Hi @STE40,
I'm not seeing any issues with the depths. You're at well over 50K reads (which would be excessive in my environment, but I tend to go shallow and high sample number over ultra deep sequencing on a few samples). I think you've exceeded expectations on your ability to do high abundance profiling, and you're likely picking up a lot of reads on the low abundance profiling.
My recommendation would be to pick a round number below the lowest depth. You can do multiple rarefaction and average if you want to make sure the models are stabilized (I tend to just run like 10 tables at the same depth, and then use q2-feature-table merge with "average" overlap to get to where I need). You may find you want to adjust for sequencing depth, particularly on your unweighted/richness metrics (Unweighted UniFrac, Jaccard, Observed Features, Chao1 - although inappropriate for denoised data, or Faiths PD) or zero-sensitive metrics, like Aitchison.
You may also want to consider how the depth impacts filtering and try to filter out your low prevalence reads based on the depth.
I would also recommend being aware of potential contamination (reagent and splashover) in your larve samples.
Best,
Justine