Fluorescence Microscopy with Deep UV, Near UV, and Visible Excitation for In Situ Detection of Microorganisms

We report a simple, inexpensive design of a fluorescence microscope with light-emitting diode (LED) excitation for detection of labeled and unlabeled microorganisms in mineral substrates. The use of deep UV (DUV) excitation with visible emission requires no specialized optics or slides and can be implemented easily and inexpensively using an oblique illumination geometry. DUV excitation (<280 nm) is preferable to near UV (365 nm) for avoidance of mineral autofluorescence. When excited with DUV, unpigmented bacteria show two emission peaks: one in the near UV ∼320 nm, corresponding to proteins, and another peak in the blue to green range, corresponding to flavins and/or reduced nicotinamide adenine dinucleotide (NADH). Many commonly used dyes also show secondary excitation peaks in the DUV, with identical emission spectra and quantum yields as their primary peak. However, DUV fails to excite key biosignature molecules, especially chlorophyll in cyanobacteria. Visible excitation (violet to blue) also results in less mineral autofluorescence than near UV, and most autofluorescence in the minerals seen here is green, so that red dyes and red autofluorescence of chlorophyll and porphyrins are readily distinguished. The pairing of DUV and near UV or visible excitation, with emission across the visible, represents the most thorough approach to detection of labeled and unlabeled bacteria in soil and rock.

Quantifying Global Origin-Diagnostic Features and Patterns in Biotic and Abiotic Acyclic Lipids for Life Detection

Lipids are a geologically robust class of organics ubiquitous to life as we know it. Lipid-like soluble organics are synthesized abiotically and have been identified in carbonaceous meteorites and on Mars. Ascertaining the origin of lipids on Mars would be a profound astrobiological achievement. We enumerate origin-diagnostic features and patterns in two acyclic lipid classes, fatty acids (i.e., carboxylic acids) and acyclic hydrocarbons, by collecting and analyzing molecular data reported in over 1500 samples from previously published studies of terrestrial and meteoritic organics. We identify 27 combined (15 for fatty acids, 12 for acyclic hydrocarbons) molecular patterns and structural features that can aid in distinguishing biotic from abiotic synthesis. Principal component analysis (PCA) demonstrates that multivariate analyses of molecular features (16 for fatty acids, 14 for acyclic hydrocarbons) can potentially indicate sample origin. Terrestrial lipids are dominated by longer straight-chain molecules (C4-C34 fatty acids, C14-C46 acyclic hydrocarbons), with predominance for specific branched and unsaturated isomers. Lipid-like meteoritic soluble organics are shorter, with random configurations. Organic solvent-extraction techniques are most commonly reported, motivating the design of our novel instrument, the Extractor for Chemical Analysis of Lipid Biomarkers in Regolith (ExCALiBR), which extracts lipids while preserving origin-diagnostic features that can indicate biogenicity.

Are Large Sulfur Isotope Variations Biosignatures in an Ancient, Impact-Induced Hydrothermal Mars Analog?

Discrepancies have emerged concerning the application of sulfur stable isotope ratios as a biosignature in impact crater paleolakes. The first in situ δ34S data from Mars at Gale crater display a ∼75‰ range that has been attributed to an abiotic mechanism. Yet biogeochemical studies of ancient environments on Earth generally interpret δ34S fractionations >21‰ as indicative of a biological origin, and studies of δ34S at analog impact crater lakes on Earth have followed the same approach. We performed analyses (including δ34S, total organic carbon wt%, and scanning electron microscope imaging) on multiple lithologies from the Nördlinger Ries impact crater, focusing on hydrothermally altered impact breccias and associated sedimentary lake-fill sequences to determine whether the δ34S properties define a biosignature. The differences in δ34S between the host lithologies may have resulted from thermochemical sulfate reduction, microbial sulfate reduction, hydrothermal equilibrium fractionation, or any combination thereof. Despite abundant samples and instrumental precision currently exclusive to Earth-bound analyses, assertions of biogenicity from δ34S variations >21‰ at the Miocene Ries impact crater are tenuous. This discourages the use of δ34S as a biosignature in similar environments without independent checks that include the full geologic, biogeochemical, and textural context, as well as a comprehensive acknowledgment of alternative hypotheses.

Raman Spectroscopic and Microbial Study of Biofilms Hosted Gypsum Deposits in the Hypersaline Wetlands: Astrobiological Perspective

Gypsum (CaSO4·2H2O) has been identified at the surface of Mars, by both orbiters and rovers. Because gypsum mostly forms in the presence of liquid water as an essential element for sustaining microbial life and has a low porosity, which is ideal for preserving organic material, it is a promising target to look for signs of past microbial life. In this article, we studied organic matter preservation within gypsum that precipitates in a salt flat or a so-called coastal sabkha located in Qatar. Sabkha's ecosystem is considered a modern analog to evaporitic environments that may have existed on early Mars. We collected the sediment cores in the areas where gypsum is formed and performed DNA analysis to characterize the community of extremophilic microorganisms that is present at the site of gypsum formation. Subsequently, we applied Raman spectroscopy, a technique available on several rovers that are currently exploring Mars, to evaluate which organic molecules can be detected through the translucent gypsum crystals. We showed that organic material can be encapsulated into evaporitic gypsum and detected via Raman microscopy with simple, straightforward sample preparation. The molecular biology data proved useful for assessing to what extent complex Raman spectra can be linked to the original microbial community, dominated by Halobacteria and methanogenic archaea, providing a reference for a signal that may be detected on Mars.

Biosignatures Preserved in Carbonate Nodules from the Western Qaidam Basin, NW China: Implications for Life Detection on Mars

The search for organic matter on Mars is one of the major objectives of Mars exploration. However, limited detection of organic signals by Mars rovers to date demands further investigation on this topic. The Curiosity rover recently discovered numerous nodules in Gale Crater on Mars. These nodules have been considered to precipitate in the neutral-to-alkaline and saline diagenetic fluids and could be beneficial for organic preservation. Here, we examine this possibility by studying the carbonate nodules in the western Qaidam Basin, NW China, one of the terrestrial analog sites for Mars. Fourier transform infrared spectra of the carbonate nodules reveal that the aliphatic and aromatic molecules can be readily preserved inside nodules in Mars-like environments. The chain-branching index of the Qaidam nodules suggests that the diagenetic fluids where nodules precipitated were able to support diverse microbial communities that could vary with the water salinity. Findings of this study provide new perspectives on the astrobiological significance of nodules in Gale Crater and the further detection of organic matter on Mars.

Planetary Mapping Using Deep Learning: A Method to Evaluate Feature Identification Confidence Applied to Habitats in Mars-Analog Terrain

The goals of Mars exploration are evolving beyond describing environmental habitability at global and regional scales to targeting specific locations for biosignature detection, sample return, and eventual human exploration. An increase in the specificity of scientific goals-from follow the water to find the biosignatures-requires parallel developments in strategies that translate terrestrial Mars-analog research into confident identification of rover-explorable targets on Mars. Precisely how to integrate terrestrial, ground-based analyses with orbital data sets and transfer those lessons into rover-relevant search strategies for biosignatures on Mars remains an open challenge. Here, leveraging small Unmanned Aerial System (sUAS) technology and state-of-the-art fully convolutional neural networks for pixel-wise classification, we present an end-to-end methodology that applies Deep Learning to map geomorphologic units and quantify feature identification confidence. We used this method to assess the identification confidence of rover-explorable habitats in the Mars-analog Salar de Pajonales over a range of spatial resolutions and found that spatial resolutions two times better than are available from Mars would be necessary to identify habitats in this study at the 1-σ (85%) confidence level. The approach we present could be used to compare the identifiability of habitats across Mars-analog environments and focus Mars exploration from the scale of regional habitability to the scale of specific habitats. Our methods could also be adapted to map dome- and ridge-like features on the surface of Mars to further understand their origin and astrobiological potential.

Testing Rover Science Protocols to Identify Possible Biosignatures on Mars: Achieving Sampling Goals Under a Highly Constrained Time Line

At a Mars analog site in Utah, we tested two science operation methods for data acquisition and decision-making protocols: a scenario where the tactical day is preplanned, but major adjustments may still be made before plan delivery; and a scenario in which the sol path must largely be planned before a given tactical planning day and very few adjustments to the plan may be made. The goal was to provide field-tested insight into operations planning for rover missions where science operations must facilitate the efficient choice of sampling locations at a site relevant to searching for habitability and biosignatures. Results of the test indicate that preplanning sol paths did not result in a sol cost savings nor did it improve science return or optimal biologically relevant sample collection. In addition because facies variations in an environment can be subtle and evident only at scales below orbital resolution, acquiring systematic observations is crucial. We also noted that while spectral data provided insight into the chemical components as a whole at this site, they did not provide a guide to targets for which the traverse should be altered. Finally, strategic science planning must include a special effort to account for terrain.

Microbial Communities in Saltpan Sediments Show Tolerance to Mars Analog Conditions, but Susceptibility to Chloride and Perchlorate Toxicity

Brines at or near the surface of present-day Mars are a potential explanation for seasonally recurring dark streaks on the walls of craters, termed recurring slope lineae (RSL). Deliquescence and freezing point depression are possible drivers of brine stability, attributable to the high salinity observed in martian regolith including chlorides and perchlorates. Investigation of life, which may inhabit RSL, and the cellular mechanisms necessary for survival, must consider the tolerance of highly variable hydration, freeze-thaw cycles, and high osmolarity in addition to the anaerobic, oligotrophic, and irradiated environment. We propose the saltpan, an ephemeral, hypersaline wetland as an analogue for putative RSL hydrology. Saltpan sediment archaeal and bacterial communities showed tolerance of the Mars-analogous atmosphere, hydration, minerology, salinity, and temperature. Although active growth and a shift to well-adapted taxa were observed, susceptibility to low-concentration chloride and perchlorate addition suggested that such a composition was insufficient for beneficial water retention relative to added salt stress.

ExoMars Mars Organic Molecule Analyzer (MOMA) Laser Desorption/Ionization Mass Spectrometry (LDI-MS) Analysis of Phototrophic Communities from a Silica-Depositing Hot Spring in Yellowstone National Park, USA

The Mars Organic Molecule Analyzer (MOMA) is a key scientific instrument on the ExoMars Rover mission. MOMA is designed to detect and characterize organic compounds, over a wide range of volatility and molecular weight, in samples obtained from up to 2 m below the martian surface. Thorough analog sample studies are required to best prepare to interpret MOMA data collected on Mars. We present here the MOMA characterization of Mars analog samples, microbial streamer communities composed primarily of oxygenic and anoxygenic phototrophs, collected from an alkaline silica-depositing hot spring in Yellowstone National Park, Wyoming, USA. Samples of partly mineralized microbial streamers and their total lipid extract (TLE) were measured on a MOMA Engineering Test Unit (ETU) instrument by using its laser desorption/ionization mass spectrometry (LDI-MS) mode. MOMA LDI-MS detected a variety of lipids and pigments such as chlorophyll a, monogalactosyldiacylglycerol, digalactosyldiacylglycerol, diacylglycerols, and β-carotene in the TLE sample. Only chlorophyll a was detected in the untreated streamer samples when using mass isolation, which was likely due to the higher background signal of this sample and the relative high ionization potential of the chlorophyll a compared with other compounds in unextracted samples. The results add to the LDI-MS sample characterization database and demonstrate the benefit of using mass isolation on the MOMA instrument to reveal the presence of complex organics and potential biomarkers preserved in a natural sample. This will also provide guidance to in situ analysis of surface samples during Mars operations.

Antarctic Water Tracks: Microbial Community Responses to Variation in Soil Moisture, pH, and Salinity

Ice-free soils in the McMurdo Dry Valleys select for taxa able to cope with challenging environmental conditions, including extreme chemical water activity gradients, freeze-thaw cycling, desiccation, and solar radiation regimes. The low biotic complexity of Dry Valley soils makes them well suited to investigate environmental and spatial influences on bacterial community structure. Water tracks are annually wetted habitats in the cold-arid soils of Antarctica that form briefly each summer with moisture sourced from snow melt, ground ice thaw, and atmospheric deposition via deliquescence and vapor flow into brines. Compared to neighboring arid soils, water tracks are highly saline and relatively moist habitats. They represent a considerable area (∼5–10 km²) of the Dry Valley terrestrial ecosystem, an area that is expected to increase with ongoing climate change. The goal of this study was to determine how variation in the environmental conditions of water tracks influences the composition and diversity of microbial communities. We found significant differences in microbial community composition between on- and off-water track samples, and across two distinct locations. Of the tested environmental variables, soil salinity was the best predictor of community composition, with members of the Bacteroidetes phylum being relatively more abundant at higher salinities and the Actinobacteria phylum showing the opposite pattern. There was also a significant, inverse relationship between salinity and bacterial diversity. Our results suggest water track formation significantly alters dry soil microbial communities, likely influencing subsequent ecosystem functioning. We highlight how Dry Valley water tracks could be a useful model system for understanding the potential habitability of transiently wetted environments found on the surface of Mars.

Team Processes and Outcomes During the AMADEE-18 Mars Analog Mission

The aim of this study was to examine team functioning within the context of the AMADEE 18 Mars analog project, which took place in Oman in the winter of 2018. Five "Analog Astronauts" participated in this study. Each completed measures of individual-level variables, including demographics and personality, before the simulated Mars mission began. At several time points during the mission, and once at the end, participants completed measures of individual stress reactions, and teamwork-related variables, including several types of team conflict, citizenship behavior, in-role behavior, counterproductive behavior, and social loafing. Each participant also reported how well he or she felt the team performed. The results indicate an overall positive, successful teamwork experience. Factors including measurement issues, psychological simulation fidelity, and qualities of the team likely influenced these results. Measuring important team- and individual-level variables during additional space analog events, while considering factors related to psychological fidelity, will allow for the compilation of data to better understand the factors affecting teams in these unusual contexts.

Bacterial Diversity of a High-Altitude Permafrost Thaw Pond Located on Ojos del Salado (Dry Andes, Altiplano-Atacama Region)

Microbial ecology of permafrost, due to its ecological and astrobiological importance, has been in the focus of studies in past decades. Although permafrost is an ancient and stable environment, it is also subjected to current climate changes. Permafrost degradation often results in generation of thaw ponds, a phenomenon not only reported mainly from polar regions but also present in high-altitude permafrost environments. Our knowledge about microbial communities of thaw ponds in these unique, remote mountain habitats is sparse. This study presents the first culture collection and results of the next-generation DNA sequencing (NGS) analysis of bacterial communities inhabiting a high-altitude permafrost thaw pond. In February 2016, a permafrost thaw pond on the Ojos del Salado at 5900 m a.s.l. (meters above sea level) was sampled as part of the Hungarian Dry Andes Research Programme. A culture collection of 125 isolates was established, containing altogether 11 genera belonging to phyla Bacteroidetes, Actinobacteria, and Proteobacteria. Simplified bacterial communities with a high proportion of candidate and hitherto uncultured bacteria were revealed by Illumina MiSeq NGS. Water of the thaw pond was dominated by Bacteroidetes and Proteobacteria, while in the sediment of the lake and permafrost, members of Acidobacteria, Actinobacteria, Bacteroidetes, Patescibacteria, Proteobacteria, and Verrucomicrobia were abundant. This permafrost habitat can be interesting as a potential Mars analog.

The Limits, Capabilities, and Potential for Life Detection with MinION Sequencing in a Paleochannel Mars Analog

No instrument capable of direct life detection has been included on a mission payload to Mars since NASA's Viking missions in the 1970s. This prevents us from discovering whether life is or ever was present on Mars. DNA is an ideal target biosignature since it is unambiguous, nonspecific, and readily detectable with nanopore sequencing. Here, we present a proof-of-concept utilization of the Oxford Nanopore Technologies (ONT) MinION sequencer for direct life detection and show how it can complement results from established space mission instruments. We used nanopore sequencing data from the MinION to detect and characterize the microbial life in a set of paleochannels near Hanksville, UT, with supporting data from X-ray diffraction, reflectance spectroscopy, Raman spectroscopy, and Life Detector Chip (LDChip) microarray immunoassay analyses. These paleochannels are analogs to martian sinuous ridges. The MinION-generated metagenomes reveal a rich microbial community dominated by bacteria and containing radioresistant, psychrophilic, and halophilic taxa. With spectral data and LDChip immunoassays, these metagenomes were linked to the surrounding Mars analog environment and potential metabolisms (e.g., methane production and perchlorate reduction). This shows a high degree of synergy between these techniques for detecting and characterizing biosignatures. We also resolved a prospective lower limit of ∼0.001 ng of DNA required for successful sequencing. This work represents the first determination of the MinION's DNA detection limits beyond ONT recommendations and the first whole metagenome analysis of a sinuous ridge analog.

Evidence for Biotic Perchlorate Reduction in Naturally Perchlorate-Rich Sediments of Pilot Valley Basin, Utah

The presence of perchlorate on Mars suggests a possible energy source for sustaining microbial life. Perchlorate-reducing microbes have been isolated from perchlorate-contaminated soils and sediments on the Earth, but to date, never from an environment that is naturally enriched in perchlorate. The arid Pilot Valley paleolake basin in Utah is a Mars analog environment whose sediments are naturally enriched with up to ∼6.5 μg kg^-1 perchlorate oxyanions. Here, we present results of field and laboratory studies indicating that perchlorate-reducing microorganisms co-occur with this potential electron acceptor. Biogeochemical data suggest ongoing perchlorate reduction; phylogenetic data indicate the presence of diverse microbial communities; and laboratory enrichments using Pilot Valley sediments show that resident microbes can reduce perchlorate. This is the first article of the co-existence of perchlorate-reducing microbes in an environment where perchlorate occurs naturally, arguing for Pilot Valley's utility as an analog for studying biogeochemical processes that may have occurred, and may yet still be occurring, in ancient martian lacustrine sediments.

Dalangtan Saline Playa in a Hyperarid Region on Tibet Plateau: I. Evolution and Environments

Since 2008, we have been studying a saline lake, Dalangtan (DLT) Playa, and its surroundings in a hyperarid region of the Qaidam Basin on the Tibetan Plateau as a potential Mars analog site. We describe the evolution of saline deposits in the Qaidam Basin (including DLT), based on investigative findings accumulated over the course of 60 years of geological surveys. In addition, we report regional meteorological patterns recorded for the past 32 years along with meteorological station recorded data at DLT since 2012. Overall, the DLT area on the Tibetan Plateau has low atmospheric pressure, high ultraviolet radiation, low annual mean temperatures (T) but large seasonal and diurnal T cycles, and extremely low relative humidity, all of which bear some similarities with the equatorial region on Mars. In addition, salt types similar to those found on Mars, such as magnesium-sulfates, chlorides, and perchlorates, are found at the surface and subsurface in the DLT area (and the other two playas in the Qaidam Basin), thus supporting DLT as a Mars analog in terms of mineralogy and geochemistry.

Biological Characterization of Microenvironments in a Hypersaline Cold Spring Mars Analog

While many habitable niches on Earth are characterized by permanently cold conditions, little is known about the spatial structure of seasonal communities and the importance of substrate-cell associations in terrestrial cyroenvironments. Here we use the 16S rRNA gene as a marker for genetic diversity to compare two visually distinct but spatially integrated surface microbial mats on Axel Heiberg Island, Canadian high arctic, proximal to a perennial saline spring. This is the first study to describe the bacterial diversity in microbial mats on Axel Heiberg Island. The hypersaline springs on Axel Heiberg represent a unique analog to putative subsurface aquifers on Mars. The Martian subsurface represents the longest-lived potentially habitable environment on Mars and a better understanding of the microbial communities on Earth that thrive in analog conditions will help direct future life detection missions. The microbial mats sampled on Axel Heiberg are only visible during the summer months in seasonal flood plains formed by melt water and run-off from the proximal spring. Targeted-amplicon sequencing revealed that not only does the bacterial composition of the two mat communities differ substantially from the sediment community of the proximal cold spring, but that the mat communities are distinct from any other microbial community in proximity to the Arctic springs studied to date. All samples are dominated by Gammaproteobacteria: Thiotichales is dominant within the spring samples while Alteromonadales comprises a significant component of the mat communities. The two mat samples differ in their Thiotichales:Alteromonadales ratio and contribution of Bacteroidetes to overall diversity. The red mats have a greater proportion of Alteromonadales and Bacteroidetes reads. The distinct bacterial composition of the mat bacterial communities suggests that the spring communities are not sourced from the surface, and that seasonal melt events create ephemerally habitable niches with distinct microbial communities in the Canadian high arctic. The finding that these surficial complex microbial communities exist in close proximity to perennial springs demonstrates the existence of a transiently habitable niche in an important Mars analog site.

Draft genome sequence of Acidithiobacillus thiooxidans CLST isolated from the acidic hypersaline Gorbea salt flat in northern Chile

10.1601/nm.2199 CLST is an extremely acidophilic gamma-proteobacteria that was isolated from the Gorbea salt flat, an acidic hypersaline environment in northern Chile. This kind of environment is considered a terrestrial analog of ancient Martian terrains and a source of new material for biotechnological applications. 10.1601/nm.2199 plays a key role in industrial bioleaching; it has the capacity of generating and maintaining acidic conditions by producing sulfuric acid and it can also remove sulfur layers from the surface of minerals, which are detrimental for their dissolution. CLST is a strain of 10.1601/nm.2199 able to tolerate moderate chloride concentrations (up to 15 g L⁻¹ Cl⁻), a feature that is quite unusual in extreme acidophilic microorganisms. Basic microbiological features and genomic properties of this biotechnologically relevant strain are described in this work. The 3,974,949 bp draft genome is arranged into 40 scaffolds of 389 contigs containing 3866 protein-coding genes and 75 RNAs encoding genes. This is the first draft genome of a halotolerant 10.1601/nm.2199 strain. The release of the genome sequence of this strain improves representation of these extreme acidophilic Gram negative bacteria in public databases and strengthens the framework for further investigation of the physiological diversity and ecological function of 10.1601/nm.2199 populations.