
Dear all

I have used permutational multivariate analysis of variance (adonis in package vegan) based on Bray-Curtis distances  to assess the signifance of carbon, nitrogen and more complex nutrient amendments on soil microbial community structure (microbial fatty acids).

I have identified signifant effects of nutrients and would like to know how to identify the fatty acids (microbial markers) that are associated with these differences.  So far I have used Pierre Legrendre's "Dufrene-Legendre Indicator Species Analysis" duleg in package 'labdsv' to do this (Calculates the indicator value (fidelity and relative abundance) of species in 
clusters or types).  However, I am not familiar with the implementation of this method and am concerned about the relevance of the output as  the 'indicator species' are not probably not based on Bray-Curtis distances.

Is there another way to identify fatty acids contributing to differences between my nutrient amendment groups?  For example, the output of the permutational multivariate analysis of variance (adonis) has the following attributes:

             
aov.tab              6        data.frame     list   
call                    2        -none-           call   
coefficients        74       -none-           numeric
coef.sites           28       -none-          numeric
f.perms             999      -none-          numeric
model.matrix     28       -none-           numeric
terms                3         terms            call

Can I use the coefficients to select fatty acids that contribute to the differences between treatment? 

Thanks

Paul      		 	   		  
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