alpha diversity wilcox.test
I think this is a bug in the input data.
At a wild guess what I think is happening is the input data is not regarded as paired, hence the error paired = paired. The other weird error is x must be numeric. Firstly,

how are you scoring missing data, its not via - by any chance? Missing data must be via nan type syntax.
are you sure there are no heading bugs? Like a header is getting dragged into the numeric data?

Wilcoxan is a non-parametric T test, so the wet root and dry root must match exactly the same sample. Thus it is not a general wet root versus generic dry root, but wet and dry from the same specimen. If this is the data you have the program doesn't think it is matching.
If it is truely paired, again I think the source of error is you have some missing value which is leaving the pairings unequal lengths or else a header bug.
If the data genuinely isn't paired, then I would look at the Mann-Whitney U test, it would be easier in this scenario.
I don't use R syntax (just pandas dataframes) so can't say whether the syntax in the first example is valid, but it is pretty clear regarding your input. In Python you'd generally just give it the entire dataframe and tell it to go figure.
The reality is that loads of programs do Wilcoxan, you don't need to use R if its a one-off test. Obviously if this a part of a pipeline (automation) thats a bit different.