66% of the sequences had no significant similarity to known sequences; presence of viral sequences (30 viral families) with significant homology to insect, human, and plant pathogens||Djikeng et al. 2009|
Abbreviations: DNase, deoxyribonuclase; MDA, multiple displacement amplification; PCR, polymerase chain reaction; RNase, ribonuclease; rRNA, ribosomal RNA.
Source: Aw and Rose 2012. Reprinted with permission; copyright 2012, Current Opinion in Biotechnology.