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Clodoré L, Foucher F, Hickman-Lewis K, Sorieul S, Jouve J, Réfrégiers M, Collet G, Petoud S, Gratuze B, Westall F. Multi-Technique Characterization of 3.45 Ga Microfossils on Earth: A Key Approach to Detect Possible Traces of Life in Returned Samples from Mars. ASTROBIOLOGY 2024; 24:190-226. [PMID: 38393828 DOI: 10.1089/ast.2023.0089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
The NASA Mars 2020 Perseverance rover is actively exploring Jezero crater to conduct analyses on igneous and sedimentary rock targets from outcrops located on the crater floor (Máaz and Séítah formations) and from the delta deposits, respectively. The rock samples collected during this mission will be recovered during the Mars Sample Return mission, which plans to bring samples back to Earth in the 2030s to conduct in-depth studies using sophisticated laboratory instrumentation. Some of these samples may contain traces of ancient martian life that may be particularly difficult to detect and characterize because of their morphological simplicity and subtle biogeochemical expressions. Using the volcanic sediments of the 3.45 Ga Kitty's Gap Chert (Pilbara, Australia), containing putative early life forms (chemolithotrophs) and considered as astrobiological analogues for potential early Mars organisms, we document the steps required to demonstrate the syngenicity and biogenicity of such biosignatures using multiple complementary analytical techniques to provide information at different scales of observation. These include sedimentological, petrological, mineralogical, and geochemical analyses to demonstrate macro- to microscale habitability. New approaches, some unavailable at the time of the original description of these features, are used to verify the syngenicity and biogenicity of the purported fossil chemolithotrophs. The combination of elemental (proton-induced X-ray emission spectrometry) and molecular (deep-ultraviolet and Fourier transform infrared) analyses of rock slabs, thin sections, and focused ion beam sections reveals that the carbonaceous matter present in the samples is enriched in trace metals (e.g., V, Cr, Fe, Co) and is associated with aromatic and aliphatic molecules, which strongly support its biological origin. Transmission electron microscopy observations of the carbonaceous matter documented an amorphous nanostructure interpreted to correspond to the degraded remains of microorganisms and their by-products (extracellular polymeric substances, filaments…). Nevertheless, a small fraction of carbonaceous particles has signatures that are more metamorphosed. They probably represent either reworked detrital biological or abiotic fragments of mantle origin. This study serves as an example of the analytical protocol that would be needed to optimize the detection of fossil traces of life in martian rocks.
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Affiliation(s)
- Laura Clodoré
- CNRS-Centre de Biophysique Moléculaire, Orléans, France
| | - Frédéric Foucher
- CNRS-Centre de Biophysique Moléculaire, Orléans, France
- CNRS-Conditions Extrêmes et Matériaux: Haute Température et Irradiation, Orléans, France
| | - Keyron Hickman-Lewis
- Natural History Museum, London, United Kingdom
- Dipartimento BiGeA, Università di Bologna, Bologna, Italy
| | | | - Jean Jouve
- University of Bordeaux, CNRS, IN2P3, CENBG, Gradignan, France
| | | | - Guillaume Collet
- CNRS-Centre de Biophysique Moléculaire, Orléans, France
- Chair of Cosmetology, AgroParisTech Innovation, Orléans, France
| | | | - Bernard Gratuze
- CNRS-Institut de Recherche sur les ArchéoMATériaux, Orléans, France
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Diaz GR, Gaire TN, Ferm P, Case L, Caixeta LS, Goldsmith TJ, Armstrong J, Noyes NR. Effect of castration timing and weaning strategy on the taxonomic and functional profile of ruminal bacteria and archaea of beef calves. Anim Microbiome 2023; 5:61. [PMID: 38041127 PMCID: PMC10691087 DOI: 10.1186/s42523-023-00284-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 11/28/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND Beef cattle experience several management challenges across their lifecycle. Castration and weaning, two major interventions in the early life of beef cattle, can have a substantial impact on animal performance. Despite the key role of the rumen microbiome on productive traits of beef cattle, the effect of castration timing and weaning strategy on this microbial community has not been formally described. We assessed the effect of four castration time windows (at birth, turnout, pre-weaning and weaning) and two weaning strategies (fence-line and truck transportation) on the rumen microbiome in a randomized controlled study with 32 male calves across 3 collection days (i.e., time points). Ruminal fluid samples were submitted to shotgun metagenomic sequencing and changes in the taxonomic (microbiota) and functional profile (metagenome) of the rumen microbiome were described. RESULTS Using a comprehensive yet stringent taxonomic classification approach, we identified 10,238 unique taxa classified under 40 bacterial and 7 archaeal phyla across all samples. Castration timing had a limited long-term impact on the rumen microbiota and was not associated with changes in alpha and beta diversity. The interaction of collection day and weaning strategy was associated with changes in the rumen microbiota, which experienced a significant decrease in alpha diversity and shifts in beta diversity within 48 h post-weaning, especially in calves abruptly weaned by truck transportation. Calves weaned using a fence-line weaning strategy had lower relative abundance of Bacteroides, Lachnospira, Fibrobacter and Ruminococcus genera compared to calves weaned by truck transportation. Some genes involved in the hydrogenotrophic methanogenesis pathway (fwdB and fwdF) had higher relative abundance in fence-line-weaned calves post-weaning. The antimicrobial resistance gene tetW consistently represented more than 50% of the resistome across time, weaning and castration groups, without significant changes in relative abundance. CONCLUSIONS Within the context of this study, castration timing had limited long-term effects on the rumen microbiota, while weaning strategy had short-term effects on the rumen microbiota and methane-associated metagenome, but not on the rumen resistome.
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Affiliation(s)
- Gerardo R Diaz
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Tara N Gaire
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Peter Ferm
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Lacey Case
- North Central Research and Outreach Center, Department of Animal Science, University of Minnesota, St. Paul, MN, 55108, USA
| | - Luciano S Caixeta
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Timothy J Goldsmith
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Joe Armstrong
- Agricultural and Natural Resource Systems, University of Minnesota Extension, University of Minnesota, St. Paul, MN, 55108, USA
| | - Noelle R Noyes
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA.
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Rodriguez JAP, Wilhelm MB, Travis B, Kargel JS, Zarroca M, Berman DC, Cohen J, Baker V, Lopez A, Buckner D. Exploring the evidence of Middle Amazonian aquifer sedimentary outburst residues in a Martian chaotic terrain. Sci Rep 2023; 13:17524. [PMID: 37853014 PMCID: PMC10584912 DOI: 10.1038/s41598-023-39060-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 07/19/2023] [Indexed: 10/20/2023] Open
Abstract
The quest for past Martian life hinges on locating surface formations linked to ancient habitability. While Mars' surface is considered to have become cryogenic ~3.7 Ga, stable subsurface aquifers persisted long after this transition. Their extensive collapse triggered megafloods ~3.4 Ga, and the resulting outflow channel excavation generated voluminous sediment eroded from the highlands. These materials are considered to have extensively covered the northern lowlands. Here, we show evidence that a lacustrine sedimentary residue within Hydraotes Chaos formed due to regional aquifer upwelling and ponding into an interior basin. Unlike the northern lowland counterparts, its sedimentary makeup likely consists of aquifer-expelled materials, offering a potential window into the nature of Mars' subsurface habitability. Furthermore, the lake's residue's estimated age is ~1.1 Ga (~3.2 Ga post-peak aquifer drainage during the Late Hesperian), enhancing the prospects for organic matter preservation. This deposit's inferred fine-grained composition, coupled with the presence of coexisting mud volcanoes and diapirs, suggest that its source aquifer existed within abundant subsurface mudstones, water ice, and evaporites, forming part of the region's extremely ancient (~ 4 Ga) highland stratigraphy. Our numerical models suggest that magmatically induced phase segregation within these materials generated enormous water-filled chambers. The meltwater, originating from varying thermally affected mudstone depths, could have potentially harbored diverse biosignatures, which could have become concentrated within the lake's sedimentary residue. Thus, we propose that Hydraotes Chaos merits priority consideration in future missions aiming to detect Martian biosignatures.
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Affiliation(s)
- J Alexis P Rodriguez
- Planetary Science Institute, 1700 East Fort Lowell Road, Suite 106, Tucson, AZ, 85719-2395, USA.
- External Geodynamics and Hydrogeology Group, Department of Geology, Autonomous University of Barcelona, Bellaterra, 08193, Barcelona, Spain.
| | | | - Bryan Travis
- Planetary Science Institute, 1700 East Fort Lowell Road, Suite 106, Tucson, AZ, 85719-2395, USA
| | - Jeffrey S Kargel
- Planetary Science Institute, 1700 East Fort Lowell Road, Suite 106, Tucson, AZ, 85719-2395, USA
| | - Mario Zarroca
- External Geodynamics and Hydrogeology Group, Department of Geology, Autonomous University of Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Daniel C Berman
- Planetary Science Institute, 1700 East Fort Lowell Road, Suite 106, Tucson, AZ, 85719-2395, USA
| | - Jacob Cohen
- NASA Ames Research Center, Moffett Field, CA, 94035, USA
| | - Victor Baker
- Department of Hydrology and Atmospheric Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Anthony Lopez
- Planetary Science Institute, 1700 East Fort Lowell Road, Suite 106, Tucson, AZ, 85719-2395, USA
| | - Denise Buckner
- Blue Marble Space Institute of Science, Seattle, WA, 98104, USA
- University of Florida, Gainesville, FL, 32611, USA
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Basapathi Raghavendra J, Zorzano MP, Kumaresan D, Martin-Torres J. DNA sequencing at the picogram level to investigate life on Mars and Earth. Sci Rep 2023; 13:15277. [PMID: 37714862 PMCID: PMC10504319 DOI: 10.1038/s41598-023-42170-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 09/06/2023] [Indexed: 09/17/2023] Open
Abstract
DNA is an incontrovertible biosignature whose sequencing aids in species identification, genome functionality, and evolutionary relationships. To study life within the rocks of Earth and Mars, we demonstrate, in an ISO5 clean room, a procedure based on nanopore technology that correctly identifies organisms at picogram levels of DNA without amplification. Our study with E. coli and S. cerevisiae DNA samples showed that MinION sequencer (Oxford Nanopore Technologies) can unequivocally detect and characterise microbes with as little as 2 pg of input with just 50 active nanopores. This result is an excellent advancement in sensitivity, immediately applicable to investigating low biomass samples. This value is also at the level of possible background contamination associated with the reagents and the environment. Cultivation of natural and heat-treated Martian analogue (MMS-2) regolith samples, exposed to atmospheric water vapour or in increasing water concentrations, led to the extraction of 600-1000 pg of DNA from 500 mg of soil. Applying the low detectability technology enabled through MinION sequencer for a natural low biomass setting, we characterised the dry MMS-2 and found few soil-related organisms and airborne contaminants. The picogram detection level and the procedure presented here, may be of interest for the future Mars sample Return program, and the life research and planetary protection studies that will be implemented through the sample safety assessment.
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Affiliation(s)
- Jyothi Basapathi Raghavendra
- Department of Planetary Sciences, School of Geosciences, University of Aberdeen, Meston Building, Aberdeen, AB24 3UE, Scotland.
| | - Maria-Paz Zorzano
- Centro de Astrobiología (CAB), CSIC-INTA, 28850, Torrejón de Ardoz, Madrid, Spain
| | - Deepak Kumaresan
- School of Biological Sciences, Queen's University Belfast (QUB), Belfast, BT9 5DL, Northern Ireland
| | - Javier Martin-Torres
- Department of Planetary Sciences, School of Geosciences, University of Aberdeen, Meston Building, Aberdeen, AB24 3UE, Scotland
- Instituto Andaluz de Ciencias de la Tierra (CSIC-UGR), 18100, Granada, Spain
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Walther-Antonio M, Schulze-Makuch D. The Hypothesis of a "Living Pulse" in Cells. Life (Basel) 2023; 13:1506. [PMID: 37511881 PMCID: PMC10381587 DOI: 10.3390/life13071506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 06/26/2023] [Accepted: 06/30/2023] [Indexed: 07/30/2023] Open
Abstract
Motility is a great biosignature and its pattern is characteristic for specific microbes. However, motion does also occur within the cell by the myriads of ongoing processes within the cell and the exchange of gases and nutrients with the outside environment. Here, we propose that the sum of these processes in a microbial cell is equivalent to a pulse in complex organisms and suggest a first approach to measure the "living pulse" in microorganisms. We emphasize that if a "living pulse" can be shown to exist, it would have far-reaching applications, such as for finding life in extreme environments on Earth and in extraterrestrial locations, as well as making sure that life is not present where it should not be, such as during medical procedures and in the food processing industry.
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Affiliation(s)
- Marina Walther-Antonio
- Department of Surgery, Division of Surgical Research, Mayo Clinic, Rochester, MN 55905, USA
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN 55905, USA
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Dirk Schulze-Makuch
- Astrobiology Group, Center of Astronomy and Astrophysics, Technical University, 10623 Berlin, Germany
- German Research Centre for Geosciences (GFZ), Section Geomicrobiology, 14473 Potsdam, Germany
- Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, 16775 Stechlin, Germany
- School of the Environment, Washington State University, Pullman, WA 99164, USA
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Fairén AG, Rodríguez N, Sánchez-García L, Rojas P, Uceda ER, Carrizo D, Amils R, Sanz JL. Ecological successions throughout the desiccation of Tirez lagoon (Spain) as an astrobiological time-analog for wet-to-dry transitions on Mars. Sci Rep 2023; 13:1423. [PMID: 36755119 PMCID: PMC9908944 DOI: 10.1038/s41598-023-28327-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 01/17/2023] [Indexed: 02/10/2023] Open
Abstract
Tirez was a small and seasonal endorheic athalassohaline lagoon that was located in central Spain. In recent years, the lagoon has totally dried out, offering for the first time the opportunity to analyze its desiccation process as a "time-analog" to similar events occurred in paleolakes with varying salinity during the wet-to-dry transition on early Mars. On the martian cratered highlands, an early period of water ponding within enclosed basins evolved to a complete desiccation of the lakes, leading to deposition of evaporitic sequences during the Noachian and into the Late Hesperian. As Tirez also underwent a process of desiccation, here we describe (i) the microbial ecology of Tirez when the lagoon was still active 20 years ago, with prokaryotes adapted to extreme saline conditions; (ii) the composition of the microbial community in the dried lake sediments today, in many case groups that thrive in sediments of extreme environments; and (iii) the molecular and isotopic analysis of the lipid biomarkers that can be recovered from the sediments today. We discuss the implications of these results to better understanding the ecology of possible Martian microbial communities during the wet-to-dry transition at the end of the Hesperian, and how they may inform about research strategies to search for possible biomarkers in Mars after all the water was lost.
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Affiliation(s)
- Alberto G Fairén
- Centro de Astrobiología (CSIC-INTA), 28850, Torrejón de Ardoz, Spain. .,Department of Astronomy, Cornell University, Ithaca, NY, 14853, USA.
| | - Nuria Rodríguez
- Centro de Astrobiología (CSIC-INTA), 28850, Torrejón de Ardoz, Spain.,Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain
| | | | - Patricia Rojas
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain
| | - Esther R Uceda
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain
| | - Daniel Carrizo
- Centro de Astrobiología (CSIC-INTA), 28850, Torrejón de Ardoz, Spain
| | - Ricardo Amils
- Centro de Astrobiología (CSIC-INTA), 28850, Torrejón de Ardoz, Spain.,Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain.,Departamento de Biología Molecular, Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain
| | - José L Sanz
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain.
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