The microbiomes of seven lichen genera reveal host specificity, a reduced core community and potential as source of antimicrobials

Abstract

The High Andean Paramo ecosystem is a unique neotropical mountain biome considered a diversity and evolutionary hotspot. Lichens, which are complex symbiotic structures that contain diverse commensal microbial communities, are prevalent in Paramos. There they play vital roles in soil formation and mineral fixation. In this study we analyzed the microbiomes of seven lichen genera in two Colombian Paramos using 16S rRNA gene analyses and provide the first description of the bacterial communities associated with Cora and Hypotrachyna lichens. Paramo lichen microbiomes were diverse, and in some cases were distinguished based on the identity of the lichen host. The majority of the lichen-associated microorganisms were not present in all lichens sampled and could be considered transient or specialists.We also uncovered sixteen shared taxa that suggest a core lichen microbiome among this diverse group of lichens, broadening our concept of these symbiotic structures. Additionally, we identified strains producing compounds active against clinically relevant pathogens. These results indicate that lichen microbiomes from the Paramo ecosystem are diverse and host-specific but share a taxonomic core and can be a source of new bacterial taxa and antimicrobials.Lichens represent some of the oldest and most diverse symbioses on Earth (16). Lichens consist of a photobiont (cyanobacterium/alga) and a mycobiont (fungus), which together form a unique structure called the thallus (17). Lichens play a vital role in ecosystems as they are essential in soil formation, naked soil colonization, and nutrient uptake and release for plants (18,19). Lichens can colonize a wide range of substrates, from natural surfaces to man-made materials such as plastic, rubber, metals and glass (20). They can also tolerate extreme environmental conditions and offer a niche for diverse microorganisms (21,22). The diversity of these lichen-associated microbial communities is not yet well characterized, and has only recently been investigated using high-throughput techniques (23, 24). These studies indicate substantial microbial and functional diversity (24-26) that has been suggested to help protect the thalli against pathogens through the production of antimicrobials (27,28). The process of community establishment within lichens is poorly understood and has been proposed to be driven either by the photobiont (29) or by geography and habitat (30).Recent studies have described the microbial communities associated with lichens using cultureindependent strategies (24, 25). However, comparisons between studies are hindered by differences in sampling methods, data analyses, and poor or complete lack of lichen description. Given the complexity of the lichen symbiotic structures, with recent evidence indicating that some lichens may be composed of multiple bacteria and more than one fungus (26), it is important to study lichen microbiomes in order to understand their ecological role in the symbiosis.A large and unexplored diversity of lichens is located in the Par...

Bacterial community of reindeer lichens differs between northern and southern lichen woodlands

“…The bacterial community of reindeer lichens does not cluster together by host species, although values of beta diversity are significant between C. stellaris and C. stygia. Our results differ from previous studies which demonstrated that the bacterial community in lichens are host-specific (e.g., Bates et al 2011;Sierra et al 2020). found species-specific bacteria in three lichens with different growth forms: fruticose, crustose, and foliose.…”

“…found species-specific bacteria in three lichens with different growth forms: fruticose, crustose, and foliose. Sierra et al (2020) also suggested bacteria host-specificity in seven genera of lichens with different thallus morphologies (Cora, Hypotrachyna, Peltigera and Sticta are foliose, and Usnea, Cladonia and Stereocaulon are fruticose). A possible explanation is that host-specificity is growthform-specific.…”

“…Bacterial diversity within each sample differs between morphological species, but it hardly varies between the eight molecular species. Sierra et al (2020) compared bacterial community in seven lichen genera, and showed differences in alpha diversity exclusively between Usnea and Hypotrachyna, although there was no information available at species level.…”

“…The bacterial community of lichens contributes to essential functions of the host (nutrient supply, resistance against biotic and abiotic factors, growth support, detoxification of metabolites or provision of vitamin B 12 ) (Grube et al 2015). Lichen bacterial community can be determined by different factors such as host-identity (Bates et al 2011;Sierra et al 2020), photoautotrophic symbiont (Hodkinson et al 2012), thallus conditions (Mushegian et al 2011;Cardinale et al 2012b;Noh et al 2020) and growth form (Park et al 2016), substrate type (Park et al 2016), habitat (Cardinale et al 2012a), or/and geography (Hodkinson and Lutzoni 2009;Aschenbrenner et al 2014). To date, studies on lichen bacterial community have been mainly carried out with Lobaria pulmonaria (L.) D r a f t Hoffm.…”

The Microbiomes of Seven Lichen Genera Reveal Host Specificity, a Reduced Core Community and Potential as Source of Antimicrobials

“…The preprint version of this manuscript has been deposited at bioRxiv-the preprint server for biology as: Sierra et al, 2019. The microbiomes of seven lichen general reveal host specificity, a reduced core community and potential as source of antimicrobials. doi: 10.1101/789032.…”