Stability and change in the lichen microbiome

Lichens represent long-living miniature ecosystems with specific bacterial communities. We extend our previous research on lichen-associated bacteria to study the effects of ecological variation on composition and function of lichen microbiomes. Lichens experience variation in humidity, temperature and irradiation in their habitat. This approach will also reveal the composition of core and transient fractions of bacterial communities in two models: Lobaria pulmonaria and Peltigera praetextata. In experimental approaches, we will expose lichens to artificial habitat disturbances, such as excessive rain or shade. These experiments will also test under which circumstances changes of microbial communities are progressive. To characterise composition of the microbiomes of individual lichens we use deep and metagenome sequencing and FISH-CLSM (fluorescence in situ hybridization and confocal laser scanning microscopy). These data will be complemented by functional characterization of the entire lichen symbiosis using an environmental proteomics approach. As a pioneering approach we also study the community mobilome to assess potential horizontal genetic transfer and evolutionary processes in the lichen microbiome. This is the first investigation of stability and change in the microbiome associated with lichens. Because lichen symbioses can be seen as miniature version of ecosystems, the results could provide new insights in the effect of environmental change on microbial services in larger ecosystems.

Traditionally, lichens are regarded as symbiotic association of a mycobiont (fungus) and a photobiont (green algae and/or cyanobacteria). While the fungus provides a suitable habitat for the photobiont, the photosynthetic partner produces energy for the mutualistic system. In the last few years this classical point of view was challenged by advanced microbiome research accompanied with new technologies. Similar to a wide range of other organisms, the positive effect of the microbiome on its host might also contribute to the wellbeing of lichens. If and which role these bacteria play for the lichen symbiosis was mostly unknown. The aim of this study was to characterize the structure and diversity of the lichen-associated microbiome by high throughput-sequencing and state of the art imaging techniques (confocal laser-scanning-microscopy), and to shed light on its functions on different molecular levels (metagenome, transcriptome, proteome).Focusing on the lung lichen (Lobaria pulmonaria) as model system, we could show that Alphaproteobacteria was the dominant group within the highly diverse bacterial community. Distant Lobaria populations share a common core-microbiome, indicating a stable correlation between specific bacterial taxa and the lichen species itself. Vertical transmission of a bacterial delegation with the lichens vegetative propagules over short distances might shape and stabilize the microbiome composition within a region. In this context, metagenome and metatranscriptome analyses revealed that the symbiotic lifestyle is supported and supplemented by various functions. These include the biosynthesis and provision of nutrients, vitamins, co-factors and growth promoting hormones as well as chemical defense mechanisms against various biotic (pathogenic bacteria and fungi) and abiotic stress factors. The latter one comprises protection against reactive oxygen species and detoxification of toxic inorganic compounds such as arsenic. More detailed approaches exploring the potential of lichen-associated bacterial isolates have shown that specific antagonistic bacteria were also producers of metabolites that are known to promote plant growth under drought and high salinity conditions.This interdisciplinary, poly-phasic study clearly showed that the lichen-associated bacterial microbiome contributes to lichen wellbeing and thus the classic lichen model should be expanded by the microbiome as third integral part. Moreover, the application of lichen-associated bacteria may prove to be a useful alternative to conventional approaches in plant protection and growth promotion.