Different sequencing runs present different alpha diversity

[CristianVillenaAlemany]

I'm working with a environmental dataset from a 3 year sampling campaign in a freshwater lake. I sequenced one marker gene from 215 samples and split randomly the sequencing of these samples in 2 illumina runs. The number of reads and quality of the sequencing files is similar in both runs. I analysed every run independently and merged before the chimera removal. When I plot the alpha diversity, one run has a substantial higher diversity than the other run, even after rarefaction. (Image attached) Any clue how to solve it? Thank you very much

[benjjneb]

Well, in downstream analyses of alpha-diversity, you will need to control for the batch effect, for example by including a batch term in any linear regression analyses of alpha-diversity.