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Lezcano MÁ, Bornemann TLV, Sánchez-García L, Carrizo D, Adam PS, Esser SP, Cabrol NA, Probst AJ, Parro V. Hyperexpansion of genetic diversity and metabolic capacity of extremophilic bacteria and archaea in ancient Andean lake sediments. MICROBIOME 2024; 12:176. [PMID: 39300577 PMCID: PMC11411797 DOI: 10.1186/s40168-024-01878-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 07/19/2024] [Indexed: 09/22/2024]
Abstract
BACKGROUND The Andean Altiplano hosts a repertoire of high-altitude lakes with harsh conditions for life. These lakes are undergoing a process of desiccation caused by the current climate, leaving terraces exposed to extreme atmospheric conditions and serving as analogs to Martian paleolake basins. Microbiomes in Altiplano lake terraces have been poorly studied, enclosing uncultured lineages and a great opportunity to understand environmental adaptation and the limits of life on Earth. Here we examine the microbial diversity and function in ancient sediments (10.3-11 kyr BP (before present)) from a terrace profile of Laguna Lejía, a sulfur- and metal/metalloid-rich saline lake in the Chilean Altiplano. We also evaluate the physical and chemical changes of the lake over time by studying the mineralogy and geochemistry of the terrace profile. RESULTS The mineralogy and geochemistry of the terrace profile revealed large water level fluctuations in the lake, scarcity of organic carbon, and high concentration of SO42--S, Na, Cl and Mg. Lipid biomarker analysis indicated the presence of aquatic/terrestrial plant remnants preserved in the ancient sediments, and genome-resolved metagenomics unveiled a diverse prokaryotic community with still active microorganisms based on in silico growth predictions. We reconstructed 591 bacterial and archaeal metagenome-assembled genomes (MAGs), of which 98.8% belonged to previously unreported species. The most abundant and widespread metabolisms among MAGs were the reduction and oxidation of S, N, As, and halogenated compounds, as well as aerobic CO oxidation, possibly as a key metabolic trait in the organic carbon-depleted sediments. The broad redox and CO2 fixation pathways among phylogenetically distant bacteria and archaea extended the knowledge of metabolic capacities to previously unknown taxa. For instance, we identified genomic potential for dissimilatory sulfate reduction in Bacteroidota and α- and γ-Proteobacteria, predicted an enzyme for ammonia oxidation in a novel Actinobacteriota, and predicted enzymes of the Calvin-Benson-Bassham cycle in Planctomycetota, Gemmatimonadota, and Nanoarchaeota. CONCLUSIONS The high number of novel bacterial and archaeal MAGs in the Laguna Lejía indicates the wide prokaryotic diversity discovered. In addition, the detection of genes in unexpected taxonomic groups has significant implications for the expansion of microorganisms involved in the biogeochemical cycles of carbon, nitrogen, and sulfur. Video Abstract.
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Affiliation(s)
- María Ángeles Lezcano
- Centro de Astrobiología (CAB), CSIC-INTA, 28850, Torrejón de Ardoz, Madrid, Spain.
- IMDEA Water Institute, Avenida Punto Com 2, 28805, Alcalá de Henares, Madrid, Spain.
| | - Till L V Bornemann
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
- Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany
| | - Laura Sánchez-García
- Centro de Astrobiología (CAB), CSIC-INTA, 28850, Torrejón de Ardoz, Madrid, Spain
| | - Daniel Carrizo
- Centro de Astrobiología (CAB), CSIC-INTA, 28850, Torrejón de Ardoz, Madrid, Spain
| | - Panagiotis S Adam
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
- Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Sarah P Esser
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Nathalie A Cabrol
- SETI Institute, 339 Bernardo Avenue, Suite 200, Mountain View, CA, 94043, USA
| | - Alexander J Probst
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
- Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany
| | - Víctor Parro
- Centro de Astrobiología (CAB), CSIC-INTA, 28850, Torrejón de Ardoz, Madrid, Spain
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Severino R, Moreno-Paz M, Puente-Sánchez F, Sánchez-García L, Risso VA, Sanchez-Ruiz JM, Cabrol N, Parro V. Immunoanalytical Approach for Detecting and Identifying Ancestral Peptide Biomarkers in Early Earth Analogue Environments. Anal Chem 2023; 95:5323-5330. [PMID: 36926836 PMCID: PMC10061368 DOI: 10.1021/acs.analchem.2c05386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/13/2023] [Indexed: 03/18/2023]
Abstract
Several mass spectrometry and spectroscopic techniques have been used in the search for molecular biomarkers on Mars. A major constraint is their capability to detect and identify large and complex compounds such as peptides or other biopolymers. Multiplex immunoassays can detect these compounds, but antibodies must be produced for a large number of sequence-dependent molecular targets. Ancestral Sequence Reconstruction (ASR) followed by protein "resurrection" in the lab can help to narrow the selection of targets. Herein, we propose an immunoanalytical method to identify ancient and universally conserved protein/peptide sequences as targets for identifying ancestral biomarkers in nature. We have developed, tested, and validated this approach by producing antibodies to eight previously described ancestral resurrected proteins (three β-lactamases, three thioredoxins, one Elongation Factor Tu, and one RuBisCO, all of them theoretically dated as Precambrian), and used them as a proxy to search for any potential feature of them that could be present in current natural environments. By fluorescent sandwich microarray immunoassays (FSMI), we have detected positive immunoreactions with antibodies to the oldest β-lactamase and thioredoxin proteins (ca. 4 Ga) in samples from a hydrothermal environment. Fine epitope mapping and inhibitory immunoassays allowed the identification of well-conserved epitope peptide sequences that resulted from ASR and were present in the sample. We corroborated these results by metagenomic sequencing and found several genes encoding analogue proteins with significant matches to the peptide epitopes identified with the antibodies. The results demonstrated that peptides inferred from ASR studies have true counterpart analogues in Nature, which validates and strengthens the well-known ASR/protein resurrection technique and our immunoanalytical approach for investigating ancient environments and metabolisms on Earth and elsewhere.
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Affiliation(s)
- Rita Severino
- Centro
de Astrobiología (CAB), CSIC-INTA, 28850 Torrejón de Ardoz, Madrid, Spain
- PhD
Program in Space Research and Astrobiology, University of Alcalá (UAH), 28805 Alcalá de Henares, Madrid, Spain
| | - Mercedes Moreno-Paz
- Centro
de Astrobiología (CAB), CSIC-INTA, 28850 Torrejón de Ardoz, Madrid, Spain
| | - Fernando Puente-Sánchez
- Department
of Aquatic Sciences and Assessment, Swedish
University of Agricultural Sciences (SLU), 75651 Uppsala, Sweden
| | - Laura Sánchez-García
- Centro
de Astrobiología (CAB), CSIC-INTA, 28850 Torrejón de Ardoz, Madrid, Spain
| | - Valeria A. Risso
- Departamento
de Química Física, Facultad de Ciencias, Unidad de Excelencia
de Química Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071 Granada, Spain
| | - Jose M. Sanchez-Ruiz
- Departamento
de Química Física, Facultad de Ciencias, Unidad de Excelencia
de Química Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071 Granada, Spain
| | - Nathalie Cabrol
- Carl
Sagan Center for the Study of Life in the Universe, SETI Institute, Mountain
View, California 94043, United States
| | - Victor Parro
- Centro
de Astrobiología (CAB), CSIC-INTA, 28850 Torrejón de Ardoz, Madrid, Spain
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