Geoscience Reference
In-Depth Information
TABLE 3-2
Metagenomic Characterization of Pathogens and Microbial Populations in Biosolids, Wastewater, Rivers, and Lakes
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
.
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