4.2. Cost factor
One of the reasons for developing metabarcoding as a future
biomonitoring tool is the decreased costs (both in terms of time and
money) compared to full metagenome reconstruction through shotgun
sequencing or classical morphological approaches. Based on recent
calculations for marine biomonitoring, the metabarcoding approach would
represent only approximately half of the costs and less than 70% of the
time compared to morphological assessments (Aylagas, Borja, Muxika, &
Rodríguez-Ezpeleta, 2018). We found that for CHB, the laboratory time
effort is nearly the same, but the costs are at present still higher
than those of metabarcoding, although considerably lower than those of
metagenome reconstruction. The major factor is the preparation of
sequencing libraries per sample for CBH compared to metabarcoding. In
addition, although multiplexing library protocols help increase cost
efficiency (for example, Förster et al., 2018; Meyer & Kircher, 2010),
the results presented here show that full metabarcodes must be targeted
to obtain satisfying read lengths and taxonomic assignments, and
multiplexing cannot encompass as many libraries in a sequencing lane as
MTB, with over 100 samples. The computational power of these methods is
also comparable: reconstruction can be demanding, yet error correction
for high-quality metabarcoding is also time- and resource-consuming.
Nevertheless, as in other recent comparable studies (Liu et al., 2016;
Seeber et al., 2019), we see the advantages of overcoming the slightly
higher prices in the long term. In particular, using CBH for baseline
studies can improve local reference databases thanks to improved
taxonomic inferences through phylogenetic reconstruction, which will be
particularly important for less described areas and taxa. These extended
libraries will in turn contribute to improving the output of massive
metabarcoding screenings.