Finally - many thanks for all the help in this long discussion!
.
.
.
And as a reference for anyone who might have a similar problem, a short summary of conclusions:
- Fungal ITS 460 bp amplicon, paired-end 2×300 bp Illumina sequencing.
- In some samples over 90% reads failed to merge with paired-end dada2.
- The results of QIIME1 looked noisy/inflated, but they also contained sequences almost perfectly matching to taxons, which dissapeared in paired-end dada2.
- Deblur workflow performed even worse than paired-end dada2.
- Single-end dada2 (on just forward reads, after removing the primers with qiime cutadapt trim-single) performed best.
- In some samples even with single-end dada2 many (up to two thirds) of sequences were removed as chimeras - but this is most likely not a problem of sequencing/analysis, but an indication of real chimeric sequences in the data (i.e. error introduced during the amplicon preparation, possibly due to very low amount of template in some samples).