Gneiss with size fractionated samples

Dear all,

I am trying to use gneiss to compare microbiomes in different size fractions of water samples and the relationship of balances to associated environmental variables ( i.e. temperature, nutrient, ect). Specifically each water sample was fractionated into whole microbiome, particle attached microbiome and free living microbiome samples. I am unsure of how to set up the formula for gneiss since I would like to identify balances different between size fraction but then also determine how any differentially abundant taxa from significant balances relate to the environmental parameters. My worry is that if I run all variables together i.e. formula “Fraction+Temperature+Nitrogen” there may be too much noise due to the size fractions to detect significant associations with the environmental parameters since the fractions are almost like pseudoreplicates as all 3 fractions from a sample are associated with the same environmental data however their compositions are quite different. For example I know from previous analyses that per sample some taxa are very abundant in one fraction but not another, however they are associated with the same temperature. Would it be better to run one regression only looking at Fraction and then separate regressions for each fraction looking at the environmental parameters? or am I overthinking this and one analysis with all the variable should still detect associations between the taxa and environmental parameters?

Any help would be much appreciated. Thanks in advance,


That’s half the reason for including fraction in the formula. I’d recommend testing it both ways and see how it changes your results.

Good luck!

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