Microbial Populations of Stony Meteorites: Substrate Controls on First Colonizers

Higher Microbial Biomass Accumulation on El Médano 464 Meteorite Compared with Adjacent Soils in the Atacama Desert

Chondritic meteorites can be appropriate substrates for the colonization of terrestrial microorganisms. However, determining whether organic compounds are intrinsic to the meteorite or come from external (terrestrial) contamination is still controversial. This research explores the molecular distribution and carbon isotopic composition of three lipid families (hydrocarbons, alkanoic acids, and alcohols) as well as DNA extracted from the interior of a CO carbonaceous chondrite named El Médano 464 (EM 464), discovered in the Atacama Desert in 2019. Three soil samples from the discovery area of EM 464 were collected and used as a background control for the composition and distribution of organic compounds. Our results revealed a higher abundance of the three lipid families in EM 464 compared with the surrounding soil samples. The organic compounds in EM 464 showed a mean δ13C value of -27.8 ± 0.5 for hydrocarbons (N = 20), -27.6 ± 1.1 for alkanoic acids (N = 17), and -27.5 ± 2.2‰ for alcohols (N = 18). These δ13C-depleted values are compatible with terrestrial biosignatures and are within isotopic values produced as a result of carbon fixation due to the Calvin cycle (δ13C of ca. from -19 to -34‰) widely used by photosynthetic terrestrial microorganisms. The DNA analysis (based on the bacterial 16S rRNA gene) showed a dominance of Proteobacteria (now Pseudomonadota) and Actinobacteriota in both meteorite and soils but exhibited different bacterial composition at the family level. This suggests that the microbial material inside the meteorite may have partially come from the adjacent soils, but we cannot rule out other sources, such as windborne microbes from distant locations. In addition, the meteorite showed higher bacterial diversity (H' = 2.4-2.8) compared with the three soil samples (H' = 0.3-1.8). Based on the distribution and δ13C value of organic compounds as well as DNA analysis, we suggest that most, if not all, of the organic compounds detected in the studied CO chondrite are of terrestrial origin (i.e., contamination). The terrestrial contamination of EM 464 by a diverse microbial community indicates that Atacama chondrites can offer distinctive ecological conditions for microorganisms to thrive in the harsh desert environment, which can result in an accumulation of microbial biomass and preservation of molecular fossils over time.

Life on Earth can grow on extraterrestrial organic carbon

The universe is a vast store of organic abiotic carbon that could potentially drive heterotrophy on habitable planets. Meteorites are one of the transporters of this carbon to planetary surfaces. Meteoritic material was accumulating on early Earth when life emerged and proliferated. Yet it is not known if this organic carbon from space was accessible to life. In this research, an anaerobic microbial community was grown with the CM2 carbonaceous chondrite Aguas Zarcas as the sole carbon, energy and nutrient source. Using a reversed 13C-stable isotope labelling experiment in combination with optical photothermal infrared (O-PTIR) spectroscopy of single cells, this paper demonstrates the direct transfer of carbon from meteorite into microbial biomass. This implies that meteoritic organics could have been used as a carbon source on early Earth and other habitable planets, and supports the potential for a heterotrophic metabolism in early living systems.

Ancestors in the Extreme: A Genomics View of Microbial Diversity in Hypersaline Aquatic Environments

The origin of eukaryotic cells, and especially naturally occurring syncytial cells, remains debatable. While a majority of our biomedical research focuses on the eukaryotic result of evolution, our data remain limiting on the prokaryotic precursors of these cells. This is particularly evident when considering extremophile biology, especially in how the genomes of organisms in extreme environments must have evolved and adapted to unique habitats. Might these rapidly diversifying organisms have created new genetic tools eventually used to enhance the evolution of the eukaryotic single nuclear or syncytial cells? Many organisms are capable of surviving, or even thriving, in conditions of extreme temperature, acidity, organic composition, and then rapidly adapt to yet new conditions. This study identified organisms found in extremes of salinity. A lake and a nearby pond in the Ethiopian Rift Valley were interrogated for life by sequencing the DNA of populations of organism collected from the water in these sites. Remarkably, a vast diversity of microbes were identified, and even though the two sites were nearby each other, the populations of organisms were distinctly different. Since these microbes are capable of living in what for humans would be inhospitable conditions, the DNA sequences identified should inform the next step in these investigations; what new gene families, or modifications to common genes, do these organisms employ to survive in these extreme conditions. The relationship between organisms and their environment can be revealed by decoding genomes of organisms living in extreme environments. These genomes disclose new biological mechanisms that enable life outside moderate environmental conditions, new gene functions for application in biotechnology, and may even result in identification of new species. In this study, we have collected samples from two hypersaline sites in the Danakil depression, the shorelines of Lake As'ale and an actively mixing salt pond called Muda'ara (MUP), to identify the microbial community by metagenomics. Shotgun sequencing was applied to high density sampling, and the relative abundance of Operational Taxonomic Units (OTUs) was calculated. Despite the broad taxonomic similarities among the salt-saturated metagenomes analyzed, MUP stood out from Lake As'ale samples. In each sample site, Archaea accounted for 95% of the total OTUs, largely to the class Halobacteria. The remaining 5% of organisms were eubacteria, with an unclassified strain of Salinibacter ruber as the dominant OTU in both the Lake and the Pond. More than 40 different genes coding for stress proteins were identified in the three sample sites of Lake As'ale, and more than 50% of the predicted stress-related genes were associated with oxidative stress response proteins. Chaperone proteins (DnaK, DnaJ, GrpE, and ClpB) were predicted, with percentage of query coverage and similarities ranging between 9.5% and 99.2%. Long reads for ClpB homologous protein from Lake As'ale metagenome datasets were modeled, and compact 3D structures were generated. Considering the extreme environmental conditions of the Danakil depression, this metagenomics dataset can add and complement other studies on unique gene functions on stress response mechanisms of thriving bio-communities that could have contributed to cellular changes leading to single and/or multinucleated eukaryotic cells.

Archaea and their interactions with bacteria in a karst ecosystem

Karst ecosystems are widely distributed around the world, accounting for 15-20% of the global land area. However, knowledge on microbial ecology of these systems does not match with their global importance. To close this knowledge gap, we sampled three niches including weathered rock, sediment, and drip water inside the Heshang Cave and three types of soils overlying the cave (forest soil, farmland soil, and pristine karst soil). All these samples were subjected to high-throughput sequencing of V4-V5 region of 16S rRNA gene and analyzed with multivariate statistical analysis. Overall, archaeal communities were dominated by Thaumarchaeota, whereas Actinobacteria dominated bacterial communities. Thermoplasmata, Nitrosopumilaceae, Aenigmarchaeales, Crossiella, Acidothermus, and Solirubrobacter were the important predictor groups inside the Heshang Cave, which were correlated to NH4 + availability. In contrast, Candidatus Nitrososphaera, Candidatus Nitrocosmicus, Thaumarchaeota Group 1.1c, and Pseudonocardiaceae were the predictors outside the cave, whose distribution was correlated with pH, Ca2+, and NO2 -. Tighter network structures were found in archaeal communities than those of bacteria, whereas the topological properties of bacterial networks were more similar to those of total prokaryotic networks. Both chemolithoautotrophic archaea (Candidatus Methanoperedens and Nitrosopumilaceae) and bacteria (subgroup 7 of Acidobacteria and Rokubacteriales) were the dominant keystone taxa within the co-occurrence networks, potentially playing fundamental roles in obtaining energy under oligotrophic conditions and thus maintaining the stability of the cave ecosystem. To be noted, all the keystone taxa of karst ecosystems were related to nitrogen cycling, which needs further investigation, particularly the role of archaea. The predicted ecological functions in karst soils mainly related to carbohydrate metabolism, biotin metabolism, and synthesis of fatty acid. Our results offer new insights into archaeal ecology, their potential functions, and archaeal interactions with bacteria, which enhance our understanding about the microbial dark matter in the subsurface karst ecosystems.

Meteorites as Food Source on Early Earth: Growth, Selection, and Inhibition of a Microbial Community on a Carbonaceous Chondrite

Meteoritic material accumulated on the surface of the anoxic early Earth during the Late Heavy Bombardment around 4.0 Gya and may have provided Earth's surface with extraterrestrial nutrients and energy sources. This research investigates the growth of an anaerobic microbial community from pond sediment on native and pyrolyzed (heat-treated) carbonaceous chondrite Cold Bokkeveld. The community was grown anaerobically in liquid media. Native Cold Bokkeveld supported the growth of a phylogenetically clustered subset of the original pond community by habitat filtering. The anaerobic community on meteorite was dominated by the Deltaproteobacteria Geobacteraceae and Desulfuromonadaceae. Members of these taxa are known to use elemental sulfur and ferric iron as electron acceptors, and organic compounds as electron donors. Pyrolyzed Cold Bokkeveld, however, was inhibitory to the growth of the microbial community. These results show that carbonaceous chondrites can support and select for a specific anaerobic microbial community, but that pyrolysis, for example by geothermal activity, could inhibit microbial growth and toxify the material. This research shows that extraterrestrial meteoritic material can shape the abundance and composition of anaerobic microbial ecosystems with implications for early Earth. These results also provide a basis to design anaerobic material processing of asteroidal material for future human settlement.

Preservation of Terrestrial Microorganisms and Organics Within Alteration Products of Chondritic Meteorites from the Nullarbor Plain, Australia

Meteorites that fall to Earth quickly become contaminated with terrestrial microorganisms. These meteorites are out of chemical equilibrium in the environments where they fall, and equilibration promotes formation of low-temperature alteration minerals that can entomb contaminant microorganisms and thus preserve them as microfossils. Given the well-understood chemistry of meteorites and their recent discovery on Mars by rovers, a similarly weathered meteorite on Mars could preserve organic and fossil evidence of a putative past biosphere at the martian surface. Here, we used several techniques to assess the potential of alteration minerals to preserve microfossils and biogenic organics in terrestrially weathered ordinary chondrites from the Nullarbor Plain, Australia. We used acid etching of ordinary chondrites to reveal entombed fungal hyphae, modern biofilms, and diatoms within alteration minerals. We employed synchrotron X-ray fluorescence microscopy of alteration mineral veins to map the distribution of redox-sensitive elements of relevance to chemolithotrophic organisms, such as Mn-cycling bacteria. We assessed the biogenicity of fungal hyphae within alteration veins using a combination of Fourier-transform infrared spectroscopy and pyrolysis gas chromatography-mass spectrometry, which showed that alteration minerals sequester and preserve organic molecules at various levels of decomposition. Our combined analyses results show that fossil microorganisms and the organic molecules they produce are preserved within calcite-gypsum admixtures in meteorites. Furthermore, the distributions of redox-sensitive elements (e.g., Mn) within alteration minerals are localized, which qualitatively suggests that climatically or microbially facilitated element mobilization occurred during the meteorite's residency on Earth. If returned as part of a sample suite from the martian surface, ordinary chondrites could preserve similar, recognizable evidence of putative past life and/or environmental change.

The smallest space miners: principles of space biomining

As we aim to expand human presence in space, we need to find viable approaches to achieve independence from terrestrial resources. Space biomining of the Moon, Mars and asteroids has been indicated as one of the promising approaches to achieve in-situ resource utilization by the main space agencies. Structural and expensive metals, essential mineral nutrients, water, oxygen and volatiles could be potentially extracted from extraterrestrial regolith and rocks using microbial-based biotechnologies. The use of bioleaching microorganisms could also be applied to space bioremediation, recycling of waste and to reinforce regenerative life support systems. However, the science around space biomining is still young. Relevant differences between terrestrial and extraterrestrial conditions exist, including the rock types and ores available for mining, and a direct application of established terrestrial biomining techniques may not be a possibility. It is, therefore, necessary to invest in terrestrial and space-based research of specific methods for space applications to learn the effects of space conditions on biomining and bioremediation, expand our knowledge on organotrophic and community-based bioleaching mechanisms, as well as on anaerobic biomining, and investigate the use of synthetic biology to overcome limitations posed by the space environments.

Prokaryotic and Fungal Characterization of the Facilities Used to Assemble, Test, and Launch the OSIRIS-REx Spacecraft

To characterize the ATLO (Assembly, Test, and Launch Operations) environment of the OSIRIS-REx spacecraft, we analyzed 17 aluminum witness foils and two blanks for bacterial, archaeal, fungal, and arthropod DNA. Under NASA’s Planetary Protection guidelines, OSIRIS-REx is a Category II outbound, Category V unrestricted sample return mission. As a result, it has no bioburden restrictions. However, the mission does have strict organic contamination requirements to achieve its primary objective of returning pristine carbonaceous asteroid regolith to Earth. Its target, near-Earth asteroid (101955) Bennu, is likely to contain organic compounds that are biologically available. Therefore, it is useful to understand what organisms were present during ATLO as part of the larger contamination knowledge effort—even though it is unlikely that any of the organisms will survive the multi-year deep space journey. Even though these samples of opportunity were not collected or preserved for DNA analysis, we successfully amplified bacterial and archaeal DNA (16S rRNA gene) from 16 of the 17 witness foils containing as few as 7 ± 3 cells per sample. Fungal DNA (ITS1) was detected in 12 of the 17 witness foils. Despite observing arthropods in some of the ATLO facilities, arthropod DNA (COI gene) was not detected. We observed 1,009 bacterial and archaeal sOTUs (sub-operational taxonomic units, 100% unique) and 167 fungal sOTUs across all of our samples (25–84 sOTUs per sample). The most abundant bacterial sOTU belonged to the genus Bacillus. This sOTU was present in blanks and may represent contamination during sample handling or storage. The sample collected from inside the fairing just prior to launch contained several unique bacterial and fungal sOTUs that describe previously uncharacterized potential for contamination during the final phase of ATLO. Additionally, fungal richness (number of sOTUs) negatively correlates with the number of carbon-bearing particles detected on samples. The total number of fungal sequences positively correlates with total amino acid concentration. These results demonstrate that it is possible to use samples of opportunity to characterize the microbiology of low-biomass environments while also revealing the limitations imposed by sample collection and preservation methods not specifically designed with biology in mind.

Rubrobacter tropicus sp. nov. and Rubrobacter marinus sp. nov., isolated from deep-sea sediment of the South China Sea

Two novel Gram-stain-positive bacteria, designated as SCSIO 52909^T and SCSIO 52915^T, were isolated from a deep-sea sediment sample collected at about 3448 m water depth of the South China Sea. Phenotypic, chemotaxonomic and genomic characteristics were investigated. These strains were aerobic and tested positive for catalase activity, oxidase activity and nitrate reduction. Optimal growth occurred at 28 °C, pH 7 and 3% salinity over 14 days cultivation. Its peptidoglycan structure was type A3α (l-Lys-l-Ala) and the only menaquinone was MK-8. Both strains possessed diphosphatidylglycerol, phosphatidylglycerol, an unidentified phosphoglycolipid, an unidentified glycolipid and an unidentified phospholipid. Their major fatty acids differed, but both contained iso-branched components of C_16 : 0 12-methyl. Genome sequencing revealed two large genomes of 4.58 Mbp with G+C content of 67.0 mol% in SCSIO 52909^T and of 4.42 Mbp with G+C content of 69.1 % in SCSIO 52915^T. The two novel strains encoded genes for metabolism that are absent in most other Rubrobacter species, and possessed many more gene copy numbers of alkaline phosphatase and thioredoxin reductase. Results of gANI and 16S rRNA gene analyses suggested that the two strains represent two new species, with 74.9, 95.0 % pairwise similarity between each other, and less than 74.3 and 93.5 % to other recognized Rubrobacter species, respectively. In the phylogenetic analysis, strains SCSIO 52909^T and SCSIO 52915^T were separately clustered together and formed a well-separated phylogenetic branch distinct from the other known species in the genus Rubrobacter. Based on the data presented here, these two strains should be recognized as two new species in the genus Rubrobacter, for which the names Rubrobacter tropicus sp. nov., with the type strain SCSIO 52909^T (=KCTC 49412^T=CGMCC 1.13853^T), and Rubrobacter marinus sp. nov., with the type strain SCSIO 52915^T (=KCTC 49411^T=CGMCC 1.13852^T), are proposed.

Eukaryotic Colonization of Micrometer-Scale Cracks in Rocks: A "Microfluidics" Experiment Using Naturally Weathered Meteorites from the Nullarbor Plain, Australia

The advent of microfluidics has revolutionized the way we understand how microorganisms propagate through microporous spaces. Here, we apply this understanding to the study of how endolithic environmental microorganisms colonize the interiors of sterile rock. The substrates used for our study are stony meteorites from the Nullarbor Plain, Australia; a semiarid limestone karst that provides an ideal setting for preserving meteorites. Periodic flooding of the Nullarbor provides a mechanism by which microorganisms and exogenous nutrients may infiltrate meteorites. Our laboratory experiments show that environmental microorganisms reach depths greater than 400 μm by propagating through existing brecciation, passing through cracks no wider than the diameter of a resident cell (i.e., ∼5 μm). Our observations are consistent with the propagation of these eukaryotic cells via growth and cell division rather than motility. The morphology of the microorganisms changed as a result of propagation through micrometer-scale cracks, as has been observed previously for bacteria on microfluidic chips. It has been suggested that meteorites could have served as preferred habitats for microorganisms on ancient Mars. Based on our results, the depths reached by terrestrial microorganisms within meteorites would be sufficient to mitigate against the harmful effects of ionizing radiation, such as UV light, in Earth's deserts and potentially on Mars, if similar processes of microbial colonization had once been active there. Thus, meteorites landing in ancient lakes on Mars, that later dried out, could have been some of the last inhabited locations on the surface, serving as refugia before the planet's surface became inhospitable. Finally, our observations suggest that terrestrial microorganisms can colonize very fine cracks within meteorites (and potentially spaceships and rovers) on unexpectedly short timescales, with important implications for both recognition of extraterrestrial life in returned geological samples and planetary protection.

Functional capabilities of bacterial biofilms on gold particles

Gold particles contain gold and other toxic, heavy metals, making them ‘extreme’ geochemical microenvironments. To date, the functional capabilities of bacterial biofilms to deal with these conditions have been inferred from taxonomic analyses. The aims of this study are to evaluate the functional capabilities of bacterial communities on gold particles from six key locations using GeoChip 5.0 and to link functional and taxonomic data. Biofilm communities displayed a wide range of functional capabilities, with up to 53 505 gene probes detected. The capability of bacterial communities to (re)cycle carbon, nitrogen, and sulphur were detected. The cycling of major nutrients is important for maintaining the biofilm community as well as enabling the biogeochemical cycling and mobilisation of heavy and noble metals. Additionally, a multitude of stress- and heavy metal resistance capabilities were also detected, most notably from the α/β/γ-Proteobacteria and Actinobacteria. The multi-copper-oxidase gene copA, which is directly involved in gold resistance and biomineralisation, was the 15th most intense response and was detected in 246 genera. The Parker Road and Belle Brooke sites were consistently the most different from other sites, which may be a result of local physicochemical conditions (extreme nutrient poverty and sulphur-richness, respectively). In conclusion, biofilms on gold particles display wide-ranging metabolic and stress-related capabilities, which may enable them to survive in these niche environments and drive biotransformation of gold particles.

Exploring the microbial biotransformation of extraterrestrial material on nanometer scale

Exploration of microbial-meteorite redox interactions highlights the possibility of bioprocessing of extraterrestrial metal resources and reveals specific microbial fingerprints left on extraterrestrial material. In the present study, we provide our observations on a microbial-meteorite nanoscale interface of the metal respiring thermoacidophile Metallosphaera sedula. M. sedula colonizes the stony meteorite Northwest Africa 1172 (NWA 1172; an H5 ordinary chondrite) and releases free soluble metals, with Ni ions as the most solubilized. We show the redox route of Ni ions, originating from the metallic Ni° of the meteorite grains and leading to released soluble Ni²⁺. Nanoscale resolution ultrastructural studies of meteorite grown M. sedula coupled to electron energy loss spectroscopy (EELS) points to the redox processing of Fe-bearing meteorite material. Our investigations validate the ability of M. sedula to perform the biotransformation of meteorite minerals, unravel microbial fingerprints left on meteorite material, and provide the next step towards an understanding of meteorite biogeochemistry. Our findings will serve in defining mineralogical and morphological criteria for the identification of metal-containing microfossils.

The Ecology of Subaerial Biofilms in Dry and Inhospitable Terrestrial Environments

The ecological relationship between minerals and microorganisms arguably represents one of the most important associations in dry terrestrial environments, since it strongly influences major biochemical cycles and regulates the productivity and stability of the Earth’s food webs. Despite being inhospitable ecosystems, mineral substrata exposed to air harbor form complex and self-sustaining communities called subaerial biofilms (SABs). Using life on air-exposed minerals as a model and taking inspiration from the mechanisms of some microorganisms that have adapted to inhospitable conditions, we illustrate the ecology of SABs inhabiting natural and built environments. Finally, we advocate the need for the convergence between the experimental and theoretical approaches that might be used to characterize and simulate the development of SABs on mineral substrates and SABs’ broader impacts on the dry terrestrial environment.