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Storz JF, Liphardt S, Quiroga-Carmona M, Bautista NM, Opazo JC, Wheeler TB, D'Elía G, Good JM. Genomic insights into the mystery of mouse mummies on the summits of Atacama volcanoes. Curr Biol 2023; 33:R1040-R1042. [PMID: 37875074 PMCID: PMC10652914 DOI: 10.1016/j.cub.2023.08.081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 08/14/2023] [Accepted: 08/17/2023] [Indexed: 10/26/2023]
Abstract
Our understanding of the limits of animal life is continually revised by scientific exploration of extreme environments. Here we report the discovery of mummified cadavers of leaf-eared mice, Phyllotis vaccarum, from the summits of three different Andean volcanoes at elevations 6,029-6,233 m above sea level in the Puna de Atacama in Chile and Argentina. Such extreme elevations were previously assumed to be completely uninhabitable by mammals. In combination with a live-captured specimen of the same species from the nearby summit of Volcán Llullaillaco (6,739 m)1, the summit mummies represent the highest altitude physical records of mammals in the world. We also report a chromosome-level genome assembly for P. vaccarum that, in combination with a whole-genome re-sequencing analysis and radiocarbon dating analysis, provides insights into the provenance and antiquity of the summit mice. Radiocarbon data indicate that the most ancient of the mummies are, at most, a few centuries old. Genomic polymorphism data revealed a high degree of continuity between the summit mice and conspecifics from lower elevations in the surrounding Altiplano. Genomic data also revealed equal numbers of males and females among the summit mice and evidence of close kinship between some individuals from the same summits. These findings bolster evidence for resident populations of Phyllotis at elevations >6,000 m and challenge assumptions about the environmental limits of vertebrate life and the physiological tolerances of small mammals.
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Affiliation(s)
- Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA.
| | - Schuyler Liphardt
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Marcial Quiroga-Carmona
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA; Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, 5090000, Chile
| | - Naim M Bautista
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA
| | - Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, 5090000, Chile; Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Valdivia, Chile; Facultad de Medicina y Ciencia, Universidad San Sebastián, Valdivia, 5090000, Chile
| | - Timothy B Wheeler
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Guillermo D'Elía
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, 5090000, Chile
| | - Jeffrey M Good
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
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Maza F, Maldonado J, Vásquez-Dean J, Mandakovic D, Gaete A, Cambiazo V, González M. Soil Bacterial Communities From the Chilean Andean Highlands: Taxonomic Composition and Culturability. Front Bioeng Biotechnol 2019; 7:10. [PMID: 30805333 PMCID: PMC6371850 DOI: 10.3389/fbioe.2019.00010] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/16/2019] [Indexed: 11/13/2022] Open
Abstract
The Atacama Desert is a highly complex, extreme ecosystem which harbors microorganisms remarkable for their biotechnological potential. Here, a soil bacterial prospection was carried out in the high Altiplano region of the Atacama Desert (>3,800 m above sea level; m a.s.l.), where direct anthropogenic interference is minimal. We studied: (1) soil bacterial community composition using high-throughput sequencing of the 16S rRNA gene and (2) bacterial culturability, by using a soil extract medium (SEM) under a factorial design of three factors: temperature (15 and 30°C), nutrient content (high and low nutrient disposal) and oxygen availability (presence and absence). A total of 4,775 OTUs were identified and a total of 101 isolates were selected for 16S rRNA sequencing, 82 of them corresponded to unique or non-redundant sequences. To expand our view of the Altiplano landscape and to obtain a better representation of its microbiome, we complemented our Operational Taxonomic Units (OTUs) and isolate collection with data from other previous data from our group and obtained a merged set of OTUs and isolates that we used to perform our study. Taxonomic comparisons between culturable microbiota and metabarcoding data showed an overrepresentation of the phylum Firmicutes (44% of isolates vs. 2% of OTUs) and an underrepresentation of Proteobacteria (8% of isolates vs. 36% of OTUs). Within the Next Generation Sequencing (NGS) results, 33% of the OTUs were unknown up to genus, revealing an important proportion of putative new species in this environment. Biochemical characterization and analysis extracted from the literature indicated that an important number of our isolates had biotechnological potential. Also, by comparing our results with similar studies on other deserts, the Altiplano highland was most similar to a cold arid desert. In summary, our study contributes to expand the knowledge of soil bacterial communities in the Atacama Desert and complements the pipeline to isolate selective bacteria that could represent new potential biotechnological resources.
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Affiliation(s)
- Felipe Maza
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile.,Center for Genome Regulation, Santiago, Chile
| | - Jonathan Maldonado
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile.,Center for Genome Regulation, Santiago, Chile
| | - Javiera Vásquez-Dean
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
| | - Dinka Mandakovic
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile.,Center for Genome Regulation, Santiago, Chile
| | - Alexis Gaete
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile.,Center for Genome Regulation, Santiago, Chile
| | - Verónica Cambiazo
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile.,Center for Genome Regulation, Santiago, Chile
| | - Mauricio González
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile.,Center for Genome Regulation, Santiago, Chile
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Crits-Christoph A, Robinson CK, Barnum T, Fricke WF, Davila AF, Jedynak B, McKay CP, DiRuggiero J. Colonization patterns of soil microbial communities in the Atacama Desert. Microbiome 2013; 1:28. [PMID: 24451153 PMCID: PMC3971613 DOI: 10.1186/2049-2618-1-28] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 11/13/2013] [Indexed: 05/20/2023]
Abstract
BACKGROUND The Atacama Desert is one of the driest deserts in the world and its soil, with extremely low moisture, organic carbon content, and oxidizing conditions, is considered to be at the dry limit for life. RESULTS Analyses of high throughput DNA sequence data revealed that bacterial communities from six geographic locations in the hyper-arid core and along a North-South moisture gradient were structurally and phylogenetically distinct (ANOVA test for observed operating taxonomic units at 97% similarity (OTU0.03), P <0.001) and that communities from locations in the hyper-arid zone displayed the lowest levels of diversity. We found bacterial taxa similar to those found in other arid soil communities with an abundance of Rubrobacterales, Actinomycetales, Acidimicrobiales, and a number of families from the Thermoleophilia. The extremely low abundance of Firmicutes indicated that most bacteria in the soil were in the form of vegetative cells. Integrating molecular data with climate and soil geochemistry, we found that air relative humidity (RH) and soil conductivity significantly correlated with microbial communities' diversity metrics (least squares linear regression for observed OTU0.03 and air RH and soil conductivity, P <0.001; UniFrac PCoA Spearman's correlation for air RH and soil conductivity, P <0.0001), indicating that water availability and salt content are key factors in shaping the Atacama soil microbiome. Mineralization studies showed communities actively metabolizing in all soil samples, with increased rates in soils from the southern locations. CONCLUSIONS Our results suggest that microorganisms in the driest soils of the Atacama Desert are in a state of stasis for most of the time, but can potentially metabolize if presented with liquid water for a sufficient duration. Over geological time, rare rain events and physicochemical factors potentially played a major role in selecting micro-organisms that are most adapted to extreme desiccating conditions.
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Affiliation(s)
- Alexander Crits-Christoph
- Biology Department, The Johns Hopkins University, 3400 N. Charles Street, Mudd Hall, Baltimore, MD 21218, USA
| | - Courtney K Robinson
- Biology Department, The Johns Hopkins University, 3400 N. Charles Street, Mudd Hall, Baltimore, MD 21218, USA
| | - Tyler Barnum
- Biology Department, The Johns Hopkins University, 3400 N. Charles Street, Mudd Hall, Baltimore, MD 21218, USA
| | - W Florian Fricke
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Bruno Jedynak
- Department of Applied Mathematics and Statistics, Whiting School of Engineering, The Johns Hopkins University, Baltimore, MD, USA
| | | | - Jocelyne DiRuggiero
- Biology Department, The Johns Hopkins University, 3400 N. Charles Street, Mudd Hall, Baltimore, MD 21218, USA
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