Careful processing of raw data excluding all low-quality reads, chimeric sequences,
or too short sequences is vital to obtaining only reliable values (Fig. 34.7). This data
processing can be provided commercially by sequencing companies, but we highly
recommend collaboration with experienced bioinformaticians, who are familiar with
appropriate software and understand the principles of molecular biology. Sequences
are then classified against various available databases (e.g., SILVA, NCBI,
Greengenes, RDP) (Balvočiūtė and Huson 2017).
NGS data can be visualized by many various diagrams and here we only describe
one of the commonly used methods. Phylum, class, or species abundance can be
displayed in column plots simply to compare the effect of nZVI between the treated
and the reference wells over certain periods of time (Fig. 34.8).
Fig. 34.7 Simplified workflow of taxonomic assignment
100%
90%
80%
70%
60%
50%
40%
30%
20%
10%
0%
–7
34
201
300
–7
34
140
201
300
Monitoring well
ZVI-treated well
Campylobacteraceae
Gallionellaceae
Helicobacteraceae
Coriobacteriaceae
Hydrogenophilaceae
Desulgobulbaceae
Eubacteriaceae
Rhodocyclaceae
SRB2
Others
Fig. 34.8 Phylum and class composition of bacterial populations present in the reference well and
ZVI-treated well over a 300-day monitoring. Phyla with higher than 3% abundance are shown
34 Tool V: Microbiological Methods for Monitoring nZVI. . .
655
or too short sequences is vital to obtaining only reliable values (Fig. 34.7). This data
processing can be provided commercially by sequencing companies, but we highly
recommend collaboration with experienced bioinformaticians, who are familiar with
appropriate software and understand the principles of molecular biology. Sequences
are then classified against various available databases (e.g., SILVA, NCBI,
Greengenes, RDP) (Balvočiūtė and Huson 2017).
NGS data can be visualized by many various diagrams and here we only describe
one of the commonly used methods. Phylum, class, or species abundance can be
displayed in column plots simply to compare the effect of nZVI between the treated
and the reference wells over certain periods of time (Fig. 34.8).
Fig. 34.7 Simplified workflow of taxonomic assignment
100%
90%
80%
70%
60%
50%
40%
30%
20%
10%
0%
–7
34
201
300
–7
34
140
201
300
Monitoring well
ZVI-treated well
Campylobacteraceae
Gallionellaceae
Helicobacteraceae
Coriobacteriaceae
Hydrogenophilaceae
Desulgobulbaceae
Eubacteriaceae
Rhodocyclaceae
SRB2
Others
Fig. 34.8 Phylum and class composition of bacterial populations present in the reference well and
ZVI-treated well over a 300-day monitoring. Phyla with higher than 3% abundance are shown
34 Tool V: Microbiological Methods for Monitoring nZVI. . .
655