Hi Qiime2 fellas,
I'm working with similar data (DNA extracted with PowerSoil, same primer pair, plus a organellar blocking primer set, Miseq sequencing),
I also lost a lot of data during dada2 step (see image below) even after trying all variations of metaparameters (FYI, I truncated fwd at 290 and rev 260, trimmed first 10 bp, this last one helped a lot),
I might sound mean, but with the combination of protocols we used, apparently we get low throughput, I even got a sample which only a 37% survived after all dada2 process.
Cheers,
Luis Alfonso.