Endolithic Communities Research Articles

Metabolomics of Dry Versus Reanimated Antarctic Lichen-Dominated Endolithic Communities.

Cryptoendolithic communities are almost the sole life form in the ice-free areas of the Antarctic desert, encompassing among the most extreme-tolerant organisms known on Earth that still assure ecosystems functioning, regulating nutrient and biogeochemical cycles under conditions accounted as incompatible with active life. If high-throughput sequencing based studies are unravelling prokaryotic and eukaryotic diversity, they are not yet characterized in terms of stress adaptations and responses, despite their paramount ecological importance. In this study, we compared the responses of Antarctic endolithic communities, with special focus on fungi, both under dry conditions (i.e., when dormant), and after reanimation by wetting, light, and optimal temperature (15 °C). We found that several metabolites were differently expressed in reanimated opposite sun exposed communities, suggesting a critical role in their success. In particular, the saccharopine pathway was up-regulated in the north surface, while the spermine/spermidine pathway was significantly down-regulated in the shaded exposed communities. The carnitine-dependent pathway is up-regulated in south-exposed reanimated samples, indicating the preferential involvement of the B-oxidation for the functioning of TCA cycle. The role of these metabolites in the performance of the communities is discussed herein.

Diversity and Colonization Strategies of Endolithic Cyanobacteria in the Cold Mountain Desert of Pamir.

Microorganisms can survive in extreme environments and oligotrophic habitats thanks to their specific adaptive capacity. Due to its severe and contrasting climate conditions, the cold mountain desert in Eastern Pamir provides a unique environment for analyzing microbial adaptation mechanisms occurring within colonization of endolithic habitats. This study aims to investigate the composition and structure of endolithic microbial communities and analyze the interactions between microorganisms and colonized lithic substrates. Endolithic biofilms were examined using scanning electron microscopy in backscattered electron mode (SEM-BSE) and next-generation sequencing (NGS) applying amplicon sequence variants (ASVs) approach. The investigation of the V3–V4 region of 16S rRNA gene revealed that endolithic communities are dominated by Actinobacteria (26%), Proteobacteria (23%), and Cyanobacteria (11.4%). Cyanobacteria were represented by Oxyphotobacteria with a predominance of subclasses of Oscillatoriophycidae, Synechococcophycideae, and Nostocophycidae as well as the rarely occurring Sericytochromatia. The positive correlation between the contribution of the orders Synechococcales and Rhizobiales to community structure suggests that some functionally closed taxa of Cyanobacteria and Proteobacteria can complement each other, for example, in nitrogen fixation in endolithic communities. The endolithic communities occurring in Eastern Pamir were identified as complex systems whose composition and structure seem to be influenced by the architecture of microhabitats and related microenvironmental conditions.

Effects of Ocean Acidification on Coral Endolithic Bacterial Communities in Isopora palifera and Porites lobata

Endolithic microbes in coral reefs may act as a nutrient source for their coral hosts. Increasing atmospheric CO2 concentrations are causing ocean acidification (OA), which may affect marine organisms and ecosystems, especially calcifying organisms such as reef-building corals. However, knowledge of how OA affects marine microbes remains limited, and little research has been done on how coral endolithic communities respond to shifting environmental baselines. In this study, the endolithic communities of two common shallow water coral species, Isopora palifera and Porites lobata, were examined to investigate the microbial community dynamics under OA treatments. The colonies were placed in an environment with a partial pressure of carbon dioxide (pCO2) of 1,000 or 400 ppm (control) for 2 months. Several I. palifera colonies bleached and died at 1,000 ppm pCO2, but the P. lobata colonies remained unaffected. Inversely, the endolithic community in P. lobata skeletons showed significant changes after OA treatment, whereas no significant dynamics were observed among the I. palifera endoliths. Our findings suggest that the skeletal structures of different coral species may play a key role in corals host and endoliths under future high-OA scenarios.

Rock structure drives the taxonomic and functional diversity of endolithic microbial communities in extreme environments.

Endolithic (rock-dwelling) microbial communities are ubiquitous in hyper-arid deserts around the world and the last resort for life under extreme aridity. These communities are excellent models to explore biotic and abiotic drivers of diversity because they are of low complexity. Using high-throughput amplicon and metagenome sequencing, combined with X-ray computed tomography, we investigated how water availability and substrate architecture modulated the taxonomic and functional composition of gypsum endolithic communities in the Atacama Desert, Chile. We found that communities inhabiting gypsum rocks with a more fragmented substrate architecture had higher taxonomic and functional diversity, despite having less water available. This effect was tightly linked with community connectedness and likely the result of niche differentiation. Gypsum communities were functionally similar, yet adapted to their unique micro-habitats by modulating their carbon and energy acquisition strategies and their growth modalities. Reconstructed population genomes showed that these endolithic microbial populations encoded potential pathways for anoxygenic phototrophy and atmospheric hydrogen oxidation as supplemental energy sources.

Marine Cyanobacteria: A Source of Lead Compounds and their Clinically-Relevant Molecular Targets.

The prokaryotic filamentous marine cyanobacteria are photosynthetic microbes that are found in diverse marine habitats, ranging from epiphytic to endolithic communities. Their successful colonization in nature is largely attributed to genetic diversity as well as the production of ecologically important natural products. These cyanobacterial natural products are also a source of potential drug leads for the development of therapeutic agents used in the treatment of diseases, such as cancer, parasitic infections and inflammation. Major sources of these biomedically important natural compounds are found predominately from marine cyanobacterial orders Oscillatoriales, Nostocales, Chroococcales and Synechococcales. Moreover, technological advances in genomic and metabolomics approaches, such as mass spectrometry and NMR spectroscopy, revealed that marine cyanobacteria are a treasure trove of structurally unique natural products. The high potency of a number of natural products are due to their specific interference with validated drug targets, such as proteasomes, proteases, histone deacetylases, microtubules, actin filaments and membrane receptors/channels. In this review, the chemistry and biology of selected potent cyanobacterial compounds as well as their synthetic analogues are presented based on their molecular targets. These molecules are discussed to reflect current research trends in drug discovery from marine cyanobacterial natural products.

Raman imaging of microbial colonization in rock-some analytical aspects.

Raman imaging allows one to obtain spatially resolved chemical information in a nondestructive manner. Herein, we present analytical aspects of effective in situ and in vivo Raman imaging of algae and cyanobacteria from within their native rock habitats. Specifically, gypsum and halite inhabited by endolithic communities from the hyperarid Atacama Desert were analyzed. Raman imaging of these phototrophic colonization reveals a pigment composition within the aggregates that helps in understanding some of their adaptation strategies to survive in this harsh polyextreme environment. The study is focused on methodical aspects of Raman imaging acquisition and subsequent data processing. Point imaging is compared with line imaging in terms of their image quality, spatial resolution, spectral signal-to-noise ratio, time requirements, and risk of laser-induced sample alteration. The roles of excitation wavelength, exposure time, and step size of the imaging grid on successful Raman imaging results are also discussed. Graphical abstract.

Succession and Colonization Dynamics of Endolithic Phototrophs within Intertidal Carbonates.

Photosynthetic endolithic communities are common in shallow marine carbonates, contributing significantly to their bioerosion. Cyanobacteria are well known from these settings, where a few are euendoliths, actively boring into the virgin substrate. Recently, anoxygenic phototrophs were reported as significant inhabitants of endolithic communities, but it is unknown if they are euendoliths or simply colonize available pore spaces secondarily. To answer this and to establish the dynamics of colonization, nonporous travertine tiles were anchored onto intertidal beach rock in Isla de Mona, Puerto Rico, and developing endolithic communities were examined with time, both molecularly and with photopigment biomarkers. By 9 months, while cyanobacterial biomass and diversity reached levels indistinguishable from those of nearby climax communities, anoxygenic phototrophs remained marginal, suggesting that they are secondary colonizers. Early in the colonization, a novel group of cyanobacteria (unknown boring cluster, UBC) without cultivated representatives, emerged as the most common euendolith, but by 6 months, canonical euendoliths such as Plectonema (Leptolyngbya) sp., Mastigocoleus sp., and Pleurocapsalean clades displaced UBC in dominance. Later, the proportion of euendolithic cyanobacterial biomass decreased, as nonboring endoliths outcompeted pioneers within the already excavated substrate. Our findings demonstrate that endolithic cyanobacterial succession within hard carbonates is complex but can attain maturity within a year’s time.

Peculiar genomic traits in the stress-adapted cryptoendolithic Antarctic fungus Friedmanniomyces endolithicus

Friedmanniomyces endolithicus is a highly melanized fungus endemic to the Antarctic, occurring exclusively in endolithic communities of the ice-free areas of the Victoria Land, including the McMurdo Dry Valleys, the coldest and most hyper-arid desert on Earth and accounted as the Martian analog on our planet. F. endolithicus is highly successful in these inhospitable environments, the most widespread and commonly isolated species from these peculiar niches, indicating a high degree of adaptation. The nature of its extremo tolerance has not been previously studied. To investigate this, we sequenced genome of F. endolithicus CCFEE 5311 to explore gene content and genomic patterns that could be attributed to its specialization. The predicted functional potential of the genes was assigned by similarity to InterPro and CAZy domains. The genome was compared to phylogenetically close relatives which are also melanized fungi occurring in extreme environments including Friedmanniomyces simplex, Baudoinia panamericana, Acidomyces acidophilus, Hortaea thailandica and Hortaea werneckii. We tested if shared genomic traits existed among these species and hyper-extremotolerant fungus F. endolithicus. We found that some characters for stress tolerance such as meristematic growth and cold tolerance are enriched in F. endolithicus that may be triggered by the exposure to Antarctic prohibitive conditions.

Trophic Selective Pressures Organize the Composition of Endolithic Microbial Communities From Global Deserts.

Studies of microbial biogeography are often convoluted by extremely high diversity and differences in microenvironmental factors such as pH and nutrient availability. Desert endolithic (inside rock) communities are relatively simple ecosystems that can serve as a tractable model for investigating long-range biogeographic effects on microbial communities. We conducted a comprehensive survey of endolithic sandstones using high-throughput marker gene sequencing to characterize global patterns of diversity in endolithic microbial communities. We also tested a range of abiotic variables in order to investigate the factors that drive community assembly at various trophic levels. Macroclimate was found to be the primary driver of endolithic community composition, with the most striking difference witnessed between hot and polar deserts. This difference was largely attributable to the specialization of prokaryotic and eukaryotic primary producers to different climate conditions. On a regional scale, microclimate and properties of the rock substrate were found to influence community assembly, although to a lesser degree than global hot versus polar conditions. We found new evidence that the factors driving endolithic community assembly differ between trophic levels. While phototrophic taxa, mostly oxygenic photosynthesizers, were rigorously selected for among different sites, heterotrophic taxa were more cosmopolitan, suggesting that stochasticity plays a larger role in heterotroph assembly. This study is the first to uncover the global drivers of desert endolithic diversity using high-throughput sequencing. We demonstrate that phototrophs and heterotrophs in the endolithic community assemble under different stochastic and deterministic influences, emphasizing the need for studies of microorganisms in context of their functional niche in the community.

Altitude and fungal diversity influence the structure of Antarctic cryptoendolithic Bacteria communities.

Endolithic growth within rocks is a critical adaptation of microbes living in harsh environments where exposure to extreme temperature, radiation, and desiccation limits the predominant life forms, such as in the ice-free regions of Continental Antarctica. The microbial diversity of the endolithic communities in these areas has been sparsely examined. In this work, diversity and composition of bacterial assemblages in the cryptoendolithic lichen-dominated communities of Victoria Land (Continental Antarctica) were explored using a high-throughput metabarcoding approach, targeting the V4 region of 16S rDNA. Rocks were collected in 12 different localities (from 14 different sites), along a gradient ranging from 1000 to 3300 m a.s.l. and at a sea distance ranging from 29 to 96 km. The results indicate Actinobacteria and Proteobacteria are the dominant taxa in all samples and defined a 'core' group of bacterial taxa across all sites. The structure of bacteria communities is correlated with the fungal counterpart and among the environmental parameters considered, altitude was found to influence bacterial biodiversity, while distance from sea had no evident influence.

Sun Exposure Shapes Functional Grouping of Fungi in Cryptoendolithic Antarctic Communities.

Antarctic cryptoendolithic microbial communities dominate ice-free areas of continental Antarctica, among the harshest environments on Earth. The endolithic lifestyle is a remarkable adaptation to the exceptional environmental extremes of this area, which is considered the closest terrestrial example to conditions on Mars. Recent efforts have attempted to elucidate composition of these extremely adapted communities, but the functionality of these microbes have remained unexplored. We have tested for interactions between measured environmental characteristics, fungal community membership, and inferred functional classification of the fungi present and found altitude and sun exposure were primary factors. Sandstone rocks were collected in Victoria Land, Antarctica along an altitudinal gradient from 834 to 3100 m a.s.l.; differently sun-exposed rocks were selected to test the influence of this parameter on endolithic settlement. Metabarcoding targeting the fungal internal transcribed spacer region 1 (ITS1) was used to catalogue the species found in these communities. Functional profile of guilds found in the samples was associated to species using FUNGuild and variation in functional groups compared across sunlight exposure and altitude. Results revealed clear dominance of lichenized and stress-tolerant fungi in endolithic communities. The main variations in composition and abundance of functional groups among sites correlated to sun exposure, but not to altitude.

A New Niche for Anoxygenic Phototrophs as Endoliths.

Anoxygenic phototrophic bacteria (APBs) occur in a wide range of aquatic habitats, from hot springs to freshwater lakes and intertidal microbial mats. Here, we report the discovery of a novel niche for APBs: endoliths within marine littoral carbonates. In a study of 40 locations around Isla de Mona, Puerto Rico, and Menorca, Spain, 16S rRNA high-throughput sequencing of endolithic community DNA revealed the presence of abundant phylotypes potentially belonging to well-known APB clades. An ad hoc phylogenetic classification of these sequences enabled us to refine the assignments more stringently. Even then, all locations contained such putative APBs, often reaching a significant proportion of all phototrophic sequences. In fact, in some 20% of samples, their contribution exceeded that of oxygenic phototrophs, previously regarded as the major type of endolithic microbe in carbonates. The communities contained representatives of APBs in the Chloroflexales, various proteobacterial groups, and Chlorobi The most abundant phylotypes varied with geography: on Isla de Mona, Roseiflexus and Chlorothrix-related phylotypes dominated, whereas those related to Erythrobacter were the most common in Menorca. The presence of active populations of APBs was corroborated through an analysis of photopigments: bacteriochlorophylls were detected in all samples, bacteriochlorophyll c and a being most abundant. We discuss the potential metabolism and geomicrobial roles of endolithic APBs. Phylogenetic inference suggests that APBs may be playing a role as photoheterotrophs, adding biogeochemical complexity to our understanding of such communities. Given the global extent of coastal carbonate platforms, they likely represent a very large and unexplored habitat for APBs.IMPORTANCE Endolithic microbial communities from carbonates, which have been explored for over 2 centuries in predominantly naturalistic studies, were thought to be primarily composed of eukaryotic algae and cyanobacteria. Our report represents a paradigm shift in this regard, at least for the marine environment, demonstrating the presence of ubiquitous and abundant populations of APBs in this habitat. It raises questions about the role of these organisms in the geological dynamics of coastal carbonates, including coral reefs.

13C and 15N assimilation and organic matter translocation by the endolithic community in the massive coral Porites lutea.

Corals evolved by establishing symbiotic relationships with various microorganisms (the zooxanthellae, filamentous algae, cyanobacteria, bacteria, archaea, fungi and viruses), forming the ‘coral holobiont'. Among them, the endolithic community is the least studied. Its main function was considered to be translocation of photo-assimilates to the coral host, particularly during bleaching. Here, we hypothesize that (i) endolithic algae may show similar primary production rates in healthy or bleached corals by changing their pigment ratios, and therefore that similar production and translocation of organic matter may occur at both conditions and (ii) diazotrophs are components of the endolithic community; therefore, N2 fixation and translocation of organic nitrogen may occur. We tested these hypotheses in incubation of Porites lutea with 13C and 15N tracers to measure primary production and N2 fixation in coral tissues and endoliths. Assimilation of the 13C atom (%) was observed in healthy and bleached corals when the tracer was injected in the endolithic band, showing translocation in both conditions. N2 fixation was found in coral tissues and endolithic communities with translocation of organic nitrogen. Thus, the endolithic community plays an important role in supporting the C and N metabolism of the holobiont, which may be crucial under changing environmental conditions.

Life in Extreme Habitats: Diversity of Endolithic Microorganisms from Cold Desert Ecosystems of Eastern Pamir

ABSTRACT The aim of this study was to identify cyanobacteria diversity in rock communities from the cold desert ecosystem in Eastern Pamir Mountains (Tajikistan) and assess if the rock type and rock`s porosity can be indicators of microbial diversity in this extreme environment. Seven samples were collected in July 2015 from hillsides (ca 4000–4500 m a.s.l.) of the Eastern Pamir Mountains. Petrographic and scanning microscopy (SEM) allowed for the characterization of the rocks inhabited by endolithic communities as granite, gneiss and limestone with variable porosity. Based on next-generation sequencing (NGS) of amplicon of V3–V4 hypervariable region of 16S rRNA gene, we established that Actinobacteria, Proteobacteria and Cyanobacteria dominated the endolithic communities of microorganisms in the rocks studied, which distinguishes these communities from those described for other cold arid regions. Chroococcidiopsis and Leptolyngbya were dominant genera in the cyanobacterial communities according to cultur...

Carbon fixation from mineral carbonates

Photoautotrophs assimilate oxidized carbon obtained from one of two sources: dissolved or atmospheric. Despite its size, the pool of lithospheric carbonate is not known to be a direct source for autotrophy. Yet, the mechanism that euendolithic cyanobacteria use to excavate solid carbonates suggests that minerals could directly supply CO2 for autotrophy. Here, we use stable isotopes and NanoSIMS to show that the cyanobacterium Mastigocoleus testarum derives most of its carbon from the mineral it excavates, growing preferentially as an endolith when lacking dissolved CO2. Furthermore, natural endolithic communities from intertidal marine carbonate outcrops present carbon isotopic signatures consistent with mineral-sourced autotrophy. These data demonstrate a direct geomicrobial link between mineral carbonate pools and reduced organic carbon, which, given the geographical extent of carbonate outcrops, is likely of global relevance. The ancient fossil record of euendolithic cyanobacteria suggests that biological fixation of solid carbonate could have been relevant since the mid-Proterozoic.

Physicochemical and Biological Controls on Carbon and Nitrogen in Permafrost from an Ultraxerous Environment, McMurdo Dry Valleys of Antarctica

Little is known about the abundance and source of soil organic carbon and biogeochemical cycling in permafrost soils from the ultraxerous environment of the Dry Valleys of Antarctica. Here, we investigate the distribution, source and cycling of organic carbon, total nitrogen and carbonates in the icy permafrost soils of University Valley, Quartermain Mountains. Results indicate that organic carbon content is lowest in icy soils from the perennially cryotic zone (<40 μg g-1 dry soils) and higher in the icy soils from the seasonally non-cryotic zone, where the highest concentrations were found in the warmer-wetter section of the valley and near a frozen pond (up to 313 μg g-1 dry soils). The δ13Corg of organic carbon in the icy soils showed that it is derived from the weathering of Beacon Supergroup sandstone that hosts active endolithic communities. The C:N ratios in icy soils formed two populations: one with ratios <5 and the other with ratios near the Redfield ratios. The low C:N ratios suggest that physico-chemical processes dominates these soils, as supported by the absence of microbial activity and atmospherically-deposited NO3 with minimal post-deposition modification. The near Redfield C:N ratios can be explained by physical processes (translocation of SOC in the soils from snow meltwater) or balanced microbial activity. The latter is supported by the δ13CCaCO3 values of carbonates that suggest a contribution from microbially-respired endolith-derived organic matter, providing indirect evidence of heterotrophic activity in permafrost soils from an ultraxerous environment.

Diversity and stability of coral endolithic microbial communities at a naturally high pCO2 reef.

The health and functioning of reef-building corals is dependent on a balanced association with prokaryotic and eukaryotic microbes. The coral skeleton harbours numerous endolithic microbes, but their diversity, ecological roles and responses to environmental stress, including ocean acidification (OA), are not well characterized. This study tests whether pH affects the diversity and structure of prokaryotic and eukaryotic algal communities associated with skeletons of Porites spp. using targeted amplicon (16S rRNA gene, UPA and tufA) sequencing. We found that the composition of endolithic communities in the massive coral Porites spp. inhabiting a naturally high pCO2 reef (avg. pCO2 811μatm) is not significantly different from corals inhabiting reference sites (avg. pCO2 357μatm), suggesting that these microbiomes are less disturbed by OA than previously thought. Possible explanations may be that the endolithic microhabitat is highly homeostatic or that the endolithic micro-organisms are well adapted to a wide pH range. Some of the microbial taxa identified include nitrogen-fixing bacteria (Rhizobiales and cyanobacteria), algicidal bacteria in the phylum Bacteroidetes, symbiotic bacteria in the family Endozoicomoniaceae, and endolithic green algae, considered the major microbial agent of reef bioerosion. Additionally, we test whether host species has an effect on the endolithic community structure. We show that the endolithic community of massive Porites spp. is substantially different and more diverse than that found in skeletons of the branching species Seriatopora hystrix and Pocillopora damicornis. This study reveals highly diverse and structured microbial communities in Porites spp. skeletons that are possibly resilient to OA.

Microbial Endoliths on East Adriatic Limestone Coast: Morphological vs. Molecular Diversity

ABSTRACTFor the first time, a combined genotype-phenotype diversity analysis of endolithic microorganisms by pyrosequencing and microscopy was carried out across the intertidal and supratidal ranges of the Adriatic limestone coast. The coastal profiles represent ecotones between the sea and land, which express gradients of water supply, solar illumination, and salinity. The use of scanning electron microscopy imagery of resin casts showed that euendolith penetration remained shallow in the uppermost zones and was progressively deeper in the lower ranges where the water supply was more frequent. Microbial genotypes and phenotypes along the coastal profile showed large differences in dominance of taxa, but less in their diversity. The linkage between morphotypes observed along the profile and sequences was achieved by sequencing single cells/filaments, which were morphologically identified prior to their amplification. Molecular signatures of Hormathonema spp., Hyella caespitosa, Scytonema endolithicum, Solentia paulocellulare and Kyrtuthrix dalmatica were found on the profile and their specific placement was confirmed by morphological observations. Most sequences obtained were affiliated with Cyanobacteria (43%), Alphaproteobacteria (18%), and Gammaproteobacteria (7%). A total of 13 cyanobacterial morphospecies and 17 genotypes were found. Most cyanobacterial sequences belonged to the Pleurocapsales (33%), only 2% of the sequences belonged to the Nostocales and Oscillatoriales. The sequences corresponding to the cyanobacterial genus Hormathonema exhibited the highest abundances among all detected sequences, which is consistent with the microscopic observations in other parts of the world. The results of our investigation underline the importance of a combined approach in comparing the molecular data with microscopic observations in all phases of the study. Further RNA studies are needed to identify the actively growing parts of the endolithic community.

Diversity and mineral substrate preference in endolithic microbial communities from marine intertidal outcrops (Isla de Mona, Puerto Rico)

Abstract. Endolithic microbial communities are prominent features of intertidal marine habitats, where they colonize a variety of substrates, contributing to their erosion. Almost 2 centuries worth of naturalistic studies focused on a few true-boring (euendolithic) phototrophs, but substrate preference has received little attention. The Isla de Mona (Puerto Rico) intertidal zone offers a unique setting to investigate substrate specificity of endolithic communities since various phosphate rock, limestone and dolostone outcrops occur there. High-throughput 16S rDNA genetic sampling, enhanced by targeted cultivation, revealed that, while euendolithic cyanobacteria were dominant operational taxonomic units (OTUs), the communities were invariably of high diversity, well beyond that reported in traditional studies and implying an unexpected metabolic complexity potentially contributed by secondary colonizers. While the overall community composition did not show differences traceable to the nature of the mineral substrate, we detected specialization among particular euendolithic cyanobacterial clades towards the type of substrate they excavate but only at the OTU phylogenetic level, implying that close relatives have specialized recurrently into particular substrates. The cationic mineral component was determinant in this preference, suggesting the existence in nature of alternatives to the boring mechanism described in culture that is based exclusively on transcellular calcium transport.

Lichen colonization and associated deterioration processes in Pasargadae, UNESCO world heritage site, Iran

Knowledge on lichen and microbial colonization as well as associated biodeterioration processes of the stone cultural heritage is needed to establish proper conservation programs, but is still poor for stonework in semi-arid regions. In this study, lichen diversity was characterized on seven monumental buildings of the Pasargadae UNESCO-world heritage site (Iran). The risk of biodeterioration processes associated to lichen occurrence on two types of limestones, and the lichen resilience to mechanical cleaning intervention were examined. Physico-chemical substrate features and climatic conditions, combined with the agricultural surrounding and tourist disturbance, supported a pervasive colonization by species-poor epi- and endolithic communities, and fast recolonization processes by nitrophytic species after mechanical removal. The endolithic growth of some lichens and the penetration of hyphal structures of epilithic ones, examined by light and electron microscopy, were associated to stone disintegration and dissolution at the lichen-rock interface. Endolithic cyanobacteria were detected under lichen thalli, likely contributing to deterioration processes. Colonization and deterioration patterns did not appear peculiar with respect to previous investigations on similar communities in different climatic regions, and were mostly related to the different examined lithologies, indicating lichens as harmful biodeteriogens of the sedimentary rock materials used in the stone cultural heritage of semi-arid regions.