Thank you for telling me more.
This is very good to hear! Sometimes people only have a few samples and don't have enough statistical power. I'm glad you have 100s of samples.
Keep all the data you have! Haveing more samples is better, even if groups are uneven.
The alpha diversity tests measure each sample independently. This means your Plant C: 100 samples would yield 100 alpha diversity values.
The beta diversity tests measure pairwise comparisons between samples, so comparing each Plant C sample against each other Plant C sample yields 100*99 = 9900 beta diversity values.
This extremely large number explains boxplots:
- most beta diversity values are near the mean, so the IQR is small, and the boxplot looks 'flat'
- outliers are calculated somehow (maybe 1.5*IQR), and even though it's a small fraction of total beta diversity values, that's still dozens of points to show on the graph