Metabolic versatility of Caldarchaeales from geothermal features of Hawai'i and Chile as revealed by five metagenome-assembled genomes

Members of the archaeal order Caldarchaeales (previously the phylum Aigarchaeota) are poorly sampled and are represented in public databases by relatively few genomes. Additional representative genomes will help resolve their placement among all known members of Archaea and provide insights into their roles in the environment. In this study, we analyzed 16S rRNA gene amplicons belonging to the Caldarchaeales that are available in public databases, which demonstrated that archaea of the order Caldarchaeales are diverse, widespread, and most abundant in geothermal habitats. We also constructed five metagenome-assembled genomes (MAGs) of Caldarchaeales from two geothermal features to investigate their metabolic potential and phylogenomic position in the domain Archaea. Two of the MAGs were assembled from microbial community DNA extracted from fumarolic lava rocks from Mauna Ulu, Hawai'i, and three were assembled from DNA obtained from hot spring sinters from the El Tatio geothermal field in Chile. MAGs from Hawai'i are high quality bins with completeness >95% and contamination <1%, and one likely belongs to a novel species in a new genus recently discovered at a submarine volcano off New Zealand. MAGs from Chile have lower completeness levels ranging from 27 to 70%. Gene content of the MAGs revealed that these members of Caldarchaeales are likely metabolically versatile and exhibit the potential for both chemoorganotrophic and chemolithotrophic lifestyles. The wide array of metabolic capabilities exhibited by these members of Caldarchaeales might help them thrive under diverse harsh environmental conditions. All the MAGs except one from Chile harbor putative prophage regions encoding several auxiliary metabolic genes (AMGs) that may confer a fitness advantage on their Caldarchaeales hosts by increasing their metabolic potential and make them better adapted to new environmental conditions. Phylogenomic analysis of the five MAGs and over 3,000 representative archaeal genomes showed the order Caldarchaeales forms a monophyletic group that is sister to the clade comprising the orders Geothermarchaeales (previously Candidatus Geothermarchaeota), Conexivisphaerales and Nitrososphaerales (formerly known as Thaumarchaeota), supporting the status of Caldarchaeales members as a clade distinct from the Thaumarchaeota.

Assessing siliceous sinter matrices for long-term preservation of lipid biomarkers in opaline sinter deposits analogous to Mars in El Tatio (Chile)

Subaerial hydrothermal systems are of great interest for paleobiology and astrobiology as plausible candidate environments to support the origin of life on Earth that offer a unique and interrelated atmosphere-hydrosphere-lithosphere interface. They harbor extensive sinter deposits of high preservation potential that are promising targets in the search for traces of possible extraterrestrial life on Hesperian Mars. However, long-term quality preservation is paramount for recognizing biosignatures in old samples and there are still significant gaps in our understanding of the impact and extent of taphonomy processes on life fingerprints. Here, we propose a study based on lipid biomarkers -highly resistant cell-membrane components- to investigate the effects of silicification on their preservation in hydrothermal opaline sinter. We explore the lipid biomarkers profile in three sinter deposits of up to ~3000 years from El Tatio, one of the best Martian analogs on Earth. The lipid profile in local living biofilms is used as a fresh counterpart of the fossil biomarkers in the centuries-old sinter deposits to qualitatively assess the taphonomy effects of silicification on the lipid's preservation. Despite the geological alteration, the preserved lipids retained a depleted stable-carbon isotopic fingerprint characteristic of biological sources, result highly relevant for astrobiology. The data allowed us to estimate for the first time the degradation rate of lipid biomarkers in sinter deposits from El Tatio, and to assess the time preservation framework of opaline silica. Auxiliary techniques of higher taxonomic resolution (DNA sequencing and metaproteomics) helped in the reconstruction of the paleobiology. The lipids were the best-preserved biomolecules, whereas the detection of DNA and proteins dropped considerably from 5 cm depth. These findings provide new insights into taphonomy processes affecting life fingerprints in hydrothermal deposits and serves as a useful baseline for assessing the time window for recovering unambiguous signs of past life on Earth and beyond.

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.

Cellular remains in a ~3.42-billion-year-old subseafloor hydrothermal environment

Subsurface habitats on Earth host an extensive extant biosphere and likely provided one of Earth's earliest microbial habitats. Although the site of life's emergence continues to be debated, evidence of early life provides insights into its early evolution and metabolic affinity. Here, we present the discovery of exceptionally well-preserved, ~3.42-billion-year-old putative filamentous microfossils that inhabited a paleo-subseafloor hydrothermal vein system of the Barberton greenstone belt in South Africa. The filaments colonized the walls of conduits created by low-temperature hydrothermal fluid. Combined with their morphological and chemical characteristics as investigated over a range of scales, they can be considered the oldest methanogens and/or methanotrophs that thrived in an ultramafic volcanic substrate.

Microbial Biomarker Transition in High-Altitude Sinter Mounds From El Tatio (Chile) Through Different Stages of Hydrothermal Activity

Geothermal springs support microbial communities at elevated temperatures in an ecosystem with high preservation potential that makes them interesting analogs for early evolution of the biogeosphere. The El Tatio geysers field in the Atacama Desert has astrobiological relevance due to the unique occurrence of geothermal features with steep hydrothermal gradients in an otherwise high altitude, hyper-arid environment. We present here results of our multidisciplinary field and molecular study of biogeochemical evidence for habitability and preservation in silica sinter at El Tatio. We sampled three morphologically similar geyser mounds characterized by differences in water activity (i.e., episodic liquid water, steam, and inactive geyser lacking hydrothermal activity). Multiple approaches were employed to determine (past and present) biological signatures and dominant metabolism. Lipid biomarkers indicated relative abundance of thermophiles (dicarboxylic acids) and sulfate reducing bacteria (branched carboxylic acids) in the sinter collected from the liquid water mound; photosynthetic microorganisms such as cyanobacteria (alkanes and isoprenoids) in the steam sinter mound; and archaea (squalane and crocetane) as well as purple sulfur bacteria (cyclopropyl acids) in the dry sinter from the inactive geyser. The three sinter structures preserved biosignatures representative of primary (thermophilic) and secondary (including endoliths and environmental contaminants) microbial communities. Sequencing of environmental 16S rRNA genes and immuno-assays generally corroborated the lipid-based microbial identification. The multiplex immunoassays and the compound-specific isotopic analysis of carboxylic acids, alkanols, and alkanes indicated that the principal microbial pathway for carbon fixation in the three sinter mounds was through the Calvin cycle, with a relative larger contribution of the reductive acetyl-CoA pathway in the dry system. Other inferred metabolic traits varied from the liquid mound (iron and sulfur chemistry), to the steam mound (nitrogen cycle), to the dry mound (perchlorate reduction). The combined results revealed different stages of colonization that reflect differences in the lifetime of the mounds, where primary communities dominated the biosignatures preserved in sinters from the still active geysers (liquid and steam mounds), in contrast to the surviving metabolisms and microbial communities at the end of lifetime of the inactive geothermal mound.

Planetary Protection and Mars Special Regions--A Suggestion for Updating the Definition

We highlight the role of COSPAR and the scientific community in defining and updating the framework of planetary protection. Specifically, we focus on Mars "Special Regions," areas where strict planetary protection measures have to be applied before a spacecraft can explore them, given the existence of environmental conditions that may be conducive to terrestrial microbial growth. We outline the history of the concept of Special Regions and inform on recent developments regarding the COSPAR policy, namely, the MEPAG SR-SAG2 review and the Academies and ESF joint committee report on Mars Special Regions. We present some new issues that necessitate the update of the current policy and provide suggestions for new definitions of Special Regions. We conclude with the current major scientific questions that remain unanswered regarding Mars Special Regions.

The United States Culture Collection Network (USCCN): Enhancing Microbial Genomics Research through Living Microbe Culture Collections

The mission of the United States Culture Collection Network (USCCN; http://usccn.org) is "to facilitate the safe and responsible utilization of microbial resources for research, education, industry, medicine, and agriculture for the betterment of human kind." Microbial culture collections are a key component of life science research, biotechnology, and emerging global biobased economies. Representatives and users of several microbial culture collections from the United States and Europe gathered at the University of California, Davis, to discuss how collections of microorganisms can better serve users and stakeholders and to showcase existing resources available in public culture collections.

Production and early preservation of lipid biomarkers in iron hot springs

The bicarbonate-buffered anoxic vent waters at Chocolate Pots hot springs in Yellowstone National Park are 51-54°C, pH 5.5-6.0, and are very high in dissolved Fe(II) at 5.8-5.9 mg/L. The aqueous Fe(II) is oxidized by a combination of biotic and abiotic mechanisms and precipitated as primary siliceous nanophase iron oxyhydroxides (ferrihydrite). Four distinct prokaryotic photosynthetic microbial mat types grow on top of these iron deposits. Lipids were used to characterize the community composition of the microbial mats, link source organisms to geologically significant biomarkers, and investigate how iron mineralization degrades the lipid signature of the community. The phospholipid and glycolipid fatty acid profiles of the highest-temperature mats indicate that they are dominated by cyanobacteria and green nonsulfur filamentous anoxygenic phototrophs (FAPs). Diagnostic lipid biomarkers of the cyanobacteria include midchain branched mono- and dimethylalkanes and, most notably, 2-methylbacteriohopanepolyol. Diagnostic lipid biomarkers of the FAPs (Chloroflexus and Roseiflexus spp.) include wax esters and a long-chain tri-unsaturated alkene. Surprisingly, the lipid biomarkers resisted the earliest stages of microbial degradation and diagenesis to survive in the iron oxides beneath the mats. Understanding the potential of particular sedimentary environments to capture and preserve fossil biosignatures is of vital importance in the selection of the best landing sites for future astrobiological missions to Mars. This study explores the nature of organic degradation processes in moderately thermal Fe(II)-rich groundwater springs--environmental conditions that have been previously identified as highly relevant for Mars exploration.

Potential fossil endoliths in vesicular pillow basalt, Coral Patch Seamount, eastern North Atlantic Ocean

The chilled rinds of pillow basalt from the Ampère-Coral Patch Seamounts in the eastern North Atlantic were studied as a potential habitat of microbial life. A variety of putative biogenic structures, which include filamentous and spherical microfossil-like structures, were detected in K-phillipsite-filled amygdules within the chilled rinds. The filamentous structures (∼2.5 μm in diameter) occur as K-phillipsite tubules surrounded by an Fe-oxyhydroxide (lepidocrocite) rich membranous structure, whereas the spherical structures (from 4 to 2 μm in diameter) are associated with Ti oxide (anatase) and carbonaceous matter. Several lines of evidence indicate that the microfossil-like structures in the pillow basalt are the fossilized remains of microorganisms. Possible biosignatures include the carbonaceous nature of the spherical structures, their size distributions and morphology, the presence and distribution of native fluorescence, mineralogical and chemical composition, and environmental context. When taken together, the suite of possible biosignatures supports the hypothesis that the fossil-like structures are of biological origin. The vesicular microhabitat of the rock matrix is likely to have hosted a cryptoendolithic microbial community. This study documents a variety of evidence for past microbial life in a hitherto poorly investigated and underestimated microenvironment, as represented by the amygdules in the chilled pillow basalt rinds. This kind of endolithic volcanic habitat would have been common on the early rocky planets in our Solar System, such as Earth and Mars. This study provides a framework for evaluating traces of past life in vesicular pillow basalts, regardless of whether they occur on early Earth or Mars.

Morphological biosignatures and the search for life on Mars

This report provides a rationale for the advances in instrumentation and understanding needed to assess claims of ancient and extraterrestrial life made on the basis of morphological biosignatures. Morphological biosignatures consist of bona fide microbial fossils as well as microbially influenced sedimentary structures. To be recognized as evidence of life, microbial fossils must contain chemical and structural attributes uniquely indicative of microbial cells or cellular or extracellular processes. When combined with various research strategies, high-resolution instruments can reveal such attributes and elucidate how morphological fossils form and become altered, thereby improving the ability to recognize them in the geological record on Earth or other planets. Also, before fossilized microbially influenced sedimentary structures can provide evidence of life, criteria to distinguish their biogenic from non-biogenic attributes must be established. This topic can be advanced by developing process-based models. A database of images and spectroscopic data that distinguish the suite of bona fide morphological biosignatures from their abiotic mimics will avoid detection of false-positives for life. The use of high-resolution imaging and spectroscopic instruments, in conjunction with an improved knowledge base of the attributes that demonstrate life, will maximize our ability to recognize and assess the biogenicity of extraterrestrial and ancient terrestrial life.

Microbial composition of near-boiling silica-depositing thermal springs throughout Yellowstone National Park

The extent of hyperthermophilic microbial diversity associated with siliceous sinter (geyserite) was characterized in seven near-boiling silica-depositing springs throughout Yellowstone National Park using environmental PCR amplification of small-subunit rRNA genes (SSU rDNA), large-subunit rDNA, and the internal transcribed spacer (ITS). We found that Thermocrinis ruber, a member of the order Aquificales, is ubiquitous, an indication that primary production in these springs is driven by hydrogen oxidation. Several other lineages with no known close relatives were identified that branch among the hyperthermophilic bacteria. Although they all branch deep in the bacterial tree, the precise phylogenetic placement of many of these lineages is unresolved at this time. While some springs contained a fair amount of phylogenetic diversity, others did not. Within the same spring, communities in the subaqueous environment were not appreciably different than those in the splash zone at the edge of the pool, although a greater number of phylotypes was found along the pool's edge. Also, microbial community composition appeared to have little correlation with the type of sinter morphology. The number of cell morphotypes identified by fluorescence in situ hybridization and scanning electron microscopy was greater than the number of phylotypes in SSU clone libraries. Despite little variation in Thermocrinis ruber SSU sequences, abundant variation was found in the hypervariable ITS region. The distribution of ITS sequence types appeared to be correlated with distinct morphotypes of Thermocrinis ruber in different pools. Therefore, species- or subspecies-level divergences are present but not detectable in highly conserved SSU sequences.

Signature lipids and stable carbon isotope analyses of Octopus Spring hyperthermophilic communities compared with those of Aquificales representatives

The molecular and isotopic compositions of lipid biomarkers of cultured Aquificales genera have been used to study the community and trophic structure of the hyperthermophilic pink streamers and vent biofilm from Octopus Spring. Thermocrinis ruber, Thermocrinis sp. strain HI 11/12, Hydrogenobacter thermophilus TK-6, Aquifex pyrophilus, and Aquifex aeolicus all contained glycerol-ether phospholipids as well as acyl glycerides. The n-C(20:1) and cy-C(21) fatty acids dominated all of the Aquificales, while the alkyl glycerol ethers were mainly C(18:0). These Aquificales biomarkers were major constituents of the lipid extracts of two Octopus Spring samples, a biofilm associated with the siliceous vent walls, and the well-known pink streamer community (PSC). Both the biofilm and the PSC contained mono- and dialkyl glycerol ethers in which C(18) and C(20) alkyl groups were prevalent. Phospholipid fatty acids included both the Aquificales n-C(20:1) and cy-C(21), plus a series of iso-branched fatty acids (i-C(15:0) to i-C(21:0)), indicating an additional bacterial component. Biomass and lipids from the PSC were depleted in (13)C relative to source water CO(2) by 10.9 and 17.2 per thousand, respectively. The C(20-21) fatty acids of the PSC were less depleted than the iso-branched fatty acids, 18.4 and 22.6 per thousand, respectively. The biomass of T. ruber grown on CO(2) was depleted in (13)C by only 3.3 per thousand relative to C source. In contrast, biomass was depleted by 19.7 per thousand when formate was the C source. Independent of carbon source, T. ruber lipids were heavier than biomass (+1.3 per thousand). The depletion in the C(20-21) fatty acids from the PSC indicates that Thermocrinis biomass must be similarly depleted and too light to be explained by growth on CO(2). Accordingly, Thermocrinis in the PSC is likely to have utilized formate, presumably generated in the spring source region.

Microbiology of ancient and modern hydrothermal systems

Hydrothermal systems have prevailed throughout geological history on earth, and ancient ARCHAEAN hydrothermal deposits could provide clues to understanding earth's earliest biosphere. Modern hydrothermal systems support a plethora of microorganisms and macroorganisms, and provide good comparisons for paleontological interpretation of ancient hydrothermal systems. However, all of the microfossils associated with ancient hydrothermal deposits reported to date are filamentous, and limited STABLE ISOTOPE analysis suggests that these microfossils were probably autotrophs. Therefore, the morphology and mode of carbon metabolism are attributes of microorganisms from modern hydrothermal systems that provide valuable information for interpreting the geological record using morphological and isotopic signatures.

Modern freshwater microbialite analogues for ancient dendritic reef structures

Microbialites are organosedimentary structures that can be constructed by a variety of metabolically distinct taxa. Consequently, microbialite structures abound in the fossil record, although the exact nature of the biogeochemical processes that produced them is often unknown. One such class of ancient calcareous structures, Epiphyton and Girvanella, appear in great abundance during the Early Cambrian. Together with Archeocyathids, stromatolites and thrombolites, they formed major Cambrian reef belts. To a large extent, Middle to Late Cambrian reefs are similar to Precambrian reefs, with the exception that the latter, including terminal Proterozoic reefs, do not contain Epiphyton or Girvanella. Here we report the discovery in Pavilion Lake, British Columbia, Canada, of a distinctive assemblage of freshwater calcite microbialites, some of which display microstructures similar to the fabrics displayed by Epiphyton and Girvanella. The morphologies of the modern microbialites vary with depth, and dendritic microstructures of the deep water (> 30 m) mounds indicate that they may be modern analogues for the ancient calcareous structures. These microbialites thus provide an opportunity to study the biogeochemical interactions that produce fabrics similar to those of some enigmatic Early Cambrian reef structures.

Fossilization processes in siliceous thermal springs: trends in preservation along thermal gradients

To enhance our ability to extract palaeobiological and palaeoenvironmental information from ancient thermal spring deposits, we have studied the processes responsible for the development and preservation of stromatolites in modern subaerial thermal spring systems in Yellowstone National Park (USA). We investigated specimens collected from silica-depositing thermal springs along the thermal gradient using petrographic techniques and scanning electron microscopy. Although it is known that thermophilic cyanobacteria control the morphogenesis of thermal spring stromatolites below 73 degrees C, we have found that biofilms which contain filamentous thermophiles contribute to the microstructural development of subaerial geyserites that occur along the inner rims of thermal spring pools and geyser effluents. Biofilms intermittently colonize the surfaces of subaerial geyserites and provide a favoured substrate for opaline silica precipitation. We have also found that the preservation of biotically produced microfabrics of thermal spring sinters reflects dynamic balances between rates of population growth, decomposition of organic matter, silica deposition and early diagenesis. Major trends in preservation of thermophilic organisms along the thermal gradient are defined by differences in the mode of fossilization, including replacement, encrustation and permineralization.