A novel Antarctic microbial endolithic community within gypsum crusts

A novel endolithic microbial habitat is described from a climatically extreme site at Two Step Cliffs, Alexander Island, Antarctic Peninsula (71 degrees 54'S, 68 degrees 13'W). Small endolithic colonies (<3 mm in diameter) are found within the translucent gypsum crust that forms on the surface of sandstone boulders. Gypsum crusts are found on ice-free rocks throughout the Antarctic and therefore offer potential colonization sites at more inhospitable locations, including sites at higher latitudes. Cyanobacterial, bacterial and fungal components were cultured from the crust material and have been identified as Chloroglea sp., Sphingomonas sp. and Verticillium sp. respectively. A non-cultured, black-pigmented fungus was also found. Cyanobacterial primary productivity is low: at depths of 1.2 and 2.5 mm within the crust, estimates of possible cell divisions per year were < 38 and four respectively. This microniche is proposed to provide protection from desiccation, rapid temperature variation and UV radiation flux while allowing penetration of photosynthetically active radiation (PAR) for utilization by phototrophs. The endolithic communities are less extensive than those of the Dry Valleys, continental Antarctica, probably owing to only recent deglaciation (<7000 year ago).     

Phylogenetic diversity of endolithic bacteria in Bole granite rock in Xinjiang

The endolithic environment is a ubiquitous microbial habitat for microorganisms, such as lichens, Cyanobacteria and fungi, and it provides mineral nutrients and growth surfaces. In extremely environments, such as hot and cold desert, endolithic communities are often the main form of life. More recently, endolithic microbial communities have been observed inhabiting a variety of rock types ranging from hard granite to porous rocks such as basalt, dolomite, limestone, sandstone and granites. Regardless of geographic location and rock type, each of these habitats is characterized by a subsurface microclimate that prevents endolithic microorganisms growth. Photosynthesis-based endolithic microbial communities commonly inhabit the outer millimeters to centimeters of rocks exposed to the surface. The ability to fix carbon dioxide and in some cases atmospheric dinitrogen, gives the Cyanobacteria a clear competitive advantage over heterotrophic bacteria, so it is been called the main primary producer. Light quality and intensity appear to be the main determinant of the maximum depth to which growth occurs in endolithic phototrophic communities. Valleys of Fantastic Rocks in Bole is close to Alashankou Port of Xinjiang which belongs to extreme continental climate. In order to investigate the structure, composition and diversity of endolithic bacterial community in exposed granitic porphyry in the Valleys of Fantastic Rocks, environmental DNA was directly extracted from granite rock, the 16S rRNA genes were amplified from the total DNA by PCR with bacterial-specific primers, and an endolithic bacterial clone library was constructed. Positive clones were randomly selected from the library and identified by Restriction Fragment Length Polymorphism (RFLP). The unique rRNA types clones were sequenced, analysised and then constructed phylogenetic tree. In total, 129 positive clones were screened and grouped into 46 operational taxonomic unites (OTUs). The clone coverage C value was 89.15%, indicating that most of the estimated endolithic bacterial diversity was sampled. BLAST analysis indicated that 46 OTUs were divided into seven phyla (Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Cyanobacteria, Planctomycetes, Proteobacteria) and five unknown groups. Cyanobacteria (43%), especially the Gp I, form the functional basis for an endolithic bacteria community which contain a wide spectrum species of chemotrophic bacteria (33%) with mainly Actinobacteria, α-Proteobacteria, Acidobacteria. Additionally, most clones that derived from the endolithic bacteria clone library showed high similarity to the sequence deposited in GenBank database with 97%–99%. Besides, 35% of the clones showed less than 97% of sequence similarity, of which 12% sequences were affiliated to genus Rubrobacter. The results suggested that endolithic bacteria in Valleys of Fantastic Rocks in Xinjiang were highly diverse in species richness, and maybe have a diversity of potential novel species and lineages.     

The Extremophile Endolithella mcmurdoensis gen. et sp. nov. (Trebouxiophyceae,Chlorellaceae), A New Chlorella-like Endolithic Alga From Antarctica

The McMurdo Dry Valleys constitute the largest ice-free region of Antarctica and one of the most extreme deserts on Earth. Despite the low temperatures, dry and poor soils and katabatic winds, some microbes are able to take advantage of endolithic microenvironments, inhabiting the pore spaces of soil and constituting photosynthesis-based communities. We isolated a green microalga, Endolithella mcmurdoensis gen. et sp. nov, from an endolithic sandstone sample collected in the McMurdo Dry Valleys (Victoria Land, East Antarctica) during the K020 expedition, in January 2013. The single non-axenic isolate (E. mcmurdoensis LEGE Z-009) exhibits cup-shaped chloroplasts, electron-dense bodies, and polyphosphate granules but our analysis did not reveal any diagnostic morphological characters. On the basis of phylogenetic analysis of the 18S rRNA (SSU) gene, the isolate was found to represent a new genus within the family Chlorellaceae.     

Endolithic microbial composition in Helliwell Hills,a newly investigated Mars-like area in Antarctica

The diversity and composition of Antarctic cryptoendolithic microbial communities in the Mars-analogue site of Helliwell Hills (Northern Victoria Land, Continental Antarctica) are investigated, for the first time, applying both culture-dependent and high-throughput sequencing approaches. The study includes all the domains of the tree of life: Eukaryotes, Bacteria and Archaea to give a complete overview of biodiversity and community structure. Furthermore, to explore the geographic distribution of endoliths throughout the Victoria Land (Continental Antarctica), we compared the fungal and bacterial community composition and structure of endolithically colonized rocks, collected in >30 sites in 10 years of Italian Antarctic Expeditions. Compared with the fungi and other eukaryotes, the prokaryotic communities were richer in species, more diverse and highly heterogeneous. Despite the diverse community compositions, shared populations were found and were dominant in all sites. Local diversification was observed and included prokaryotes as members of Alphaproteobacteria and Crenarchaeota (Archaea), the last detected for the first time in these cryptoendolithic communities. Few eukaryotes, namely lichen-forming fungal species as Lecidella grenii, were detected in Helliwell Hills only. These findings suggest that geographic distance and isolation in these remote areas may promote the establishment of peculiar locally diversified microorganisms.     

Phylogenetic Composition of Rocky Mountain Endolithic Microbial Ecosystems

The endolithic environment, the pore space in rocks, is a ubiquitous microbial habitat. Photosynthesis-based endolithic communities inhabit the outer few millimeters to centimeters of rocks exposed to the surface. Such endolithic ecosystems have been proposed as simple, tractable models for understanding basic principles in microbial ecology. In order to test previously conceived hypotheses about endolithic ecosystems, we studied selected endolithic communities in the Rocky Mountain region of the United States with culture-independent molecular methods. Community compositions were determined by determining rRNA gene sequence contents, and communities were compared using statistical phylogenetic methods. The results indicate that endolithic ecosystems are seeded from a select, global metacommunity and form true ecological communities that are among the simplest microbial ecosystems known. Statistical analysis showed that biogeographical characteristics that control community composition, such as rock type, are more complex than predicted. Collectively, results of this study support the idea that patterns of microbial diversity found in endolithic communities are governed by principles similar to those observed in macroecological systems.     

Phylogenetic composition of Rocky Mountain endolithic microbial ecosystems

The endolithic environment, the pore space in rocks, is a ubiquitous microbial habitat. Photosynthesis-based endolithic communities inhabit the outer few millimeters to centimeters of rocks exposed to the surface. Such endolithic ecosystems have been proposed as simple, tractable models for understanding basic principles in microbial ecology. In order to test previously conceived hypotheses about endolithic ecosystems, we studied selected endolithic communities in the Rocky Mountain region of the United States with culture-independent molecular methods. Community compositions were determined by determining rRNA gene sequence contents, and communities were compared using statistical phylogenetic methods. The results indicate that endolithic ecosystems are seeded from a select, global metacommunity and form true ecological communities that are among the simplest microbial ecosystems known. Statistical analysis showed that biogeographical characteristics that control community composition, such as rock type, are more complex than predicted. Collectively, results of this study support the idea that patterns of microbial diversity found in endolithic communities are governed by principles similar to those observed in macroecological systems.     

Fundamental drivers for endolithic microbial community assemblies in the hyperarid Atacama Desert

In hyperarid deserts, endolithic microbial communities colonize the rocks’ interior as a survival strategy. Yet, the composition of these communities and the drivers promoting their assembly are still poorly understood. We analysed the diversity and community composition of endoliths from four different lithic substrates – calcite, gypsum, ignimbrite and granite – collected in the hyperarid zone of the Atacama Desert, Chile. By combining microscopy, mineralogy, spectroscopy and high throughput sequencing, we found these communities to be highly specific to their lithic substrate, although they were all dominated by the same four main phyla, Cyanobacteria, Actinobacteria, Chloroflexi and Proteobacteria. Our finding indicates a fine scale diversification of the microbial reservoir driven by substrate properties. The data suggest that the overall rock chemistry and the light transmission properties of the substrates are not essential drivers of community structure and composition. Instead, we propose that the architecture of the rock, i.e., the space available for colonization and its physical structure, linked to water retention capabilities, is ultimately the driver of community diversity and composition at the dry limit of life.     

Community structure of epilithic and endolithic algae and cyanobacteria on cliffs of the Niagara Escarpment

Abstract. In order to understand how communities of rock-inhabiting micro-organisms are spatially organized, rock samples and environmental variables were collected from five cliff sites in Ontario, Canada. Algae and cyanobacteria were extracted from the epilithic zone (rock surface) and endolithic zone (subsurface) of 180 samples, and the frequency of each taxon (genus or larger) was determined. Multivariate statistical analyses were used to determine (1) the variation in community composition on different spatial scales; (2) differences in community composition between surface and subsurface; and (3) the environmental constraints of community structure. 13 taxa of cyanobacteria and 12 taxa of eukaryotic algae were identified in the endolithic zone, and 17 and 14 in the epilithic zone, respectively. The most frequent taxa were similar in both zones, but MANOVA of species frequencies showed significant differences between endolithic and epilithic communities. DCA and CCA showed that geographic-scale variation in community composition was the dominant trend in the data for both surface and subsurface. Cyanobacteria and eukaryotic algae showed a clear separation on the first ordination axis. When the geographic-scale variation was removed in a partial ordination, the separation of organisms by kingdoms disappeared and epi- and endolithic ordinations were no longer similar. Light then appeared to control the endolithic species composition, while other factors, possibly moisture-related, were suggested for the epilithic community. Despite biomass and productivity that varies mostly at scales of < 1m², we conclude here that species composition and its environmental constraints vary at small as well as larger scales.     

Lithic cyanobacterial communities in the polyextreme Sahara Desert: implications for the search for the limits of life

The hyperarid Sahara Desert presents extreme and persistent dry conditions with a limited number of hours during which the moisture availability, temperature and light allow phototrophic growth. Some cyanobacteria can live in these hostile conditions by seeking refuge under (hypolithic) or inside (endolithic) rocks, by colonizing porous spaces (cryptoendoliths) or fissures in stones (chasmoendoliths). Chroococcidiopsis spp. have been reported as the dominant or even the only phototrophs in these hot desert lithic communities. However, the results of this study reveal the high diversity of and variability in cyanobacteria among the sampled habitats in the Sahara Desert. The chasmoendolithic samples presented high coccoid cyanobacteria abundances, although the dominant cyanobacteria were distinct among different locations. A high predominance of a newly described cyanobacterium, Pseudoacaryochloris sahariense, was found in hard, compact, and more opaque stones with cryptoendolithic colonization. On the other hand, the hypolithic samples were dominated by filamentous, non-heterocystous cyanobacteria. Thermophysiological bioassays confirmed desiccation and extreme temperature tolerance as drivers in the cyanobacterial community composition of these lithic niches. The results of the present study provide key factors for understanding life strategies under polyextreme environmental conditions. The isolated strains, especially the newly described cyanobacterium P. sahariense, might represent suitable microorganisms in astrobiology studies aimed at investigating the limits of life.     

Endolithic Phototrophs from an Active Geothermal Region in New Zealand

Endolithic photosynthetic communities in geothermal siliceous rocks in the area of Rotorua, New Zealand, were analysed using traditional microbiological and molecular biology techniques. Rock surface temperatures varied between 40°C and 60°C. Major endoliths included cyanobacteria of subsections I, II and V. Few subsection IV organisms were found and subsection III (filamentous, non-heterocystous) cyanobacteria were present only as epiliths or chasmoendoliths. Therefore, the endolithic cyanobacterial communities in these sites resembled assemblages as reported for carbonate rocks in other geothermal regions. Cells of the rhodophyte family Cyanidiaceae were detected within rock at various sites. Some of these phototrophic organisms were associated with mineral (presumably silica) deposits and could be important geological agents in siliceous rock deposition.     

Diversity of endolithic fungal communities in dolomite and limestone rocks from Nanjiang Canyon in Guizhou karst area, China

The endolithic environment, the tiny pores and cracks in rocks, buffer microbial communities from a number of physical stresses, such as desiccation, rapid temperature variations, and UV radiation. Considerable knowledge has been acquired about the diversity of microorganisms in these ecosystems, but few culture-independent studies have been carried out on the diversity of fungi to date. Scanning electron microscopy of carbonate rock fragments has revealed that the rock samples contain certain kinds of filamentous fungi. We evaluated endolithic fungal communities from bare dolomite and limestone rocks collected from Nanjiang Canyon (a typical karst canyon in China) using culture-independent methods. Results showed that Ascomycota was absolutely dominant both in the dolomite and limestone fungal clone libraries. Basidiomycota and other eukaryotic groups (Bryophyta and Chlorophyta) were only detected occasionally or at low frequencies. The most common genus in the investigated carbonate rocks was Verrucaria. Some other lichen-forming fungi (e.g., Caloplaca, Exophiala, and Botryolepraria), Aspergillus, and Penicillium were also identified from the rock samples. The results provide a cross-section of the endolithic fungal communities in carbonate rocks and help us understand more about the role of microbes (fungi and other rock-inhabiting microorganisms) in rock weathering and pedogenesis.     

Antarctic terrestrial ecosystems: The Vestfold Hills in context

Antarctic terrestrial ecosystems are briefly described, with emphasis on Signy Island in the maritime antarctic region, and the McMurdo oasis, southern Victoria Land, and Vestfold Hills in the continental antarctic region.As the largest and best known coastal ice-free oasis, the Vestfold Hills contain excellent examples of terrestrial sublithic, epilithic, chasmoendolithic, epiphytic and terricolous algal communities, as well as epilithic, endolithic, and epiphytic lichen communities, and moss communities. Many of the numerous lakes support dense communities of aquatic algae.     

Microscopic and biomolecular complementary approaches to characterize bioweathering processes at petroglyph sites from the Negev Desert,Israel

Throughout the Negev Desert highlands, thousands of ancient petroglyphs sites are susceptible to deterioration processes that may result in the loss of this unique rock art. Therefore, the overarching goal of the current study was to characterize the composition, diversity and effects of microbial colonization of the rocks to find ways of protecting these unique treasures. The spatial organization of the microbial colonizers and their relationships with the lithic substrate were analysed using scanning electron microscopy. This approach revealed extensive epilithic and endolithic colonization and close microbial–mineral interactions. Shotgun sequencing analysis revealed various taxa from the archaea, bacteria and some eukaryotes. Metagenomic coding sequences (CDS) of these microbial lithobionts exhibited specific metabolic pathways involved in the rock elements' cycles and uptake processes. Thus, our results provide evidence for the potential participation of the microorganisms colonizing these rocks during different solubilization and mineralization processes. These damaging actions may contribute to the deterioration of this extraordinary rock art and thus threaten this valuable heritage. Shotgun metagenomic sequencing, in conjunction with the in situ scanning electron microscopy study, can thus be considered an effective strategy to understand the complexity of the weathering processes occurring at petroglyph sites and other cultural heritage assets.     

Studies on the life cycle of Lemanea using natural and artificial substrates

A comparison of the ability ofLemanea to colonize a variety of artificial and natural substrates indicated that limestone and sandstone were most densely colonized. Germination ofLemanea carpospores and establishment of the plant was succesfully accomplished in the laboratory using coarse sandstone rock units as a substrate. Subsequent transplanting of these colonized units to the original site of collection on the River Usk was also succesfull. Similar clean, prepared rock units were used for colonization studies at the same river site and the life cycle stages compared with those on the natural sandstone rocks and on the laboratory colonized rock units.     

Endolithic Microbial Colonization of Limestone in a High-altitude Arid Environment

The morphology of endolithic colonization in a limestone escarpment and surrounding rocky debris (termed float) at a high-altitude arid site in central Tibet was documented using scanning electron microscopy. Putative lichenized structures and extensive coccoid bacterial colonization were observed. Absolute and relative abundance of rRNA gene signatures using real-time quantitative polymerase chain reaction and phylogenetic analysis of environmental phylotypes were used to characterize community structure across all domains. Escarpment endoliths were dominated by eukaryotic phylotypes suggestive of lichenised associations (a Trebouxia lichen phycobiont and Leptodontidium lichen mycobiont), whereas float endoliths were dominated by bacterial phylotypes, including the cyanobacterium Chroococcidiopsis plus several unidentified beta proteobacteria and crenarchaea. Among a range of abiotic variables tested, ultraviolet (UV) transmittance by rock substrates was the factor best able to explain differences in community structure, with eukaryotic lichen phylotypes more abundant under conditions of greater UV-exposure compared to prokaryotes. Variously pigmented float rocks did not support significantly different communities. Estimates of in situ carbon fixation based upon ¹⁴C radio-labelled bicarbonate uptake indicated endolithic productivity of approximately 2.01 g C/m²/year^?1, intermediate between estimates for Antarctic and temperate communities.     

Life, decay and fossilisation of endolithic microorganisms from the Ross Desert, Antarctica

The adaptation and survival of the endolithic microorganisms that colonise the near-surface layer of porous sandstone rock in the Ross Desert (Antarctica) depend upon a precarious equilibrium of biological, geological and climatic factors. Any unfavourable change in external conditions can result in the death and disappearance of microscopic organisms, and this may be followed by trace microfossil formation. The sequence of events leading to the extinction of life in the Antarctic desert is considered to be a terrestrial analogue of the disappearance of possible life on early Mars. The present paper reviews the current state of knowledge on the endolithic microorganisms of the Ross Desert with particular reference to their decay and fossilisation processes. Ideas for in situ further research on this microbial ecosystem are also proposed, including several new microscopy techniques such as CLSM, LTSEM, SEM-BSE and EDS. Preliminary images are presented and it is proposed that, for the first time, such techniques will permit the in situ study of the ecology of Antarctic lithobiontic microorganisms and the identification and characterisation of fossilised traces of past life.     

Effect of environmental parameters on biodiversity of the fungal component in lithic Antarctic communities

Extremophiles - A wide sampling of rocks, colonized by microbial epi–endolithic communities, was performed along an altitudinal gradient from sea level to 3600&nbsp;m asl and sea distance...     

Geomicrobiology of the ocean crust: a role for chemoautotrophic Fe-bacteria

The delicate balance of the major global biogeochemical cycles greatly depends on the transformation of Earth materials at or near its surface. The formation and degradation of rocks, minerals, and organic matter are pivotal for the balance, maintenance, and future of many of these cycles. Microorganisms also play a crucial role, determining the transformation rates, pathways, and end products of these processes. While most of Earth's crust is oceanic rather than terrestrial, few studies have been conducted on ocean crust transformations, particularly those mediated by endolithic (rock-hosted) microbial communities. The biology and geochemistry of deep-sea and sub-seafloor environments are generally more complicated to study than in terrestrial or near-coastal regimes. As a result, fewer, and more targeted, studies usually homing in on specific sites, are most common. We are studying the role of endolithic microorganisms in weathering seafloor crustal materials, including basaltic glass and sulfide minerals, both in the vicinity of seafloor hydrothermal vents and off-axis at unsedimented (young) ridge flanks. We are using molecular phylogenetic surveys and laboratory culture studies to define the size, diversity, physiology, and distribution of microorganisms in the shallow ocean crust. Our data show that an unexpected diversity of microorganisms directly participate in rock weathering at the seafloor, and imply that endolithic microbial communities contribute to rock, mineral, and carbon transformations.     

Epilithic and Endolithic Bacterial Communities in Limestone from a Maya Archaeological Site

Biodeterioration of archaeological sites and historic buildings is a major concern for conservators, archaeologists, and scientists involved in preservation of the world's cultural heritage. The Maya archaeological sites in southern Mexico, some of the most important cultural artifacts in the Western Hemisphere, are constructed of limestone. High temperature and humidity have resulted in substantial microbial growth on stone surfaces at many of the sites. Despite the porous natureof limestone and the common occurrence of endolithic microorganisms in many habitats, little is known about the microbial flora living inside the stone. We found a large endolithic bacterial community in limestone from the interior of the Maya archaeological site Ek' Balam. Analysis of 16S rDNA clones demonstrated disparate communities (endolithic: >80% Actinobacteria, Acidobacteria, and Low GC Firmicutes; epilithic: >50% Proteobacteria). The presence of differing epilithic and endolithic bacterial communities may be a significant factor for conservation of stone cultural heritage materials and quantitative prediction of carbonate weathering.     

Nitrogen economy of endolithic microbial communities in hot and cold deserts

The source of combined nitrogen in endolithic microbial communities was studied in samples from desert localities in North and South America, the Middle East, South Africa, and Antarctica. Nitrogen fixation (acetylene reduction) seems to occur only exceptionally. Evidence suggests that, in general, the nitrogen source for endolithic microorganisms in deserts is abiotically fixed nitrogen produced by atmospheric electric discharges (lightning or aurorae), conveyed to the rock by atmospheric precipitation. Nitrogen is apparently not a limiting factor in these low-productivity communities. An incomplete nitrogen cycle seems to be present which includes the following pathways: supply of nitrates and ammonia from the atmosphere; decomposition of organic matter to ammonia; reassimilation of ammonia; ammonia volatilization; loss of organic matter through weathering (only in certain Antarctic rocks); biological nitrogen fixation (exceptional).