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Background  Recent evidence of specific bacterial communities extended the traditional concept of fungal-algal lichen symbioses by a further organismal kingdom. Although functional roles were already assigned to dominant members of the highly diversified microbiota, a substantial fraction of the ubiquitous colonizers remained unexplored. We employed a multi-omics approach to further characterize functional guilds in an unconventional model system.    Results  The general community structure of the lichen-associated microbiota was shown to be highly similar irrespective of the employed omics approach. Five highly abundant bacterial orders— Sphingomonadales ,  Rhodospirillales ,  Myxococcales ,  Chthoniobacterales , and  Sphingobacteriales— harbor functions that are of substantial importance for the holobiome. Identified functions range from the provision of vitamins and cofactors to the degradation of phenolic compounds like phenylpropanoid, xylenols, and cresols.    Conclusions  Functions that facilitate the persistence of  Lobaria pulmonaria  under unfavorable conditions were present in previously overlooked fractions of the microbiota. So far, unrecognized groups like  Chthoniobacterales  ( Verrucomicrobia ) emerged as functional protectors in the lichen microbiome. By combining multi-omics and imaging techniques, we highlight previously overlooked participants in the complex microenvironment of the lichens.    Electronic supplementary material  The online version of this article (doi:10.1186/s40168-017-0303-5) contains supplementary material, which is available to authorized users.

Deciphering functional diversification within the lichen microbiota by meta-omics