Figure 5 - uploaded by Luigimaria Borruso
Content may be subject to copyright.
Pie-charts displaying the proportions of proteins annotated within each COG category (upper part of the picture), and histograms of aggregated data for MAGs retrieved from varnish (orange) and non-varnish (blue) samples.
Source publication
Rock varnish is a microbial habitat, characterized by thin (5-500 μm) and shiny coatings of iron (Fe) and manganese (Mn) oxides associated with clay minerals. This structure is well studied by geologists, and recently there have been reports about the taxonomical composition of its microbiome. In this study, we investigated the rock varnish microbi...
Contexts in source publication
Context 1
... compared to non-varnish. Those results were consistent with our previous study based on 16S (i.e. Chloroflexi, represented mostly by the species Ktedonobacter racemifer, Esposito et al. 2015), However, this study revealed different structure of the abundant species that may have been overlooked by the 16S rRNA metabarcoding approach (Fig. 3 and Fig. S5, Supporting Information). For example, in the present study we found among the varnish biomarkers Acidiphilium cryptum, a heterotrophic alpha-proteobacterium previously isolated from acidic rocks and Rubrobacter xylanophilus, which was consistently found in previous studies on rock varnish microbiome ( Kuhlman et al. 2006a;Zhang et al. 2012;Lang-Yona et al. ...
Context 2
... assembled mainly from varnished surfaces ( Table 2). None of the genome bins could be classified at the genus or species level, meaning every bin had an ANI below 85% to the known closest relative. Sequences of the genome bins are available as Supplementary Files 2. Most proteins encoded in the MAGs genomes were classified with unknown functions (Fig. 5), despite this, proteins connected to amino-acid and carbohydrate metabolism and transport, proteins involved in replication and repair machinery and outer structures were represented with an abundance >5% in all genomes. No significant differences were found in the abundance of proteins classified in any given COG category in genomes ...
Similar publications
Motivation:
Sequencing technologies allow the sequencing of microbial communities directly from the environment without prior culturing. Because assembly typically produces only genome fragments, also known as contigs, it is crucial to group them into putative species for further taxonomic profiling and down-streaming functional analysis. Taxonomi...
Citations
... Other cyanobacteria strains were already found to contain these genes (Ng and Pakrasi, 2001;Earl et al., 2002;Cassier-Chauvat et al., 2016). Interestingly, recent metagenomic analyses of microorganisms making up "desert varnish" have uncovered a similar gene cluster indicating similar capabilities in these organisms (Nir et al., 2021;Esposito et al., 2019;Lang-Yona et al., 2018). Understanding the cyanobacterial mechanism of repair could provide information about its stress protection pathways (Rajaram et al., 2020). ...
... This finding agrees with a recent phylogenetic analysis of 322 GST sequences retrieved from 126 cyanobacteria strains. The glutathione gene cluster was found in additional members of the cyanobacterial phylum (Shylaja Naciyar et al., 2020), including in a recent rock varnish microbiome metagenomic investigation (Esposito et al., 2019). According to Oren (2007) and Roberts (2005), cells with high quantities of glutathione molecules have low water potentials in their cytoplasm that help the cell resist desiccation stress. ...
The Negev petroglyphs are considered valuable cultural heritage sites, but unfortunately, they are exposed to deterioration processes caused by anthropogenic and natural forces. Despite the many studies that have already pointed to the role of cyanobacteria in biogenic rock weathering, the knowledge involved in the process is still lacking. In this study, a cyanobacterial strain was isolated from the Negev Desert petroglyphs aiming to reveal its involvement in geochemical cycles and in the weathering processes of the rock substrate. The strain was characterized using morphological, molecular, and microscopic studies. The morphological research revealed a green-bluish, bundle-forming filamentous strain characterized by trichomes embedded in a common sheath. A combination of Nanopore and Illumina sequencing technologies facilitated the assembly of a near-complete genome containing 5,458,034 base pairs. A total of 5027 coding sequences were revealed by implementing PROKKA software. Annotation of five replicas of the 16S ribosomal RNA genes revealed that the Negev cyanobacteria isolate is closely (99.73 %) related to Trichocoleus desertorum LSB90_MW403957 isolated from the Sahara Desert, Algeria. The local strain was thus named Trichocoleus desertorum NBK24 CP116619. Several gene sequences that code for possible environmental adaptation mechanisms were found. Our study also identified genes for membrane transporters involved in the exchange of chemical elements, suggesting a possible interaction with rock minerals. Microscopic observations of T. desertorum NBK24 CP116619 infected onto calcareous stone slabs under laboratory conditions demonstrated the effect of the isolated cyanobacteria on stone surface degradation. In conclusion, the findings of this study further our understanding of terrestrial cyanobacterial genomes and functions and highlight the role of T. desertorum NBK24 CP116619 in stone weathering processes. This information may contribute to the creation of efficient restoration strategies for stone monuments affected by cyanobacteria.
... Under different climate conditions, the progress of the physical and chemical deterioration is significantly accelerated by the microbial activities, especially biofilm formation, pigmentation, invasion, and the elution of the stone components by biochemical metabolites produced by the colonizing microorganisms (Sand and Bock, 1991;Papida et al., 2000;Warscheid and Braams, 2000;McNamara et al., 2006;Zhang et al., 2019;Liu et al., 2020). Previous studies have demonstrated that stone surfaces are a habitat capable of supporting a rich diversity of bacteria, archaea and eukarya, including fungi (Lan et al., 2010;Gaylarde et al., 2012;Cutler et al., 2013;Kusumi et al., 2013;Esposito et al., 2019;Ding et al., 2021). At the Angkor site, sulfate formed by microbial oxidation of elemental sulfur (S 0 ) and/or H 2 S in bat droppings is one of the major factors contributing to stone deterioration (Uchida et al., 2000;Hosono et al., 2006;Li et al., 2008;Siedel et al., 2010). ...
... [33]. The threshold on the logarithmic LDA score for discriminative features is generally set to 2 and was set to 2.5 in a rock varnish study [34]; this study set it to 4 to only focus on biomarkers with large statistical differences between samples. ...
The diversity of microorganisms associated with speleological sources has mainly been studied in limestone caves, while studies in silicate caves are still under development. Here, we profiled the microbial diversity of opal speleothems from a silicate cave in Guiana Highlands. Bulk DNAs were extracted from three speleothems of two types, i.e., one soft whitish mushroom-like speleothem and two hard blackish coral-like speleothems. The extracted DNAs were amplified for sequencing the V3–V4 region of the bacterial 16S rRNA gene by MiSeq. A total of 210,309 valid reads were obtained and clustered into 3184 phylotypes or operational taxonomic units (OTUs). The OTUs from the soft whitish speleothem were mostly affiliated with Acidobacteriota, Pseudomonadota (formerly, Proteobacteria), and Chloroflexota, with the OTUs ascribed to Nitrospirota being found specifically in this speleothem. The OTUs from the hard blackish speleothems were similar to each other and were mostly affiliated with Pseudomonadota, Acidobacteriota, and Actinomycetota (formerly, Actinobacteria). These OTU compositions were generally consistent with those reported for limestone and silicate caves. The OTUs were further used to infer metabolic features by using the PICRUSt bioinformatic tool, and membrane transport and amino acid metabolism were noticeably featured. These and other featured metabolisms may influence the pH microenvironment and, consequently, the formation, weathering, and re-deposition of silicate speleothems.
... High relative abundances of Ktedonobacteria are commonly found in extreme environments [44,45]. However, the enormous variety of environmental conditions (high and low temperatures, nutrient-rich and oligotrophic substrates, high and low pH), where Ktedonobacteria class can thrive, suggests that these Gram-positive, aerobic and mycelia-forming actinomycetes-like bacteria could be able to produce secondary metabolites, to survive in extremely different conditions and different geochemical rock surfaces [46,47]. In all samples, few reads were assigned to Thermosporothrix, which belonged to Ktedonobacteria. ...
The diversity and composition of endolithic bacterial diversity of several locations in McMurdo Dry Valleys (Continental Antarctica) were explored using amplicon sequencing, targeting the V3 and V4 of the 16S region. Despite the increasing interest in edaphic factors that drive bacterial community composition in Antarctic rocky communities, few researchers focused attention on the direct effects of sun exposure on bacterial diversity; we herein reported significant differences in the northern and southern communities. The analysis of β-diversity showed significant differences among sampled localities. For instance, the most abundant genera found in the north-exposed rocks were Rhodococcus and Blastococcus in Knobhead Mt.; Ktedonobacter and Cyanobacteria Family I Group I in Finger Mt.; Rhodococcus and Endobacter in University Valley; and Segetibacter and Tetrasphaera in Siegfried Peak samples. In south-exposed rocks, instead, the most abundant genera were Escherichia/Shigella and Streptococcus in Knobhead Mt.; Ktedonobacter and Rhodococcus in Finger Mt.; Ktedonobacter and Roseomonas in University Valley; and Blastocatella, Cyanobacteria Family I Group I and Segetibacter in Siegfried Peak. Significant biomarkers, detected by the Linear discriminant analysis Effect Size, were also found among north-and south-exposed communities. Besides, the large number of positive significant co-occurrences may suggest a crucial role of positive associations over competitions under the harsher conditions where these rock-inhabiting microorganisms spread. Although the effect of geographic distances in these extreme environments play a significant role in shaping biodiversity, the study of an edaphic factor, such as solar exposure, adds an important contribution to the mosaic of microbial biodiversity of Antarctic bacterial cryptoendolithic communities.
... Now, metagenomic analyses have begun to be applied to these ecological systems; these can lead to the identification of functional genes in the microbial population, allowing us to detect cells with the abilities to produce chelating molecules, to metabolise sulfur, manganese, nitrogen, and to produce relevant organic acids and pigments. Esposito et al. 83 used shotgun metagenomic sequencing to analyse the microbial population of a siliceous rock varnish in the Matsch Valley, Italy. Interestingly, they found a high number of Archaea in the varnish. ...
Dimension stone is natural rock prepared for building use. It is rapidly colonised by microorganisms that cause discoloration (mainly cyanobacteria, algae and fungi) and structural damage. Microbial mobilisation of ions leads to new superficial or internal deposits, weakening the structure. Cyanobacteria and fungi may penetrate, filling pores or creating new spaces. Lichens, fungus/phototroph associations, colonise surfaces and damage stone through ingrowing rhizines and acid production. Initial degradation produces conditions suitable for germination of seeds of higher plants and further destruction. Emerging techniques to elucidate stone-cell interactions and control of initial biofilm formation that eventuates in stone disintegration are discussed.
... This process affects many types of historical rock artifacts as well as natural rocks and stones (Sabev et al., 2006;Sterflinger and Piñar, 2013). Different groups of microorganisms, including bacteria, fungi, and archaea, in addition to algae and lichens, very often organized to form biofilm, contribute to the deterioration of stone monuments around the world under different conditions (outdoor, indoor, sheltered areas) (Cutler et al., 2013;Esposito et al., 2019;Gaylarde et al., 2012;Kusumi et al., 2013;Lan et al., 2010;Sterflinger and Piñar, 2013) as due to different microclimatic conditions and to the bioreceptivity of stone. The way microorganisms can act as biodeteriogens of rocks and stones is very different, such as patina formations, pigment release, desert varnish, lichenic crust, biopitting, dissolution and biomineralization processes as described in literature (Antonelli et al., 2020;Gorbushina, 2007;Krumbein, 2003) and in the international glossary (Vergès-Belmin, 2008). ...
Microorganisms can accelerate the deterioration of stone monuments. In this study, we used next-generation sequencing (Illumina MiSeq PE300 Platform) to investigate the microbial biofilm communities that have developed on sandstone in two famous Buddhist cave temples, the Maijishan Grottoes and Tiantishan Grottoes, located on the historical Silk Road in western China. We found high bacterial diversity and relatively low eukaryota diversity based on 16S and 18S ribosomal RNA (rRNA) sequencing analysis. The dominant bacterial groups were Cyanobacteria, Actinobacteria, Proteobacteria, Bacteroidetes, and Chloroflexi. The dominant eukaryota were Ascomycota, Basidiomycota, and Chytridiomycota. The most dominant genes among the bacteria were from Cyanobacteria (unclassified and no rank), Pseudonocardia, Kribbella, and Rubrobacter; the dominant fungal genes were from unclassified Lecanorales and Capnodiales (unclassified and norank). These microbes form biofilms that will contribute to biodeterioration of the underlying sandstone. Combining with field monitoring and microscopic analysis, we determined that high bioreceptivity of the sandstone and locally available water were two important exogenous and endogenous factors that promoted microbial colonization, proliferation, and subsequent biofilm formation. The aforementioned microbes usually coexisted on the sandstone surfaces by building an inter-connected and dynamic community capable of adapting to and resisting the harsh local environmental conditions to survive and undergo succession.
... These results confirmed that most of the non-photosynthetic prokaryotic cells observed by SEM could correspond to bacteria cells. These findings are consistent with the results obtained recently by other authors, using shotgun metagenomics analysis on microbial communities of oligotrophic environments(Northup et al., 2010;Lang-yona et al., 2018;Esposito et al., 2019: Wiseschart et al., 2019 ...
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.
... Figure 6 shows red autofluorescent cyanobacterial cells visualized by confocal laser scanning microscopy within a sample of soapstone from the church of São Francisco de Paula in Tiradentes, Minas Gerais, Brazil. Endolithic organisms disrupt stone structure physically and by production of organic and inorganic acids [28], as well as by dissolution and remobilization of ions such as iron and manganese from the rock [29]. The arenitous sandstone of the Argentine missions was shown to have an outer layer enriched in Fe and Mn, produced by these biogenic processes [30], while the augen gneiss facades of churches in the city of Rio de Janeiro, Brazil, were found to contain endolithic filamentous cyanobacteria encrusted with neogypsum, redeposited after dissolution from the deteriorated crust [31]. ...
... This is particularly damaging to carbonate stones, but can also affect siliceous rocks ( [34], and references therein). Endolithic organisms disrupt stone structure physically and by production of organic and inorganic acids [28], as well as by dissolution and remobilization of ions such as iron and manganese from the rock [29]. The arenitous sandstone of the Argentine missions was shown to have an outer layer enriched in Fe and Mn, produced by these biogenic processes [30], while the augen gneiss facades of churches in the city of Rio de Janeiro, Brazil, were found to contain endolithic filamentous cyanobacteria encrusted with neogypsum, redeposited after dissolution from the deteriorated crust [31]. ...
Microbial cells that produce biofilms, or patinas, on historic buildings are affected by climatic changes, mainly temperature, rainfall and air pollution, all of which will alter over future decades. This review considers the colonization of stone buildings by microorganisms and the effects that the resultant biofilms have on the degradation of the structure. Conservation scientists require a knowledge of the potential effects of microorganisms, and the subsequent growth of higher organisms such as vascular plants, in order to formulate effective control strategies. The vulnerability of various structural materials ("bioreceptivity") and the ways in which the environmental factors of temperature, precipitation, wind-driven rain and air pollution influence microbial colonization are discussed. The photosynthetic microorganisms, algae and cyanobacteria, are acknowledged to be the primary colonizers of stone surfaces and many cyanobacterial species are able to survive climate extremes; hence special attention is paid to this group of organisms. Since cyanobacteria require only light and water to grow, can live endolithically and are able to survive most types of stress, they may become even more important as agents of stone cultural property degradation in the future.
... For more than 200 years after Humboldt's first observation in the early nineteenth century, rock and desert varnish have been studied from different perspectives such as microbiology (Dorn and Oberlander, 1981;Perry et al., 2004), geochemistry (Goldsmith et al., 2014), astrobiology (Krinsley et al., 2009;Lanza et al., 2012), paleoclimatology (Dorn and DeNiro, 1985;Dietzel et al., 2008), geomorphology (Oberlander, 1994), edaphology (Sarmast et al., 2017;Lebedeva et al., 2019), archeology (Dragovich, 1984;Macholdt et al., 2019), metagenomics (Esposito et al., 2019), the ecology of extreme environments (Krumbein and Jens, 1981;Zhang et al., 2012), and climate change (Dorn, 1994;Lee and Bland, 2003), among other fields. ...
... Another recent metagenomic approach to rock varnish also shows the contribution of the phylum Chloroflexi to these microbial communities, which was also relevant in our survey (Fig. 8b). This phylum has been related to C-fixing strategies, such as the Wood-Ljungdahl pathway (Esposito et al., 2019). These autotrophic metabolisms have been found to be relevant in the core microbiota of rock varnish (Esposito et al., 2019), contributing to the C-input in the microbial biomass. ...
... This phylum has been related to C-fixing strategies, such as the Wood-Ljungdahl pathway (Esposito et al., 2019). These autotrophic metabolisms have been found to be relevant in the core microbiota of rock varnish (Esposito et al., 2019), contributing to the C-input in the microbial biomass. ...
Desert varnish is a dark microlayer that forms on rocky surfaces that is usually associated with arid and desert
environments. It consists mainly of clay minerals (60%), while the rest are Fe and Mn oxides. Growth rates are
very slow and vary from <1 to 40 μm/ky. Although different proposals exist to explain their formation mechanisms,
these processes are still unknown. Around the world, various groups and human communities have
created petroglyphs with different meanings in desert varnish. In the Sonoran Desert, the archaeological site La
Proveedora is known for having many petroglyphs made in granite rock varnishes. It is believed that people
groups occupied the area during the mid-Holocene (ca 5000-3000 BC). The research was carried out by analyzing
and looking for possible signals and contributions from past environments and current processes that are preserved
in the varnish layers. The X-ray diffraction, laser breakdown spectra and scanning electron microscopy
with energy dispersive spectroscopy analyses in varnish samples, showed that the distribution and concentrations
of Fe and Mn exhibit an alternating behavior on a depth scale from the surface until contact with granite.
The DNA analysis showed a major presence of the Proteobacteria and Actinobacteria groups. Notably, some of
these microorganisms can incorporate Fe and Mn into their metabolic processes and mobilize them through the
varnish for its formation. The 14C radiocarbon dating (370 ± 54 cal BP) indicates a very young age associated
primarily with recent microorganisms. However, a first approximation was obtained for the minimum age (5000-
1000 yr BP). The comparison between the areas of varnish and the surfaces within the petroglyphs suggests that
the varnish formation occurred under conditions in the past when the humidity was higher, and that it is
probably a very slow, intermittent or uncoated formation mechanism today.
... Those papers concentrating on Antarctic ecosystems included: the impacts of a warming world on enzymatic activity in Antarctic soils (Barnard et al. 2020), how abiotic factors influence microbial diversity in the McMurdo Dry Valleys (Bottos et al. 2020), the diversity, distribution, and role of heterotrophic diazotrophs in Antarctic soils (Coyne et al. 2020), and the energetic constraints in benthic microbial mats of an Antarctic Lake (Dillon et al. 2020). Those submissions specifically addressing questions in Alpine ecosystems included: resolving the diversity and functional role of the rock varnish microbiome (Esposito et al. 2019), microbial succession in Tibetan Plateau glaciers (Kong et al. 2019), microbial biogeography in Tibetan Plateau lakes ecosystems (Liu et al. 2019), prokaryotic and fungal communities in Tibetan lake sediments (Yang et al. 2020), and a comprehensive characterization of two new snow algae (Procházková et al. 2019). The special issue also contains one bi-polar study examining the diversity of natural product encoding genes in High Arctic and Antarctic soils (Benaud et al. 2019) and a more general mini review on the role of outer membrane glycolipids in bacteria from cold environments (Casillo et al. 2019). ...
