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.