Deciphering functional diversification within the lichen microbiota by meta-omics

Abstract

BackgroundRecent 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.ResultsThe 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.ConclusionsFunctions 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 materialThe online version of this article (doi:10.1186/s40168-017-0303-5) contains supplementary material, which is available to authorized users.

Hydrolytic Capabilities as a Key to Environmental Success: Chitinolytic and Cellulolytic Acidobacteria From Acidic Sub-arctic Soils and Boreal Peatlands

“…The bacterium examined in our study, strain SBC82 T , was isolated from a habitat enriched with fungal-derived chitin, i.e., an organic soil layer underlying lichen cover. Although Acidobacteria are not recognized as an important component of the lichen-associated microbiome ( Cernava et al, 2017 ), decaying lichen thalli or underlying organic layers are abundantly colonized by these bacteria ( Pankratov, 2012 ).…”

Comparing Sanger sequencing and high-throughput metabarcoding for inferring photobiont diversity in lichens

“…16 , 20 ). This previously unrecognized lichen-associated biosphere may act as a significant functional component of the symbiosis, supporting the growth and regeneration of the thallus, and modulating the holobiont’s response to environmental triggers 21 – 23 .…”

Adaptions of Lichen Microbiota Functioning Under Persistent Exposure to Arsenic Contamination

“…Such adaptations facilitate persistence of the microbiota and thus might be crucial to preserve symbiosis-relevant functioning (Figure 5 ). By enduring unfavorable conditions in typical lichen habitats, which primarily include high fluctuations in humidity and temperature, the associated bacteria can fulfill their main roles as (i) protectors against biotic and abiotic stresses, (ii) providers of nutrients, vitamins and co-factors, and (iii) detoxifiers of organic and inorganic compounds ( Grube et al, 2015 ; Cernava et al, 2017 ; Eymann et al, 2017 ).…”

“…Considering lichens as microbial multi-species symbioses, also including additional fungi ( Spribille et al, 2016 ), provides the basis for understanding how highly complex functional networks persist under recurrently changing climatic and sometimes hostile conditions. In one of our recent works, we divided beneficial groups of lichen-colonizing microorganisms in two general groups, the “feeders” and the “protectors” ( Cernava et al, 2017 ). The role of the “feeders” fraction is more obvious and often easier to access with various experiment setups.…”