Astrobiological implications of rock varnish in Tibet

Forced Biomineralization: A Review

Biologically induced and controlled mineralization of metals promotes the development of protective structures to shield cells from thermal, chemical, and ultraviolet stresses. Metal biomineralization is widely considered to have been relevant for the survival of life in the environmental conditions of ancient terrestrial oceans. Similar behavior is seen among extremophilic biomineralizers today, which have evolved to inhabit a variety of industrial aqueous environments with elevated metal concentrations. As an example of extreme biomineralization, we introduce the category of "forced biomineralization", which we use to refer to the biologically mediated sequestration of dissolved metals and metalloids into minerals. We discuss forced mineralization as it is known to be carried out by a variety of organisms, including polyextremophiles in a range of psychrophilic, thermophilic, anaerobic, alkaliphilic, acidophilic, and halophilic conditions, as well as in environments with very high or toxic metal ion concentrations. While much additional work lies ahead to characterize the various pathways by which these biominerals form, forced biomineralization has been shown to provide insights for the progression of extreme biomimetics, allowing for promising new forays into creating the next generation of composites using organic-templating approaches under biologically extreme laboratory conditions relevant to a wide range of industrial conditions.

An ecophysiological explanation for manganese enrichment in rock varnish

Rock varnish is a prominent feature of desert landscapes and the canvas for many prehistoric petroglyphs. How it forms—and, in particular, the basis for its extremely high manganese content—has been an enduring mystery. The work presented here establishes a biological mechanism for this manganese enrichment, underpinned by an apparent antioxidant strategy that enables microbes to survive in the harsh environments where varnish forms. The understanding that varnish is the residue of life using manganese to thrive in the desert illustrates that, even in extremely stark environments, the imprint of life is omnipresent on the landscape.

Desert varnish is a dark rock coating that forms in arid environments worldwide. It is highly and selectively enriched in manganese, the mechanism for which has been a long-standing geological mystery. We collected varnish samples from diverse sites across the western United States, examined them in petrographic thin section using microscale chemical imaging techniques, and investigated the associated microbial communities using 16S amplicon and shotgun metagenomic DNA sequencing. Our analyses described a material governed by sunlight, water, and manganese redox cycling that hosts an unusually aerobic microbial ecosystem characterized by a remarkable abundance of photosynthetic Cyanobacteria in the genus Chroococcidiopsis as the major autotrophic constituent. We then showed that diverse Cyanobacteria, including the relevant Chroococcidiopsis taxon, accumulate extraordinary amounts of intracellular manganese—over two orders of magnitude higher manganese content than other cells. The speciation of this manganese determined by advanced paramagnetic resonance techniques suggested that the Cyanobacteria use it as a catalytic antioxidant—a valuable adaptation for coping with the substantial oxidative stress present in this environment. Taken together, these results indicated that the manganese enrichment in varnish is related to its specific uptake and use by likely founding members of varnish microbial communities.

Taxonomic and functional insights into rock varnish microbiome using shotgun metagenomics

Rock varnish is a microbial habitat, characterised 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 microbiome using shotgun metagenomics together with analyses of elemental composition, lipid and small molecule biomarkers, and rock surface analyses to explore the biogeography of microbial communities and their functional features. We report taxa and encoded functions represented in metagenomes retrieved from varnish or non-varnish samples, additionally, eight nearly complete genomes have been reconstructed spanning four phyla (Acidobacteria, Actinobacteria, Chloroflexi and TM7). The functional and taxonomic analyses presented in this study provide new insights into the ecosystem dynamics and survival strategies of microbial communities inhabiting varnish and non-varnish rock surfaces.

Photoelectric conversion on Earth's surface via widespread Fe- and Mn-mineral coatings

Sunlight drives photosynthesis and associated biological processes, and also influences inorganic processes that shape Earth's climate and geochemistry. Bacterial solar-to-chemical energy conversion on this planet evolved to use an intricate intracellular process of phototrophy. However, a natural nonbiological counterpart to phototrophy has yet to be recognized. In this work, we reveal the inherent "phototrophic-like" behavior of vast expanses of natural rock/soil surfaces from deserts, red soils, and karst environments, all of which can drive photon-to-electron conversions. Using scanning electron microscopy, transmission electron microscopy, micro-Raman spectroscopy, and X-ray absorption spectroscopy, Fe and Mn (oxyhydr)oxide-rich coatings were found in rock varnishes, as were Fe (oxyhydr)oxides on red soil surfaces and minute amounts of Mn oxides on karst rock surfaces. By directly fabricating a photoelectric detection device on the thin section of a rock varnish sample, we have recorded an in situ photocurrent micromapping of the coatings, which behave as highly sensitive and stable photoelectric systems. Additional measurements of red soil and powder separated from the outermost surface of karst rocks yielded photocurrents that are also sensitive to irradiation. The prominent solar-responsive capability of the phototrophic-like rocks/soils is ascribed to the semiconducting Fe- and Mn (oxyhydr)oxide-mineral coatings. The native semiconducting Fe/Mn-rich coatings may play a role similar, in part, to photosynthetic systems and thus provide a distinctive driving force for redox (bio)geochemistry on Earth's surfaces.

Nanoscale Observations Support the Importance of Chemical Processes in Rock Decay and Rock Coating Development in Cold Climates

Conventional scholarship long held that rock fracturing from physical processes dominates over chemical rock decay processes in cold climates. The paradigm of the supremacy of cold-climate shattering was questioned by Rapp’s discovery (1960) that the flux of dissolved solids leaving a Kärkevagge, Swedish Lapland, watershed exceeded physical denudation processes. Many others since have gone on to document the importance of chemical rock decay in all cold climate landscapes, using a wide variety of analytical approaches. This burgeoning scholarship, however, has only generated a few nanoscale studies. Thus, this paper’s purpose rests in an exploration of the potential for nanoscale research to better understand chemical processes operating on rock surfaces in cold climates. Samples from several Antarctica locations, Greenland, the Tibetan Plateau, and high altitude tropical and mid-latitude mountains all illustrate ubiquitous evidence of chemical decay at the nanoscale, even though the surficial appearance of each landscape is dominated by “bare fresh rock.” With the growing abundance of focused ion beam (FIB) instruments facilitating sample preparation, the hope is that that future rock decay researchers studying cold climates will add nanoscale microscopy to their bag of tools.

Natural Extracellular Electron Transfer Between Semiconducting Minerals and Electroactive Bacterial Communities Occurred on the Rock Varnish

Rock varnish is a thin coating enriched with manganese (Mn) and iron (Fe) oxides. The mineral composition and formation of rock varnish elicit considerable attention from geologists and microbiologists. However, limited research has been devoted to the semiconducting properties of these Fe/Mn oxides in varnish and relatively little attention is paid to the mineral-microbe interaction under sunlight. In this study, the mineral composition and the bacterial communities on varnish from the Gobi Desert in Xinjiang, China were analyzed. Results of principal components analysis and t-test indicated that more electroactive genera such as Acinetobacter, Staphylococcus, Dietzia, and Pseudomonas gathered on varnish bacterial communities than on substrate rock and surrounding soils. We then explored the culture of varnish, substrate and soil samples in media and the extracellular electron transfer (EET) between bacterial communities and mineral electrodes under light/dark conditions for the first time. Orthogonal electrochemical experiments demonstrated that the most remarkable photocurrent density of 6.1 ± 0.4 μA/cm2 was observed between varnish electrode and varnish microflora. Finally, based on Raman and 16S rRNA gene-sequencing results, coculture system of birnessite and Pseudomonas (the major Mn oxide and a common electroactive bacterium in varnish) was established to study underlying mechanism. A steadily growing photocurrent (205 μA at 100 h) under light was observed with a stable birnessite after 110 h. However, only 47 μA was generated in the dark control and birnessite was reduced to Mn2+ in 13 h, suggesting that birnessite helped deliver electrons instead of serving as an electron acceptor under light. Our study demonstrated that electroactive bacterial communities were positively correlated with Fe/Mn semiconducting minerals in varnish, and diversified EET process occurred on varnish under sunlight. Overall, these phenomena may influence bacterial-community structure in natural environments over time.

Oxygen isotope analysis of bacterial and fungal manganese oxidation

The ability of micro-organisms to oxidize manganese (Mn) from Mn(II) to Mn(III/IV) oxides transcends boundaries of biological clade or domain. Many bacteria and fungi oxidize Mn(II) to Mn(III/IV) oxides directly through enzymatic activity or indirectly through the production of reactive oxygen species. Here, we determine the oxygen isotope fractionation factors associated with Mn(II) oxidation via various biotic (bacteria and fungi) and abiotic Mn(II) reaction pathways. As oxygen in Mn(III/IV) oxides may be derived from precursor water and molecular oxygen, we use a twofold approach to determine the isotope fractionation with respect to each oxygen source. Using both ¹⁸ O-labeled water and closed-system Rayleigh distillation approaches, we constrain the kinetic isotope fractionation factors associated with O atom incorporation during Mn(II) oxidation to -17.3‰ to -25.9‰ for O₂ and -1.9‰ to +1.8‰ for water. Results demonstrate that stable oxygen isotopes of Mn(III/IV) oxides have potential to distinguish between two main classes of biotic Mn(II) oxidation: direct enzymatic oxidation in which O₂ is the oxidant and indirect enzymatic oxidation in which superoxide is the oxidant. The fraction of Mn(III/IV) oxide-associated oxygen derived from water varies significantly (38%-62%) among these bio-oxides with only weak relationship to Mn oxidation state, suggesting Mn(III) disproportionation may account for differences in the fraction of mineral-bound oxygen from water and O₂ . Additionally, direct incorporation of molecular O₂ suggests that Mn(III/IV) oxides contain a yet untapped proxy of δ18OO2 of environmental O₂ , a parameter reflecting the integrated influence of global respiration, photorespiration, and several other biogeochemical reactions of global significance.

Insights into microbial involvement in desert varnish formation retrieved from metagenomic analysis

Desert varnishes are dark rock coatings observed in arid environments and might resemble Mn-rich coatings found on Martian rocks. Their formation mechanism is not fully understood and the possible microbial involvement is under debate. In this study, we applied DNA metagenomic Shotgun sequencing of varnish and surrounding soil to evaluate the composition of the microbial community and its potential metabolic function. We found that the α diversity was lower in varnish compared to soil samples (p value < 0.05), suggesting distinct populations with significantly higher abundance of Actinobacteria, Proteobacteria and Cyanobacteria within the varnish. Additionally, we observed increased levels of transition metal metabolic processes in varnish compared to soil samples. Nevertheless, potentially relevant enzymes for varnish formation were detected at low to insignificant levels in both niches, indicating no current direct microbial involvement in Mn oxidation. This finding is supported by quantitative genomic analysis, elemental analysis, fluorescence imaging and scanning transmission X-ray microscopy. We thus conclude that the distinct microbial communities detected in desert varnish originate from settled Aeolian microbes, which colonized this nutrient-enriched niche, and discuss possible indirect contributions of microorganisms to the formation of desert varnish.

The Characterization of Biosignatures in Caves Using an Instrument Suite

The search for life and habitable environments on other Solar System bodies is a major motivator for planetary exploration. Due to the difficulty and significance of detecting extant or extinct extraterrestrial life in situ, several independent measurements from multiple instrument techniques will bolster the community's confidence in making any such claim. We demonstrate the detection of subsurface biosignatures using a suite of instrument techniques including IR reflectance spectroscopy, laser-induced breakdown spectroscopy, and scanning electron microscopy/energy dispersive X-ray spectroscopy. We focus our measurements on subterranean calcium carbonate field samples, whose biosignatures are analogous to those that might be expected on some high-interest astrobiology targets. In this work, we discuss the feasibility and advantages of using each of the aforementioned instrument techniques for the in situ search for biosignatures and present results on the autonomous characterization of biosignatures using multivariate statistical analysis techniques. Key Words: Biosignature suites-Caves-Mars-Life detection. Astrobiology 17, 1203-1218.

Comparison of Rock Varnish Bacterial Communities with Surrounding Non-Varnished Rock Surfaces: Taxon-Specific Analysis and Morphological Description

Rock varnish is a thin layer of Fe and Mn oxyhydroxides with embedded clay minerals that contain an increased Mn/Fe ratio compared to that of the Earth's crust. Even if the study of rock varnish has important implications in several fields, the composition of epilithic bacterial communities and the distribution of taxa on varnish surfaces are still not wholly described. The aim of this study was (i) to identify the bacterial taxa which show the greatest variation between varnish and non-varnish environments, collected from the same rock, and (ii) to describe the morphology of epilithic communities through scanning electron microscopy (SEM). Triplicate samples of rock surfaces with varnish and triplicate samples without varnish were collected from five sites in Matsch Valley (South Tyrol, Italy). The V4 region of 16S rRNA gene was analyzed by Illumina sequencing. Fifty-five ubiquitous taxa have been examined to assess variation between varnish and non-varnish. Cyanobacteria, Chloroflexi, Proteobacteria along with minor taxa such as Solirubrobacterales, Conexibaxter, and Rhodopila showed significant variations of abundance, diversity, or both responding to the ecology (presence/absence of varnish). Other taxa, such as the genus Edaphobacter, showed a more marked spatial variation responding to the sampling site. SEM images showed a multitude of bacterial morphologies and structures involved in the process of attachment and creation of a suitable environment for growth. The features emerging from this analysis suggest that the highly oxidative Fe and Mn-rich varnish environment favors anoxigenic autotrophy and establishment of highly specialized bacteria.

Localized grounding, excavation, and dissection using in-situ probe techniques for focused ion beam and scanning electron microscopy: experiments with rock varnish

While investigating rock varnish, we explored novel uses for an in-situ micromanipulator, including charge collection, sample manipulation, as well as digging and dissection at the micron level. Dual-beam focused ion beam microscopes (DB-FIB or FIBSEM) equipped with micromanipulators have proven to be valuable tools for material science, semiconductor research, and product failure analysis. Researchers in many other disciplines utilize the DB-FIB and micromanipulator for site-specific transmission electron microscope (TEM) foil preparation. We have demonstrated additional applications for in-situ micromanipulators.

Investigation of Tibetian Plateau varnish: new findings at the nanoscale using focused ion beam and transmission electron microscopy techniques

Dual-beam focused ion beam microscopy (FIB/SEM) preparation of rock varnish for high-resolution transmission electron microscopy (HR-TEM) has enabled us to characterize unreported nanostructures. Fossils, unreported textures, and compositional variability were observed at the nanoscale. These techniques could provide a method for studying ancient terrestrial and extra-terrestrial environments to better understand geological processes at the nanoscale.