1
|
Reverdy A, Hathaway D, Jha J, Michaels G, Sullivan J, McAdoo DD, Riquelme C, Chai Y, Godoy-Carter V. Insights into the diversity and survival strategies of soil bacterial isolates from the Atacama Desert. Front Microbiol 2024; 15:1335989. [PMID: 38516016 PMCID: PMC10955380 DOI: 10.3389/fmicb.2024.1335989] [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: 11/09/2023] [Accepted: 02/16/2024] [Indexed: 03/23/2024] Open
Abstract
The Atacama Desert, the driest, with the highest radiation, and one of the most ancient deserts in the world, is a hostile environment for life. We have a collection of 74 unique bacterial isolates after cultivation and confirmation by 16S rRNA gene sequencing. Pigmentation, biofilm formation, antimicrobial production against Escherichia coli MG1655 and Staphylococcus aureus HG003, and antibiotic resistance were assessed on these isolates. We found that approximately a third of the colonies produced pigments, 80% of isolates formed biofilms, many isolates produce growth inhibiting activities against E. coli and/or S. aureus, and many were resistant to antibiotics. The functional characterization of these isolates gives us insight into the adaptive bacterial strategies in harsh environments and enables us to learn about their possible use in agriculture, healthcare, or biotechnology.
Collapse
Affiliation(s)
| | | | - Jessica Jha
- Northeastern University, Boston, MA, United States
| | | | | | - Daniela Diaz McAdoo
- Facultad de Ciencias Básicas, Universidad de Antofagasta, Antofagasta, Chile
| | - Carlos Riquelme
- Facultad de Ciencias Básicas, Universidad de Antofagasta, Antofagasta, Chile
| | - Yunrong Chai
- Northeastern University, Boston, MA, United States
| | | |
Collapse
|
2
|
Runzheimer K, Lozano C, Boy D, Boy J, Godoy R, Matus FJ, Engel D, Pavletic B, Leuko S, Armengaud J, Moeller R. Exploring Andean High-Altitude Lake Extremophiles through Advanced Proteotyping. J Proteome Res 2024; 23:891-904. [PMID: 38377575 PMCID: PMC10913102 DOI: 10.1021/acs.jproteome.3c00538] [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: 08/25/2023] [Revised: 01/05/2024] [Accepted: 01/11/2024] [Indexed: 02/22/2024]
Abstract
Quickly identifying and characterizing isolates from extreme environments is currently challenging while very important to explore the Earth's biodiversity. As these isolates may, in principle, be distantly related to known species, techniques are needed to reliably identify the branch of life to which they belong. Proteotyping these environmental isolates by tandem mass spectrometry offers a rapid and cost-effective option for their identification using their peptide profiles. In this study, we document the first high-throughput proteotyping approach for environmental extremophilic and halophilic isolates. Microorganisms were isolated from samples originating from high-altitude Andean lakes (3700-4300 m a.s.l.) in the Chilean Altiplano, which represent environments on Earth that resemble conditions on other planets. A total of 66 microorganisms were cultivated and identified by proteotyping and 16S rRNA gene amplicon sequencing. Both the approaches revealed the same genus identification for all isolates except for three isolates possibly representing not yet taxonomically characterized organisms based on their peptidomes. Proteotyping was able to indicate the presence of two potentially new genera from the families of Paracoccaceae and Chromatiaceae/Alteromonadaceae, which have been overlooked by 16S rRNA amplicon sequencing approach only. The paper highlights that proteotyping has the potential to discover undescribed microorganisms from extreme environments.
Collapse
Affiliation(s)
- Katharina Runzheimer
- Department
of Radiation Biology, Institute of Aerospace
Medicine, German Aerospace Center (DLR), 51147 Cologne, Germany
| | - Clément Lozano
- Département
Médicaments et Technologies pour la Santé (DMTS), CEA,
INRAE, SPI, Université, Paris-Saclay, F-30200 Bagnols-sur-Cèze, France
| | - Diana Boy
- Institute
of Microbiology, Leibniz University Hannover, 30419 Hannover, Germany
| | - Jens Boy
- Institute
of Soil Science, Leibniz University Hannover, 30419 Hannover, Germany
| | - Roberto Godoy
- Instituto
de Ciencias Ambientales y Evolutivas, Universidad
Austral de Chile, 509000 Valdivia, Chile
| | - Francisco J. Matus
- Laboratory
of Conservation and Dynamics of Volcanic Soils, Department of Chemical
Sciences and Natural Resources, Universidad
de La Frontera, 4811230 Temuco, Chile
- Network
for Extreme Environmental Research (NEXER), Universidad de La Frontera, 4811230 Temuco, Chile
| | - Denise Engel
- Department
of Radiation Biology, Institute of Aerospace
Medicine, German Aerospace Center (DLR), 51147 Cologne, Germany
| | - Bruno Pavletic
- Department
of Radiation Biology, Institute of Aerospace
Medicine, German Aerospace Center (DLR), 51147 Cologne, Germany
| | - Stefan Leuko
- Department
of Radiation Biology, Institute of Aerospace
Medicine, German Aerospace Center (DLR), 51147 Cologne, Germany
| | - Jean Armengaud
- Département
Médicaments et Technologies pour la Santé (DMTS), CEA,
INRAE, SPI, Université, Paris-Saclay, F-30200 Bagnols-sur-Cèze, France
| | - Ralf Moeller
- Department
of Radiation Biology, Institute of Aerospace
Medicine, German Aerospace Center (DLR), 51147 Cologne, Germany
| |
Collapse
|
3
|
Veloso M, Waldisperg A, Arros P, Berríos-Pastén C, Acosta J, Colque H, Varas MA, Allende ML, Orellana LH, Marcoleta AE. Diversity, Taxonomic Novelty, and Encoded Functions of Salar de Ascotán Microbiota, as Revealed by Metagenome-Assembled Genomes. Microorganisms 2023; 11:2819. [PMID: 38004830 PMCID: PMC10673233 DOI: 10.3390/microorganisms11112819] [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: 09/21/2023] [Revised: 11/12/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
Salar de Ascotán is a high-altitude arsenic-rich salt flat exposed to high ultraviolet radiation in the Atacama Desert, Chile. It hosts unique endemic flora and fauna and is an essential habitat for migratory birds, making it an important site for conservation and protection. However, there is limited information on the resident microbiota's diversity, genomic features, metabolic potential, and molecular mechanisms that enable it to thrive in this extreme environment. We used long- and short-read metagenomics to investigate the microbial communities in Ascotán's water, sediment, and soil. Bacteria predominated, mainly Pseudomonadota, Acidobacteriota, and Bacteroidota, with a remarkable diversity of archaea in the soil. Following hybrid assembly, we recovered high-quality bacterial (101) and archaeal (6) metagenome-assembled genomes (MAGs), including representatives of two putative novel families of Patescibacteria and Pseudomonadota and two novel orders from the archaeal classes Halobacteriota and Thermoplasmata. We found different metabolic capabilities across distinct lineages and a widespread presence of genes related to stress response, DNA repair, and resistance to arsenic and other metals. These results highlight the remarkable diversity and taxonomic novelty of the Salar de Ascotán microbiota and its rich functional repertoire, making it able to resist different harsh conditions. The highly complete MAGs described here could serve future studies and bioprospection efforts focused on salt flat extremophiles, and contribute to enriching databases with microbial genome data from underrepresented regions of our planet.
Collapse
Affiliation(s)
- Marcelo Veloso
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile; (M.V.); (A.W.); (P.A.); (C.B.-P.); (J.A.); (H.C.); (M.A.V.)
| | - Angie Waldisperg
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile; (M.V.); (A.W.); (P.A.); (C.B.-P.); (J.A.); (H.C.); (M.A.V.)
| | - Patricio Arros
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile; (M.V.); (A.W.); (P.A.); (C.B.-P.); (J.A.); (H.C.); (M.A.V.)
| | - Camilo Berríos-Pastén
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile; (M.V.); (A.W.); (P.A.); (C.B.-P.); (J.A.); (H.C.); (M.A.V.)
| | - Joaquín Acosta
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile; (M.V.); (A.W.); (P.A.); (C.B.-P.); (J.A.); (H.C.); (M.A.V.)
| | - Hazajem Colque
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile; (M.V.); (A.W.); (P.A.); (C.B.-P.); (J.A.); (H.C.); (M.A.V.)
| | - Macarena A. Varas
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile; (M.V.); (A.W.); (P.A.); (C.B.-P.); (J.A.); (H.C.); (M.A.V.)
- Millenium Institute Center for Genome Regulation, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile;
| | - Miguel L. Allende
- Millenium Institute Center for Genome Regulation, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile;
| | - Luis H. Orellana
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359 Bremen, Germany;
| | - Andrés E. Marcoleta
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile; (M.V.); (A.W.); (P.A.); (C.B.-P.); (J.A.); (H.C.); (M.A.V.)
| |
Collapse
|
4
|
Dopson M, González-Rosales C, Holmes DS, Mykytczuk N. Eurypsychrophilic acidophiles: From (meta)genomes to low-temperature biotechnologies. Front Microbiol 2023; 14:1149903. [PMID: 37007468 PMCID: PMC10050440 DOI: 10.3389/fmicb.2023.1149903] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 02/16/2023] [Indexed: 03/17/2023] Open
Abstract
Low temperature and acidic environments encompass natural milieus such as acid rock drainage in Antarctica and anthropogenic sites including drained sulfidic sediments in Scandinavia. The microorganisms inhabiting these environments include polyextremophiles that are both extreme acidophiles (defined as having an optimum growth pH < 3), and eurypsychrophiles that grow at low temperatures down to approximately 4°C but have an optimum temperature for growth above 15°C. Eurypsychrophilic acidophiles have important roles in natural biogeochemical cycling on earth and potentially on other planetary bodies and moons along with biotechnological applications in, for instance, low-temperature metal dissolution from metal sulfides. Five low-temperature acidophiles are characterized, namely, Acidithiobacillus ferriphilus, Acidithiobacillus ferrivorans, Acidithiobacillus ferrooxidans, “Ferrovum myxofaciens,” and Alicyclobacillus disulfidooxidans, and their characteristics are reviewed. Our understanding of characterized and environmental eurypsychrophilic acidophiles has been accelerated by the application of “omics” techniques that have aided in revealing adaptations to low pH and temperature that can be synergistic, while other adaptations are potentially antagonistic. The lack of known acidophiles that exclusively grow below 15°C may be due to the antagonistic nature of adaptations in this polyextremophile. In conclusion, this review summarizes the knowledge of eurypsychrophilic acidophiles and places the information in evolutionary, environmental, biotechnological, and exobiology perspectives.
Collapse
Affiliation(s)
- Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
- *Correspondence: Mark Dopson
| | - Carolina González-Rosales
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - David S. Holmes
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastian, Santiago, Chile
| | - Nadia Mykytczuk
- Goodman School of Mines, Laurentian University, Sudbury, ON, Canada
| |
Collapse
|
5
|
Paquis P, Hengst MB, Florez JZ, Tapia J, Molina V, Pérez V, Pardo-Esté C. Short-term characterisation of climatic-environmental variables and microbial community diversity in a high-altitude Andean wetland (Salar de Huasco, Chile). THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 859:160291. [PMID: 36410480 DOI: 10.1016/j.scitotenv.2022.160291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 11/11/2022] [Accepted: 11/15/2022] [Indexed: 06/16/2023]
Abstract
Microbial community structures are shaped by geochemical factors and their interactions with the lithosphere, hydrosphere, and atmosphere through the processes of chemical mobilisation and mineralisation. High-altitude wetlands and salt flats in the central Andes are characterised by pronounced physicochemical gradients and extreme climatic conditions, representing hotspots of microbial diversity. We here hypothesise about the existence of direct relationships between the local microbiology and the climate cyclicity variables based on meteorological and biogeochemical patterns that develop over a short time scale (five years). We have here analysed the interactions between hydrometeorological and biogeochemical variables and the microbial communities of the Salar de Huasco. These results were obtained by correlating 16S cDNA and DNA gene Illumina sequences with meteorological/satellite data collected both at monitoring stations and by remote sensing between the years 2015 and 2020. The precipitation levels and flooded areas (i.e., areas covered and/or saturated with permanent water) detected in the Salar de Huasco revealed a marked hydric cyclicity that correlated seasonally with intra-annual wet and dry seasons. Overall, at this site, wet periods occurred from December to April, and dry periods from May to November. Meteorological variables such as solar radiation, air temperature, relative humidity, wind speed, atmospheric pressure, and wind direction were well-defined, showing a potential association with the hydrogeology of the area, which is directly related to the wetlands' flooded areas. Finally, the microbial presence and potentially active microbial communities were determined through the sequencing of the 16S gene (DNA and cDNA, respectively), this were associated with climatic seasonality and spatially distributed physical and chemical heterogeneity. Other non-local inter-annual scale processes, such as El Niño-Southern Oscillation (ENSO) events, modify the physical and chemical context of the wetland, thus forming unique ecological niches in the Andean Mountains.
Collapse
Affiliation(s)
- Pablo Paquis
- Departamento de Ciencias Farmacéuticas, Facultad de Ciencias, Universidad Católica del Norte, Antofagasta, Chile; Departamento de Ciencias Geológicas, Facultad de Ingeniería y Ciencias Geológicas, Universidad Católica del Norte, Antofagasta, Chile; Programa de Doctorado en Ciencias mención Geología, Universidad Católica del Norte, Antofagasta, Chile.
| | - Martha B Hengst
- Departamento de Ciencias Farmacéuticas, Facultad de Ciencias, Universidad Católica del Norte, Antofagasta, Chile.
| | - July Z Florez
- Departamento de Ciencias Farmacéuticas, Facultad de Ciencias, Universidad Católica del Norte, Antofagasta, Chile; Departamento de Ciencias y Geografía, Facultad de Ciencias Naturales y Exactas y HUB Ambiental UPLA, Universidad de Playa Ancha, Valparaíso, Chile.
| | - Joseline Tapia
- Departamento de Ciencias Geológicas, Facultad de Ingeniería y Ciencias Geológicas, Universidad Católica del Norte, Antofagasta, Chile.
| | - Verónica Molina
- Departamento de Ciencias y Geografía, Facultad de Ciencias Naturales y Exactas y HUB Ambiental UPLA, Universidad de Playa Ancha, Valparaíso, Chile; Centro COPAS Coastal, Universidad de Concepción, Concepción, Chile.
| | - Vilma Pérez
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Australia.
| | - Coral Pardo-Esté
- Departamento de Ciencias Farmacéuticas, Facultad de Ciencias, Universidad Católica del Norte, Antofagasta, Chile.
| |
Collapse
|
6
|
Schoenle A, Hohlfeld M, Rybarski A, Sachs M, Freches E, Wiechmann K, Nitsche F, Arndt H. Cafeteria in extreme environments: investigations on C. burkhardae and three new species from the atacama desert and the deep ocean. Eur J Protistol 2022; 85:125905. [DOI: 10.1016/j.ejop.2022.125905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 06/10/2022] [Accepted: 06/15/2022] [Indexed: 11/03/2022]
|
7
|
Valladares MA, Fabres AA, Collado GA, Sáez PA, Méndez MA. Coping With Dynamism: Phylogenetics and Phylogeographic Analyses Reveal Cryptic Diversity in Heleobia Snails of Atacama Saltpan, Chile. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.869626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The species that inhabit systems highly affected by anthropic activities usually exhibit this external influence in their gene pool. In this study, we investigated the genetic patterns of populations of Heleobia atacamensis, a freshwater microgastropod endemic to the Atacama Saltpan, a system historically exposed to environmental changes, and currently subjected to conditions associated with metallic and non-metallic mining and other anthropic activities. Molecular analyses based on nuclear and mitochondrial sequences indicate that the saltpan populations are highly fragmented and that the genetic structure is mainly explained by historical geographic isolation, with little influence of contemporary factors. The microsatellite results suggest a moderate genetic diversity and sharp differentiation mediated by isolation by distance. Additionally, despite the high environmental heterogeneity detected and the marked historical dynamism of the region, our data reveal no signs of demographic instability. The patterns of contemporary gene flow suggest a change in the current genetic structure, based on the geographic proximity and specific environmental conditions for each population. Our results, highlight the role of fragmentation as a modulator of genetic diversity, but also suggest that the historical persistence of isolated populations in naturally dynamic environments could explain the apparent demographic stability detected.
Collapse
|
8
|
Vignale FA, Lencina AI, Stepanenko TM, Soria MN, Saona LA, Kurth D, Guzmán D, Foster JS, Poiré DG, Villafañe PG, Albarracín VH, Contreras M, Farías ME. Lithifying and Non-Lithifying Microbial Ecosystems in the Wetlands and Salt Flats of the Central Andes. MICROBIAL ECOLOGY 2022; 83:1-17. [PMID: 33730193 DOI: 10.1007/s00248-021-01725-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 02/22/2021] [Indexed: 06/12/2023]
Abstract
The wetlands and salt flats of the Central Andes region are unique extreme environments as they are located in high-altitude saline deserts, largely influenced by volcanic activity. Environmental factors, such as ultraviolet (UV) radiation, arsenic content, high salinity, low dissolved oxygen content, extreme daily temperature fluctuation, and oligotrophic conditions, resemble the early Earth and potentially extraterrestrial conditions. The discovery of modern microbialites and microbial mats in the Central Andes during the past decade has increased the interest in this area as an early Earth analog. In this work, we review the current state of knowledge of Central Andes region environments found within lakes, small ponds or puquios, and salt flats of Argentina, Chile, and Bolivia, many of them harboring a diverse range of microbial communities that we have termed Andean Microbial Ecosystems (AMEs). We have integrated the data recovered from all the known AMEs and compared their biogeochemistry and microbial diversity to achieve a better understanding of them and, consequently, facilitate their protection.
Collapse
Affiliation(s)
- Federico A Vignale
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI)-CCT-CONICET, San Miguel de Tucumán, Tucumán, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN)-CONICET, Universidad de Buenos Aires (UBA), Buenos Aires, Argentina
| | - Agustina I Lencina
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI)-CCT-CONICET, San Miguel de Tucumán, Tucumán, Argentina
| | - Tatiana M Stepanenko
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI)-CCT-CONICET, San Miguel de Tucumán, Tucumán, Argentina
| | - Mariana N Soria
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI)-CCT-CONICET, San Miguel de Tucumán, Tucumán, Argentina
| | - Luis A Saona
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI)-CCT-CONICET, San Miguel de Tucumán, Tucumán, Argentina
| | - Daniel Kurth
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI)-CCT-CONICET, San Miguel de Tucumán, Tucumán, Argentina
| | - Daniel Guzmán
- Centro de Biotecnología (CBT), Facultad de Ciencias y Tecnología, Universidad Mayor de San Simón (UMSS), Cochabamba, Bolivia
| | - Jamie S Foster
- Space Life Science Lab, Department of Microbiology and Cell Science, University of Florida, Merritt Island, FL, USA
| | - Daniel G Poiré
- Centro de Investigaciones Geológicas (CIG), Universidad Nacional de La Plata (UNLP)-CONICET, La Plata, Argentina
| | - Patricio G Villafañe
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI)-CCT-CONICET, San Miguel de Tucumán, Tucumán, Argentina
| | - Virginia H Albarracín
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI)-CCT-CONICET, San Miguel de Tucumán, Tucumán, Argentina
- Centro Integral de Microscopía Electrónica (CIME)-CCT-CONICET, Universidad Nacional de Tucumán (UNT), Tucumán, Argentina
| | | | - María E Farías
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI)-CCT-CONICET, San Miguel de Tucumán, Tucumán, Argentina.
| |
Collapse
|
9
|
Di Genova A, Nardocci G, Maldonado-Agurto R, Hodar C, Valdivieso C, Morales P, Gajardo F, Marina R, Gutiérrez RA, Orellana A, Cambiazo V, González M, Glavic A, Mendez MA, Maass A, Allende ML, Montecino MA. Genome sequencing and transcriptomic analysis of the Andean killifish Orestias ascotanensis reveals adaptation to high-altitude aquatic life. Genomics 2021; 114:305-315. [PMID: 34954349 DOI: 10.1016/j.ygeno.2021.12.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 11/26/2021] [Accepted: 12/17/2021] [Indexed: 12/21/2022]
Abstract
Orestias ascotanensis (Cyprinodontidae) is a teleost pupfish endemic to springs feeding into the Ascotan saltpan in the Chilean Altiplano (3,700 m.a.s.l.) and represents an opportunity to study adaptations to high-altitude aquatic environments. We have de novo assembled the genome of O. ascotanensis at high coverage. Comparative analysis of the O. ascotanensis genome showed an overall process of contraction, including loss of genes related to G-protein signaling, chemotaxis and signal transduction, while there was expansion of gene families associated with microtubule-based movement and protein ubiquitination. We identified 818 genes under positive selection, many of which are involved in DNA repair. Additionally, we identified novel and conserved microRNAs expressed in O. ascotanensis and its closely-related species, Orestias gloriae. Our analysis suggests that positive selection and expansion of genes that preserve genome stability are a potential adaptive mechanism to cope with the increased solar UV radiation to which high-altitude animals are exposed to.
Collapse
Affiliation(s)
- Alex Di Genova
- FONDAP Center for Genome Regulation, Santiago, Chile; Center for Mathematical Modeling, Department of Mathematical Engineering, Faculty of Physical and Mathematical Sciences, Universidad de Chile and IRL CNRS, 2807 Santiago, Chile
| | - Gino Nardocci
- FONDAP Center for Genome Regulation, Santiago, Chile; Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Rodrigo Maldonado-Agurto
- FONDAP Center for Genome Regulation, Santiago, Chile; Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Christian Hodar
- FONDAP Center for Genome Regulation, Santiago, Chile; Institute of Nutrition and Food Technology, Universidad de Chile, Santiago, Chile
| | - Camilo Valdivieso
- FONDAP Center for Genome Regulation, Santiago, Chile; Faculty of Sciences, Universidad de Chile, Santiago, Chile
| | - Pamela Morales
- FONDAP Center for Genome Regulation, Santiago, Chile; Faculty of Sciences, Universidad de Chile, Santiago, Chile
| | - Felipe Gajardo
- FONDAP Center for Genome Regulation, Santiago, Chile; Faculty of Sciences, Universidad de Chile, Santiago, Chile
| | - Raquel Marina
- FONDAP Center for Genome Regulation, Santiago, Chile; Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Rodrigo A Gutiérrez
- FONDAP Center for Genome Regulation, Santiago, Chile; Department of Molecular Genetics and Microbiology, Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - Ariel Orellana
- FONDAP Center for Genome Regulation, Santiago, Chile; Center of Plant Biotechnology, Universidad Andres Bello, Santiago, Chile
| | - Veronica Cambiazo
- FONDAP Center for Genome Regulation, Santiago, Chile; Institute of Nutrition and Food Technology, Universidad de Chile, Santiago, Chile
| | - Mauricio González
- FONDAP Center for Genome Regulation, Santiago, Chile; Institute of Nutrition and Food Technology, Universidad de Chile, Santiago, Chile
| | - Alvaro Glavic
- FONDAP Center for Genome Regulation, Santiago, Chile; Faculty of Sciences, Universidad de Chile, Santiago, Chile
| | - Marco A Mendez
- FONDAP Center for Genome Regulation, Santiago, Chile; Faculty of Sciences, Universidad de Chile, Santiago, Chile; Center of Applied Ecology and Sustainability (CAPES), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Chile; Institute of Ecology and Biodiversity, Chile
| | - Alejandro Maass
- FONDAP Center for Genome Regulation, Santiago, Chile; Center for Mathematical Modeling, Department of Mathematical Engineering, Faculty of Physical and Mathematical Sciences, Universidad de Chile and IRL CNRS, 2807 Santiago, Chile
| | - Miguel L Allende
- FONDAP Center for Genome Regulation, Santiago, Chile; Faculty of Sciences, Universidad de Chile, Santiago, Chile.
| | - Martin A Montecino
- FONDAP Center for Genome Regulation, Santiago, Chile; Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile.
| |
Collapse
|
10
|
Cárcamo-Tejer V, Vila I, Llanquín-Rosas F, Sáez-Arteaga A, Guerrero-Jiménez C. Phylogeography of high Andean killifishes Orestias (Teleostei: Cyprinodontidae) in Caquena and Lauca sub-basins of the Altiplano (Chile): mitochondrial and nuclear analysis of an endangered fish. PeerJ 2021; 9:e11917. [PMID: 34484986 DOI: 10.7717/peerj.11917] [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: 10/30/2020] [Accepted: 07/15/2021] [Indexed: 11/20/2022] Open
Abstract
From the early Miocene, the uplift of the Andes Mountains, intense volcanic activity and the occurrence of successive periods of dryness and humidity would have differentially influenced the modification of Altiplano watersheds, and consequently the evolutionary history of the taxa that live there. We analyzed Orestias populations from the Caquena and Lauca Altiplanic sub-basins of northern Chile to determine their genetic differentiation and relationship to their geographical distribution using mitochondrial (D-loop) and nuclear (microsatellite) molecular markers and to reconstruct its biogeographic history on these sub-basins. The results allowed reconstructing and reevaluating the evolutionary history of the genus in the area; genic diversity and differentiation together with different founding genetic groups suggest that Orestias have been spread homogeneously in the study area and would have experienced local disturbances that promoted isolation and diversification in restricted zones of their distribution.
Collapse
Affiliation(s)
- Violeta Cárcamo-Tejer
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Región Metropolitana, Chile
| | - Irma Vila
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Región Metropolitana, Chile
| | - Francisco Llanquín-Rosas
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Región Metropolitana, Chile
| | - Alberto Sáez-Arteaga
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Temuco, Región de la Araucanía, Chile
| | - Claudia Guerrero-Jiménez
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Temuco, Región de la Araucanía, Chile
| |
Collapse
|
11
|
Castro-Severyn J, Pardo-Esté C, Mendez KN, Fortt J, Marquez S, Molina F, Castro-Nallar E, Remonsellez F, Saavedra CP. Living to the High Extreme: Unraveling the Composition, Structure, and Functional Insights of Bacterial Communities Thriving in the Arsenic-Rich Salar de Huasco Altiplanic Ecosystem. Microbiol Spectr 2021; 9:e0044421. [PMID: 34190603 PMCID: PMC8552739 DOI: 10.1128/spectrum.00444-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 06/07/2021] [Indexed: 01/03/2023] Open
Abstract
Microbial communities inhabiting extreme environments such as Salar de Huasco (SH) in northern Chile are adapted to thrive while exposed to several abiotic pressures and the presence of toxic elements such as arsenic (As). Hence, we aimed to uncover the role of As in shaping bacterial composition, structure, and functional potential in five different sites in this altiplanic wetland using a shotgun metagenomic approach. The sites exhibit wide gradients of As (9 to 321 mg/kg), and our results showed highly diverse communities and a clear dominance exerted by the Proteobacteria and Bacteroidetes phyla. Functional potential analyses show broadly convergent patterns, contrasting with their great taxonomic variability. As-related metabolism, as well as other functional categories such as those related to the CH4 and S cycles, differs among the five communities. Particularly, we found that the distribution and abundance of As-related genes increase as the As concentration rises. Approximately 75% of the detected genes for As metabolism belong to expulsion mechanisms; arsJ and arsP pumps are related to sites with higher As concentrations and are present almost exclusively in Proteobacteria. Furthermore, taxonomic diversity and functional potential are reflected in the 12 reconstructed high-quality metagenome assembled genomes (MAGs) belonging to the Bacteroidetes (5), Proteobacteria (5), Cyanobacteria (1), and Gemmatimonadetes (1) phyla. We conclude that SH microbial communities are diverse and possess a broad genetic repertoire to thrive under extreme conditions, including increasing concentrations of highly toxic As. Finally, this environment represents a reservoir of unknown and undescribed microorganisms, with great metabolic versatility, which needs further study. IMPORTANCE As microbial communities inhabiting extreme environments are fundamental for maintaining ecosystems, many studies concerning composition, functionality, and interactions have been carried out. However, much is still unknown. Here, we sampled microbial communities in the Salar de Huasco, an extreme environment subjected to several abiotic stresses (high UV radiation, salinity and arsenic; low pressure and temperatures). We found that although microbes are taxonomically diverse, functional potential seems to have an important degree of convergence, suggesting high levels of adaptation. Particularly, arsenic metabolism showed differences associated with increasing concentrations of the metalloid throughout the area, and it effectively exerts a significant pressure over these organisms. Thus, the significance of this research is that we describe highly specialized communities thriving in little-explored environments subjected to several pressures, considered analogous of early Earth and other planets, that have the potential for unraveling technologies to face the repercussions of climate change in many areas of interest.
Collapse
Affiliation(s)
- Juan Castro-Severyn
- Laboratorio de Microbiología Aplicada y Extremófilos, Facultad de Ingeniería y Ciencias Geológicas, Universidad Católica del Norte, Antofagasta, Chile
| | - Coral Pardo-Esté
- Laboratorio de Microbiología Aplicada y Extremófilos, Facultad de Ingeniería y Ciencias Geológicas, Universidad Católica del Norte, Antofagasta, Chile
- Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Katterinne N. Mendez
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Jonathan Fortt
- Laboratorio de Microbiología Aplicada y Extremófilos, Facultad de Ingeniería y Ciencias Geológicas, Universidad Católica del Norte, Antofagasta, Chile
| | - Sebastian Marquez
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Franck Molina
- Sys2Diag, UMR9005 CNRS ALCEDIAG, Montpellier, France
| | - Eduardo Castro-Nallar
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Francisco Remonsellez
- Laboratorio de Microbiología Aplicada y Extremófilos, Facultad de Ingeniería y Ciencias Geológicas, Universidad Católica del Norte, Antofagasta, Chile
- Centro de Investigación Tecnológica del Agua en el Desierto-CEITSAZA, Universidad Católica del Norte, Antofagasta, Chile
| | - Claudia P. Saavedra
- Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| |
Collapse
|
12
|
Benison KC, O'Neill WK, Blain D, Hallsworth JE. Water Activities of Acid Brine Lakes Approach the Limit for Life. ASTROBIOLOGY 2021; 21:729-740. [PMID: 33819431 PMCID: PMC8219186 DOI: 10.1089/ast.2020.2334] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 02/09/2021] [Indexed: 05/19/2023]
Abstract
Water activity is an important characteristic for describing unusual waters and is a determinant of habitability for microorganisms. However, few empirical studies of water activity have been done for natural waters exhibiting an extreme chemistry. Here, we investigate water activity for acid brines from Western Australia and Chile with pH as low as 1.4, salinities as high as 32% total dissolved solids, and complex chemical compositions. These acid brines host diverse communities of extremophilic microorganisms, including archaea, bacteria, algae, and fungi, according to metagenomic analyses. For the most extreme brine, its water activity (0.714) was considerably lower than that of saturated (pure) NaCl brine. This study provides a thermodynamic insight into life within end-member natural waters that lie at, or possibly beyond, the very edge of habitable space on Earth.
Collapse
Affiliation(s)
- Kathleen C. Benison
- Department of Geology and Geography, West Virginia University, Morgantown, West Virginia, USA
- Address correspondence to: Kathleen C. Benison, Department of Geology and Geography, West Virginia University, Morgantown, WV 26506-6300, USA
| | - William K. O'Neill
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, Northern Ireland
| | - David Blain
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, Northern Ireland
| | - John E. Hallsworth
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, Northern Ireland
- Address correspondence to: John E. Hallsworth, Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Garden, Belfast, BT9 5DL, Northern Ireland
| |
Collapse
|
13
|
Physicochemical Parameters Affecting the Distribution and Diversity of the Water Column Microbial Community in the High-Altitude Andean Lake System of La Brava and La Punta. Microorganisms 2020; 8:microorganisms8081181. [PMID: 32756460 PMCID: PMC7464526 DOI: 10.3390/microorganisms8081181] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/31/2020] [Accepted: 08/01/2020] [Indexed: 11/23/2022] Open
Abstract
Due to the low incidence of precipitation attributed to climate change, many high-altitude Andean lakes (HAALs) and lagoons distributed along the central Andes in South America may soon disappear. This includes La Brava–La Punta, a brackish lake system located south of the Salar de Atacama within a hyper-arid and halophytic biome in the Atacama Desert. Variations in the physicochemical parameters of the water column can induce changes in microbial community composition, which we aimed to determine. Sixteen sampling points across La Brava–La Punta were studied to assess the influence of water physicochemical properties on the aquatic microbial community, determined via 16S rRNA gene analysis. Parameters such as pH and the concentrations of silica, magnesium, calcium, salinity, and dissolved oxygen showed a more homogenous pattern in La Punta samples, whereas those from La Brava had greater variability; pH and total silica were significantly different between La Brava and La Punta. The predominant phyla were Proteobacteria, Bacteroidetes, Actinobacteria, and Verrucomicrobia. The genera Psychroflexus (36.85%), Thiomicrospira (12.48%), and Pseudomonas (7.81%) were more abundant in La Brava, while Pseudospirillum (20.73%) and Roseovarius (17.20%) were more abundant in La Punta. Among the parameters, pH was the only statistically significant factor influencing the diversity within La Brava lake. These results complement the known microbial diversity and composition in the HAALs of the Atacama Desert.
Collapse
|
14
|
Genome-scale metabolic models of Microbacterium species isolated from a high altitude desert environment. Sci Rep 2020; 10:5560. [PMID: 32221328 PMCID: PMC7101325 DOI: 10.1038/s41598-020-62130-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 02/28/2020] [Indexed: 01/09/2023] Open
Abstract
The Atacama Desert is the most arid desert on Earth, focus of important research activities related to microbial biodiversity studies. In this context, metabolic characterization of arid soil bacteria is crucial to understand their survival strategies under extreme environmental stress. We investigated whether strain-specific features of two Microbacterium species were involved in the metabolic ability to tolerate/adapt to local variations within an extreme desert environment. Using an integrative systems biology approach we have carried out construction and comparison of genome-scale metabolic models (GEMs) of two Microbacterium sp., CGR1 and CGR2, previously isolated from physicochemically contrasting soil sites in the Atacama Desert. Despite CGR1 and CGR2 belong to different phylogenetic clades, metabolic pathways and attributes are highly conserved in both strains. However, comparison of the GEMs showed significant differences in the connectivity of specific metabolites related to pH tolerance and CO2 production. The latter is most likely required to handle acidic stress through decarboxylation reactions. We observed greater GEM connectivity within Microbacterium sp. CGR1 compared to CGR2, which is correlated with the capacity of CGR1 to tolerate a wider pH tolerance range. Both metabolic models predict the synthesis of pigment metabolites (β-carotene), observation validated by HPLC experiments. Our study provides a valuable resource to further investigate global metabolic adaptations of bacterial species to grow in soils with different abiotic factors within an extreme environment.
Collapse
|
15
|
Contador CA, Veas-Castillo L, Tapia E, Antipán M, Miranda N, Ruiz-Tagle B, García-Araya J, Andrews BA, Marin M, Dorador C, Asenjo JA. Atacama Database: a platform of the microbiome of the Atacama Desert. Antonie van Leeuwenhoek 2019; 113:185-195. [PMID: 31535335 DOI: 10.1007/s10482-019-01328-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 09/07/2019] [Indexed: 11/30/2022]
Abstract
The Atacama Desert is one of the oldest and driest places on Earth. In the last decade, microbial richness and diversity has been acknowledged as an important biological resource of this region. Owing to the value of the microbial diversity apparent in potential biotechnology applications and conservation purposes, it is necessary to catalogue these microbial communities to promote research activities and help to preserve the wide range of ecological niches of the Atacama region. A prototype Atacama Database has been designed and it provides a description of the rich microbial diversity of the Atacama Desert, and helps to visualise available literature resources. Data has been collected, curated, and organised into several categories to generate a single record for each organism in the database that covers classification, isolation metadata, morphology, physiology, genome and metabolism information. The current version of Atacama Database contains 2302 microorganisms and includes cultured and uncultured organisms retrieved from different environments within the desert between 1984 and 2016. These organisms are distributed in bacterial, archaeal or eukaryotic domains, along with those that are unclassified taxonomically. The initial prototype of the Atacama Database includes a basic search and taxonomic and advanced search tools to allow identification and comparison of microbial populations, and space distribution within this biome. A geolocation search was implemented to visualise the microbial diversity of the ecological niches defined by sectors and extract general information of the sampling sites. This effort will aid understanding of the microbial ecology of the desert, microbial population dynamics, seasonal behaviour, impact of climate change over time, and reveal further biotechnological applications of these microorganisms. The Atacama Database is freely available at: https://www.atacamadb.cl.
Collapse
Affiliation(s)
- Carolina A Contador
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, 8370456, Santiago, Chile.
| | - Luis Veas-Castillo
- Centre for Biotechnology and Bioengineering (CeBiB), Departamento de Ingeniería Informática (DIINF), Universidad de Santiago de Chile, Santiago, Chile
| | - Emilio Tapia
- Centre for Biotechnology and Bioengineering (CeBiB), Departamento de Ingeniería Informática (DIINF), Universidad de Santiago de Chile, Santiago, Chile
| | - Marcela Antipán
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, 8370456, Santiago, Chile
| | - Noemi Miranda
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, 8370456, Santiago, Chile
| | - Benjamín Ruiz-Tagle
- Centre for Biotechnology and Bioengineering (CeBiB), Departamento de Ingeniería Informática (DIINF), Universidad de Santiago de Chile, Santiago, Chile
| | - Jonathan García-Araya
- Centre for Biotechnology and Bioengineering (CeBiB), Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta & Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Barbara A Andrews
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, 8370456, Santiago, Chile
| | - Mauricio Marin
- Centre for Biotechnology and Bioengineering (CeBiB), Departamento de Ingeniería Informática (DIINF), Universidad de Santiago de Chile, Santiago, Chile
| | - Cristina Dorador
- Centre for Biotechnology and Bioengineering (CeBiB), Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta & Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Juan A Asenjo
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, 8370456, Santiago, Chile
| |
Collapse
|
16
|
Saleem F, Azim MK, Mustafa A, Kori JA, Hussain MS. Metagenomic profiling of fresh water lakes at different altitudes in Pakistan. ECOL INFORM 2019. [DOI: 10.1016/j.ecoinf.2019.02.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
17
|
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: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [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.
Collapse
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
| |
Collapse
|
18
|
Portero LR, Alonso-Reyes DG, Zannier F, Vazquez MP, Farías ME, Gärtner W, Albarracín VH. Photolyases and Cryptochromes in UV-resistant Bacteria from High-altitude Andean Lakes. Photochem Photobiol 2019; 95:315-330. [DOI: 10.1111/php.13061] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 11/18/2018] [Indexed: 11/30/2022]
Affiliation(s)
- Luciano Raúl Portero
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA); Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI); CCT; CONICET; Tucumán Argentina
- Centro de Investigaciones y Servicios de Microscopía Electrónica (CISME-CONICET-UNT); CCT, CONICET; Tucumán Argentina
| | - Daniel G. Alonso-Reyes
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA); Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI); CCT; CONICET; Tucumán Argentina
- Centro de Investigaciones y Servicios de Microscopía Electrónica (CISME-CONICET-UNT); CCT, CONICET; Tucumán Argentina
| | - Federico Zannier
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA); Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI); CCT; CONICET; Tucumán Argentina
- Centro de Investigaciones y Servicios de Microscopía Electrónica (CISME-CONICET-UNT); CCT, CONICET; Tucumán Argentina
| | - Martín P. Vazquez
- Instituto de Agrobiotecnología de Rosario (INDEAR); Predio CCT Rosario; Santa Fe Argentina
| | - María Eugenia Farías
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA); Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI); CCT; CONICET; Tucumán Argentina
| | - Wolfgang Gärtner
- Institute for Analytical Chemistry; University of Leipzig; Leipzig Germany
| | - Virginia Helena Albarracín
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA); Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI); CCT; CONICET; Tucumán Argentina
- Centro de Investigaciones y Servicios de Microscopía Electrónica (CISME-CONICET-UNT); CCT, CONICET; Tucumán Argentina
- Facultad de Ciencias Naturales; Instituto Miguel Lillo; Universidad Nacional de Tucumán; Tucumán Argentina
| |
Collapse
|
19
|
Ordoñez OF, Rasuk MC, Soria MN, Contreras M, Farías ME. Haloarchaea from the Andean Puna: Biological Role in the Energy Metabolism of Arsenic. MICROBIAL ECOLOGY 2018; 76:695-705. [PMID: 29520450 DOI: 10.1007/s00248-018-1159-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 02/13/2018] [Indexed: 05/25/2023]
Abstract
Biofilms, microbial mats, and microbialites dwell under highly limiting conditions (high salinity, extreme aridity, pH, and elevated arsenic concentration) in the Andean Puna. Only recent pioneering studies have described the microbial diversity of different Altiplano lakes and revealed their unexpectedly diverse microbial communities. Arsenic metabolism is proposed to be an ancient mechanism to obtain energy by microorganisms. Members of Bacteria and Archaea are able to exploit arsenic as a bioenergetic substrate in either anaerobic arsenate respiration or chemolithotrophic growth on arsenite. Only six aioAB sequences coding for arsenite oxidase and three arrA sequences coding for arsenate reductase from haloarchaea were previously deposited in the NCBI database. However, no experimental data on their expression and function has been reported. Recently, our working group revealed the prevalence of haloarchaea in a red biofilm from Diamante Lake and microbial mat from Tebenquiche Lake using a metagenomics approach. Also, a surprisingly high abundance of genes used for anaerobic arsenate respiration (arr) and arsenite oxidation (aio) was detected in the Diamante's metagenome. In order to study in depth the role of arsenic in these haloarchaeal communities, in this work, we obtained 18 haloarchaea belonging to the Halorubrum genus, tolerant to arsenic. Furthermore, the identification and expression analysis of genes involved in obtaining energy from arsenic compounds (aio and arr) showed that aio and arr partial genes were detected in 11 isolates, and their expression was verified in two selected strains. Better growth of two isolates was obtained in presence of arsenic compared to control. Moreover, one of the isolates was able to oxidize As[III]. The confirmation of the oxidation of arsenic and the transcriptional expression of these genes by RT-PCR strongly support the hypothesis that the arsenic can be used in bioenergetics processes by the microorganisms flourishing in these environments.
Collapse
Affiliation(s)
- Omar Federico Ordoñez
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI), CCT, CONICET, Av. Belgrano y Pasaje Caseros, 4000, Tucumán, Argentina
| | - María Cecilia Rasuk
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI), CCT, CONICET, Av. Belgrano y Pasaje Caseros, 4000, Tucumán, Argentina
| | - Mariana Noelia Soria
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI), CCT, CONICET, Av. Belgrano y Pasaje Caseros, 4000, Tucumán, Argentina
| | - Manuel Contreras
- Centro de Ecología Aplicada (CEA), Suecia 3304, 56-2-2741872, Ñuñoa, Santiago, Chile
| | - María Eugenia Farías
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI), CCT, CONICET, Av. Belgrano y Pasaje Caseros, 4000, Tucumán, Argentina.
| |
Collapse
|
20
|
Remonsellez F, Castro-Severyn J, Pardo-Esté C, Aguilar P, Fortt J, Salinas C, Barahona S, León J, Fuentes B, Areche C, Hernández KL, Aguayo D, Saavedra CP. Characterization and Salt Response in Recurrent Halotolerant Exiguobacterium sp. SH31 Isolated From Sediments of Salar de Huasco, Chilean Altiplano. Front Microbiol 2018; 9:2228. [PMID: 30294311 PMCID: PMC6158405 DOI: 10.3389/fmicb.2018.02228] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 08/31/2018] [Indexed: 12/22/2022] Open
Abstract
Poly-extremophiles microorganisms have the capacity to inhabit hostile environments and can survive several adverse conditions that include as variations in temperature, pH, and salinity, high levels UV light and atmospheric pressure, and even the presence of toxic compounds and the formation of reactive oxygen species (ROS). A halotolerant Exiguobacterium strain was isolated from Salar de Huasco (Chilean Altiplano), a well-known shallow lake area with variable salinity levels, little human intervention, and extreme environmental conditions, which makes it ideal for the study of resistant mechanisms and the evolution of adaptations. This bacterial genus has not been extensively studied, although its cosmopolitan location indicates that it has high levels of plasticity and adaptive capacity. However, to date, there are no studies regarding the tolerance and resistance to salinity and osmotic pressure. We set out to characterize the Exiguobacterium sp. SH31 strain and describe its phenotypical and genotypical response to osmotic stress. In this context, as a first step to characterize the response to the SH31 strain to salinity and to establish the bases for a molecular study, we proposed to compare its response under three salt conditions (0, 25, and 50 g/l NaCl). Using different physiology, genomic, and transcriptomic approaches, we determined that the bacterium is able to grow properly in a NaCl concentration of up to 50 g/l; however, the best growth rate was observed at 25 g/l. Although the presence of flagella is not affected by salinity, motility was diminished at 25 g/l NaCl and abolished at 50 g/l. Biofilm formation was induced proportionally with increases in salinity, which was expected. These phenotypic results correlated with the expression of related genes: fliG and fliS Motility); opuBA and putP (transport); glnA, proC, gltA, and gbsA (compatible solutes); ywqC, bdlA, luxS y pgaC (biofilm and stress response); and therefore, we conclude that this strain effectively modifies gene expression and physiology in a differential manner when faced with different concentrations of NaCl and these modifications aid survival.
Collapse
Affiliation(s)
- Francisco Remonsellez
- Departamento de Ingeniería Química, Facultad de Ingeniería y Ciencias Geológicas, Universidad Católica del Norte, Antofagasta, Chile
- Centro de Investigación Tecnológica del Agua en el Desierto (CEITSAZA), Universidad Católica del Norte, Antofagasta, Chile
| | - Juan Castro-Severyn
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Coral Pardo-Esté
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Pablo Aguilar
- Lake and Glacier Ecology Research Group, Institute of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Jonathan Fortt
- Departamento de Ingeniería Química, Facultad de Ingeniería y Ciencias Geológicas, Universidad Católica del Norte, Antofagasta, Chile
| | - Cesar Salinas
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Sergio Barahona
- Departamento de Ingeniería Química, Facultad de Ingeniería y Ciencias Geológicas, Universidad Católica del Norte, Antofagasta, Chile
| | - Joice León
- Departamento de Ingeniería Química, Facultad de Ingeniería y Ciencias Geológicas, Universidad Católica del Norte, Antofagasta, Chile
| | - Bárbara Fuentes
- Departamento de Ingeniería Química, Facultad de Ingeniería y Ciencias Geológicas, Universidad Católica del Norte, Antofagasta, Chile
| | - Carlos Areche
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Klaudia L. Hernández
- Centro de Investigación Marina Quintay, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile
| | - Daniel Aguayo
- Center for Bioinformatics and Integrative Biology, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Claudia P. Saavedra
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| |
Collapse
|
21
|
Solon AJ, Vimercati L, Darcy JL, Arán P, Porazinska D, Dorador C, Farías ME, Schmidt SK. Microbial Communities of High-Elevation Fumaroles, Penitentes, and Dry Tephra "Soils" of the Puna de Atacama Volcanic Zone. MICROBIAL ECOLOGY 2018; 76:340-351. [PMID: 29305629 DOI: 10.1007/s00248-017-1129-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 12/12/2017] [Indexed: 06/07/2023]
Abstract
The aim of this study was to understand the spatial distribution of microbial communities (18S and 16S rRNA genes) across one of the harshest terrestrial landscapes on Earth. We carried out Illumina sequencing using samples from two expeditions to the high slopes (up to 6050 m.a.s.l.) of Volcán Socompa and Llullaillaco to describe the microbial communities associated with the extremely dry tephra compared to areas that receive water from fumaroles and ice fields made up of nieves penitentes. There were strong spatial patterns relative to these landscape features with the most diverse (alpha diversity) communities being associated with fumaroles. Penitentes did not significantly increase alpha diversity compared to dry tephra at the same elevation (5825 m.a.s.l.) on Volcán Socompa, but the structure of the 18S community (beta diversity) was significantly affected by the presence of penitentes on both Socompa and Llullaillaco. In addition, the 18S community was significantly different in tephra wetted by penitentes versus dry tephra sites across many elevations on Llullaillaco. Traditional phototrophs (algae and cyanobacteria) were abundant in wetter tephra associated with fumaroles, and algae (but not cyanobacteria) were common in tephra associated with penitentes. Dry tephra had neither algae nor cyanobacteria but did host potential phototrophs in the Rhodospirillales on Volcán Llullaillaco, but not on Socompa. These results provide new insights into the distribution of microbes across one of the most extreme terrestrial environments on Earth and provide the first ever glimpse of life associated with nieves penitentes, spire-shaped ice structures that are widespread across the mostly unexplored high-elevation Andean Central Volcanic Zone.
Collapse
Affiliation(s)
- Adam J Solon
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
| | - Lara Vimercati
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
| | - J L Darcy
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
| | - Pablo Arán
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta & Centre for Biotechnology and Bioengineering (CeBiB), Universidad de Antofagasta, Antofagasta, Chile
- Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Dorota Porazinska
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
| | - C Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta & Centre for Biotechnology and Bioengineering (CeBiB), Universidad de Antofagasta, Antofagasta, Chile
- Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - M E Farías
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas, PROIMI, Tucumán, Argentina
| | - S K Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA.
| |
Collapse
|
22
|
Stewart LC, Stucker VK, Stott MB, de Ronde CEJ. Marine-influenced microbial communities inhabit terrestrial hot springs on a remote island volcano. Extremophiles 2018; 22:687-698. [PMID: 29713821 DOI: 10.1007/s00792-018-1029-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 04/19/2018] [Indexed: 11/25/2022]
Abstract
Raoul Island is a subaerial island volcano approximately 1000 km northeast of New Zealand. Its caldera contains a circumneutral closed-basin volcanic lake and several associated pools, as well as intertidal coastal hot springs, all fed by a hydrothermal system sourced from both meteoric water and seawater. Here, we report on the geochemistry, prokaryotic community diversity, and cultivatable abundance of thermophilic microorganisms of four terrestrial features and one coastal feature on Raoul. Hydrothermal fluid contributions to the volcanic lake and pools make them brackish, and consequently support unusual microbial communities dominated by Planctomycetes, Chloroflexi, Alphaproteobacteria, and Thaumarchaeota, as well as up to 3% of the rare sister phylum to Cyanobacteria, Candidatus Melainabacteria. The dominant taxa are mesophilic to moderately thermophilic, phototrophic, and heterotrophic marine groups related to marine Planctomycetaceae. The coastal hot spring/shallow hydrothermal vent community is similar to other shallow systems in the Western Pacific Ocean, potentially due to proximity and similarities of geochemistry. Although rare in community sequence data, thermophilic methanogens, sulfur-reducers, and iron-reducers are present in culture-based assays.
Collapse
Affiliation(s)
- Lucy C Stewart
- Marine Geosciences, GNS Science, PO Box 30368, Lower Hutt, 5040, New Zealand.
| | - Valerie K Stucker
- Marine Geosciences, GNS Science, PO Box 30368, Lower Hutt, 5040, New Zealand
| | - Matthew B Stott
- Marine Geosciences, GNS Science, PO Box 30368, Lower Hutt, 5040, New Zealand
- University of Canterbury, Christchurch, 8140, New Zealand
| | - Cornel E J de Ronde
- Marine Geosciences, GNS Science, PO Box 30368, Lower Hutt, 5040, New Zealand
| |
Collapse
|
23
|
Mandakovic D, Maldonado J, Pulgar R, Cabrera P, Gaete A, Urtuvia V, Seeger M, Cambiazo V, González M. Microbiome analysis and bacterial isolation from Lejía Lake soil in Atacama Desert. Extremophiles 2018; 22:665-673. [PMID: 29687212 DOI: 10.1007/s00792-018-1027-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 04/13/2018] [Indexed: 12/31/2022]
Abstract
As a consequence of the severe climatic change affecting our entire world, many lakes in the Andes Cordillera are likely to disappear within a few decades. One of these lakes is Lejía Lake, located in the central Atacama Desert. The objectives of this study were: (1) to characterize the bacterial community from Lejía Lake shore soil (LLS) using 16S rRNA sequencing and (2) to test a culture-based approach using a soil extract medium (SEM) to recover soil bacteria. This extreme ecosystem was dominated by three phyla: Bacteroidetes, Proteobacteria, and Firmicutes with 29.2, 28.2 and 28.1% of the relative abundance, respectively. Using SEM, we recovered 7.4% of the operational taxonomic units from LLS, all of which belonged to the same three dominant phyla from LLS (6.9% of Bacteroidetes, 77.6% of Proteobacteria, and 15.3% of Firmicutes). In addition, we used SEM to recover isolates from LLS and supplemented the culture medium with increasing salt concentrations to isolate microbial representatives of salt tolerance (Halomonas spp.). The results of this study complement the list of microbial taxa diversity from the Atacama Desert and assess a pipeline to isolate selective bacteria that could represent useful elements for biotechnological approaches.
Collapse
Affiliation(s)
- Dinka Mandakovic
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile
- Fondap Center for Genome Regulation (CGR), Avenida Blanco Encalada, 2085, Santiago, Chile
| | - Jonathan Maldonado
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile
- Fondap Center for Genome Regulation (CGR), Avenida Blanco Encalada, 2085, Santiago, Chile
| | - Rodrigo Pulgar
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile
- Fondap Center for Genome Regulation (CGR), Avenida Blanco Encalada, 2085, Santiago, Chile
- Laboratorio de Genómica Aplicada, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile
| | - Pablo Cabrera
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile
- Fondap Center for Genome Regulation (CGR), Avenida Blanco Encalada, 2085, Santiago, Chile
| | - Alexis Gaete
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile
| | - Viviana Urtuvia
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química, Center for Nanotechnology, Systems Biology and Centro de Biotecnología, Universidad Técnica Federico Santa María, Avenida España, 1680, Valparaiso, Chile
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Avenida Brasil, 2147, Valparaiso, Chile
| | - Michael Seeger
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química, Center for Nanotechnology, Systems Biology and Centro de Biotecnología, Universidad Técnica Federico Santa María, Avenida España, 1680, Valparaiso, Chile
| | - Verónica Cambiazo
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile
- Fondap Center for Genome Regulation (CGR), Avenida Blanco Encalada, 2085, Santiago, Chile
- Laboratorio de Genómica Aplicada, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile
| | - Mauricio González
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile.
- Fondap Center for Genome Regulation (CGR), Avenida Blanco Encalada, 2085, Santiago, Chile.
- Laboratorio de Genómica Aplicada, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile.
| |
Collapse
|
24
|
Molina V, Dorador C, Fernández C, Bristow L, Eissler Y, Hengst M, Hernandez K, Olsen LM, Harrod C, Marchant F, Anguita C, Cornejo M. The activity of nitrifying microorganisms in a high-altitude Andean wetland. FEMS Microbiol Ecol 2018; 94:4969675. [DOI: 10.1093/femsec/fiy062] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 04/09/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Verónica Molina
- Departamento de Biología, Observatorio de Ecología Microbiana, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha. Avenida Leopoldo Carvallo 270, Playa Ancha, Valparaíso, Chile
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto de Antofagasta, Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta. Avenida Universidad de Antofagasta s/n, Antofagasta, Chile
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Beaucheff 851 (Piso 7)
| | - Camila Fernández
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique, F-66650, Banyuls/mer, France
- Interdisciplinary Center for Aquaculture Research (INCAR), COPAS SUR-AUSTRAL Program, Barrio Universitario s/n, Universidad de Concepción, Concepción, Chile
| | - Laura Bristow
- Nordic Center for Earth Evolution (NordCEE), Department of Biology, University of Southern Denmark, Campusvej 55-5230, Odense, Denmark
| | - Yoanna Eissler
- Centro de Investigación y Gestión de Recursos Naturales, Instituto de Química y Bioquímica, Facultad de Ciencias, Universidad de Valparaíso, Gran Bretaña 1111, Playa Ancha, Valparaíso, Chile
| | - Martha Hengst
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Beaucheff 851 (Piso 7)
- Departamento de Ciencias Farmacéuticas, Facultad de Ciencias, Universidad Católica del Norte. Av Angamos 0610 Antofagasta, Chile
| | - Klaudia Hernandez
- Centro de Investigacion Marina Quintay, Facultad de Ecología y Recursos Naturales, Universidad Andres Bello, Avenida República 440, Santiago, Chile10
| | | | - Chris Harrod
- Fish and Stable Isotope Ecology Laboratory, Instituto de Ciencias Naturales Alexander von Humboldt, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Francisca Marchant
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto de Antofagasta, Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta. Avenida Universidad de Antofagasta s/n, Antofagasta, Chile
| | - Cristobal Anguita
- Departamento de Ecologia y Biodiversidad, Facultad de Ecologia y Recursos Naturales, Universidad Andres Bello, Av. Republica 440, Santiago, Chile
| | - Marcela Cornejo
- Escuela de Ciencias del Mar e Instituto Milenio de Oceanografía , Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile, Altamirano 1480, Valparaíso
| |
Collapse
|
25
|
Cabrol NA. The Coevolution of Life and Environment on Mars: An Ecosystem Perspective on the Robotic Exploration of Biosignatures. ASTROBIOLOGY 2018; 18:1-27. [PMID: 29252008 PMCID: PMC5779243 DOI: 10.1089/ast.2017.1756] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 11/27/2017] [Indexed: 05/09/2023]
Abstract
Earth's biological and environmental evolution are intertwined and inseparable. This coevolution has become a fundamental concept in astrobiology and is key to the search for life beyond our planet. In the case of Mars, whether a coevolution took place is unknown, but analyzing the factors at play shows the uniqueness of each planetary experiment regardless of similarities. Early Earth and early Mars shared traits. However, biological processes on Mars, if any, would have had to proceed within the distinctive context of an irreversible atmospheric collapse, greater climate variability, and specific planetary characteristics. In that, Mars is an important test bed for comparing the effects of a unique set of spatiotemporal changes on an Earth-like, yet different, planet. Many questions remain unanswered about Mars' early environment. Nevertheless, existing data sets provide a foundation for an intellectual framework where notional coevolution models can be explored. In this framework, the focus is shifted from planetary-scale habitability to the prospect of habitats, microbial ecotones, pathways to biological dispersal, biomass repositories, and their meaning for exploration. Critically, as we search for biosignatures, this focus demonstrates the importance of starting to think of early Mars as a biosphere and vigorously integrating an ecosystem approach to landing site selection and exploration. Key Words: Astrobiology-Biosignatures-Coevolution of Earth and life-Mars. Astrobiology 18, 1-27.
Collapse
|
26
|
Strahsburger E, Zapata F, Pedroso I, Fuentes D, Tapia P, Ponce R, Valdes J. Draft genome sequence of Exiguobacterium aurantiacum strain PN47 isolate from saline ponds, known as "Salar del Huasco", located in the Altiplano in the North of Chile. Braz J Microbiol 2018; 49:7-9. [PMID: 28757098 PMCID: PMC5790568 DOI: 10.1016/j.bjm.2017.03.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 02/14/2017] [Accepted: 03/10/2017] [Indexed: 11/24/2022] Open
Abstract
In this report, we present a draft genome of 2,886,173bp of an Exiguobacterium aurantiacum strain PN47 isolate from the sediment of a saline pond named "Salar del Huasco" in the Altiplano in the North of Chile. Strain PN47 encodes adaptive characteristics enabling survival in extreme environmental conditions of high heavy metal and salt concentrations and high alkalinity.
Collapse
Affiliation(s)
- Erwin Strahsburger
- Universidad Arturo Prat, Faculty of Renewable Naturals Resources, Molecular Biotechnology Laboratory, Iquique, Chile.
| | - Felipe Zapata
- Center for Systems Biotechnology, Fraunhofer Chile Research Foundation, Bio-Computing and Applied Genetics Division, Santiago, Chile
| | - Inti Pedroso
- Center for Systems Biotechnology, Fraunhofer Chile Research Foundation, Bio-Computing and Applied Genetics Division, Santiago, Chile
| | - Derie Fuentes
- Center for Systems Biotechnology, Fraunhofer Chile Research Foundation, Bio-Computing and Applied Genetics Division, Santiago, Chile
| | - Paz Tapia
- Center for Systems Biotechnology, Fraunhofer Chile Research Foundation, Bio-Computing and Applied Genetics Division, Santiago, Chile
| | - Raul Ponce
- Universidad Arturo Prat, Faculty of Renewable Naturals Resources, Molecular Biotechnology Laboratory, Iquique, Chile
| | - Jorge Valdes
- Center for Systems Biotechnology, Fraunhofer Chile Research Foundation, Bio-Computing and Applied Genetics Division, Santiago, Chile.
| |
Collapse
|
27
|
Serrano AE, Escudero LV, Tebes-Cayo C, Acosta M, Encalada O, Fernández-Moroso S, Demergasso C. First draft genome sequence of a strain from the genus Fusibacter isolated from Salar de Ascotán in Northern Chile. Stand Genomic Sci 2017; 12:43. [PMID: 28770028 PMCID: PMC5525254 DOI: 10.1186/s40793-017-0252-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 07/12/2017] [Indexed: 11/18/2022] Open
Abstract
Fusibacter sp. 3D3 (ATCC BAA-2418) is an arsenate-reducing halotolerant strain within the Firmicutes phylum, isolated from the Salar de Ascotán, a hypersaline salt flat in Northern Chile. This high-Andean closed basin is an athalassohaline environment located at the bottom of a tectonic basin surrounded by mountain range, including some active volcanoes. This landscape can be an advantageous system to explore the effect of salinity on microorganisms that mediate biogeochemical reactions. Since 2000, microbial reduction of arsenic has been evidenced in the system, and the phylogenetic analysis of the original community plus the culture enrichments has revealed the predominance of Firmicutes phylum. Here, we describe the first whole draft genome sequence of an arsenic-reducing strain belonging to the Fusibacter genus showing the highest 16S rRNA gene sequence similarity (98%) with Fusibacter sp. strain Vns02. The draft genome consists of 57 contigs with 5,111,250 bp and an average G + C content of 37.6%. Out of 4780 total genes predicted, 4700 genes code for proteins and 80 genes for RNAs. Insights from the genome sequence and some microbiological features of the strain 3D3 are available under Bioproject accession PRJDB4973 and Biosample SAMD00055724. The release of the genome sequence of this strain could contribute to the understanding of the arsenic biogeochemistry in extreme environments.
Collapse
Affiliation(s)
- Antonio E Serrano
- Centro de Biotecnología, Universidad Católica del Norte, Antofagasta, Chile
| | - Lorena V Escudero
- Centro de Biotecnología, Universidad Católica del Norte, Antofagasta, Chile.,Centro de Investigación Científica y Tecnológica para la Minería, Antofagasta, Chile
| | - Cinthya Tebes-Cayo
- Centro de Biotecnología, Universidad Católica del Norte, Antofagasta, Chile
| | - Mauricio Acosta
- Centro de Biotecnología, Universidad Católica del Norte, Antofagasta, Chile
| | - Olga Encalada
- Centro de Biotecnología, Universidad Católica del Norte, Antofagasta, Chile
| | | | - Cecilia Demergasso
- Centro de Biotecnología, Universidad Católica del Norte, Antofagasta, Chile.,Centro de Investigación Científica y Tecnológica para la Minería, Antofagasta, Chile
| |
Collapse
|
28
|
Schmidt SK, Vimercati L, Darcy JL, Arán P, Gendron EM, Solon AJ, Porazinska D, Dorador C. A Naganishia in high places: functioning populations or dormant cells from the atmosphere? Mycology 2017; 8:153-163. [PMID: 30123637 PMCID: PMC6059072 DOI: 10.1080/21501203.2017.1344154] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 06/15/2017] [Indexed: 12/16/2022] Open
Abstract
Here, we review the current state of knowledge concerning high-elevation members of the extremophilic Cryptococcus albidus clade (now classified as the genus Naganishia). These fungi dominate eukaryotic microbial communities across the highest elevation, soil-like material (tephra) on volcanoes such as Llullaillaco, Socompa, and Saírecabur in the Atacama region of Chile, Argentina, and Bolivia. Recent studies indicate that Naganishia species are among the most resistant organisms to UV radiation, and a strain of N. friedmannii from Volcán Llullaillaco is the first organism that is known to grow during the extreme, diurnal freeze-thaw cycles that occur on a continuous basis at elevations above 6000 m.a.s.l. in the Atacama region. These and other extremophilic traits discussed in this review may serve a dual purpose of allowing Naganishia species to survive long-distance transport through the atmosphere and to survive the extreme conditions found at high elevations. Current evidence indicates that there are frequent dispersal events between high-elevation volcanoes of Atacama region and the Dry Valleys of Antarctica via "Rossby Wave" merging of the polar and sub-tropical jet streams. This dispersal hypothesis needs further verification, as does the hypothesis that Naganishia species are flexible "opportunitrophs" that can grow during rare periods of water (from melting snow) and nutrient availability (from Aeolian inputs) in one of the most extreme terrestrial habitats on Earth.
Collapse
Affiliation(s)
- Steven K Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Lara Vimercati
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - John L Darcy
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Pablo Arán
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta & Centre for Biotechnology and Bioengineering (CeBiB), Universidad de Antofagasta, Antofagasta, Chile
- Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Eli M.S Gendron
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
- Molecular, Cellular, and Developmental Biology Department, University of Colorado, Boulder, CO, USA
| | - Adam J Solon
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Dorota Porazinska
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta & Centre for Biotechnology and Bioengineering (CeBiB), Universidad de Antofagasta, Antofagasta, Chile
- Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| |
Collapse
|
29
|
Freeze-thaw revival of rotifers and algae in a desiccated, high-elevation (5500 meters) microbial mat, high Andes, Perú. Extremophiles 2017; 21:573-580. [PMID: 28321614 DOI: 10.1007/s00792-017-0926-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/06/2017] [Indexed: 12/24/2022]
Abstract
This is the first study of the highest elevation cyanobacteria-dominated microbial mat yet described. The desiccated mat was sampled in 2010 from an ephemeral rock pool at 5500 m above sea level in the Cordillera Vilcanota of southern Perú. After being frozen for 6 years at -20 °C in the lab, pieces of the mat were sequenced to fully characterize both the 16 and 18S microbial communities and experiments were conducted to determine if organisms in the mat could revive and become active under the extreme freeze-thaw conditions that these mats experience in the field. Sequencing revealed an unexpectedly diverse, multi-trophic microbial community with 16S OTU richness comparable to similar, seasonally desiccated mats from the Dry Valleys of Antarctica and low elevation sites in the Atacama Desert region. The bacterial community of the mat was dominated by phototrophs in the Cyanobacteria (Nostoc) and the Rhodospirillales, whereas the eukaryotic community was dominated by predators such as bdelloid rotifers (Philodinidae). Microcosm experiments showed that bdelloid rotifers in the mat were able to come out of dormancy and actively forage even under realistic field conditions (diurnal temperature fluctuations of -12 °C at night to + 27 °C during the day), and after being frozen for 6 years. Our results broaden our understanding of the diversity of life in periodically desiccated, high-elevation habitats and demonstrate that extreme freeze-thaw cycles per se are not a major factor limiting the development of at least some members of these unique microbial mat systems.
Collapse
|
30
|
Hernández KL, Yannicelli B, Olsen LM, Dorador C, Menschel EJ, Molina V, Remonsellez F, Hengst MB, Jeffrey WH. Microbial Activity Response to Solar Radiation across Contrasting Environmental Conditions in Salar de Huasco, Northern Chilean Altiplano. Front Microbiol 2016; 7:1857. [PMID: 27920763 PMCID: PMC5118629 DOI: 10.3389/fmicb.2016.01857] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 11/04/2016] [Indexed: 11/13/2022] Open
Abstract
In high altitude environments, extreme levels of solar radiation and important differences of ionic concentrations over narrow spatial scales may modulate microbial activity. In Salar de Huasco, a high-altitude wetland in the Andean mountains, the high diversity of microbial communities has been characterized and associated with strong environmental variability. Communities that differed in light history and environmental conditions, such as nutrient concentrations and salinity from different spatial locations, were assessed for bacterial secondary production (BSP, 3H-leucine incorporation) response from short-term exposures to solar radiation. We sampled during austral spring seven stations categorized as: (a) source stations, with recently emerged groundwater (no-previous solar exposure); (b) stream running water stations; (c) stations connected to source waters but far downstream from source points; and (d) isolated ponds disconnected from ground sources or streams with a longer isolation and solar exposure history. Very high values of 0.25 μE m-2 s-1, 72 W m-2 and 12 W m-2 were measured for PAR, UVA, and UVB incident solar radiation, respectively. The environmental factors measured formed two groups of stations reflected by principal component analyses (near to groundwater sources and isolated systems) where isolated ponds had the highest BSP and microbial abundance (35 microalgae taxa, picoeukaryotes, nanoflagellates, and bacteria) plus higher salinities and PO43- concentrations. BSP short-term response (4 h) to solar radiation was measured by 3H-leucine incorporation under four different solar conditions: full sun, no UVB, PAR, and dark. Microbial communities established in waters with the longest surface exposure (e.g., isolated ponds) had the lowest BSP response to solar radiation treatments, and thus were likely best adapted to solar radiation exposure contrary to ground source waters. These results support our light history (solar exposure) hypothesis where the more isolated the community is from ground water sources, the better adapted it is to solar radiation. We suggest that factors other than solar radiation (e.g., salinity, PO43-, NO3-) are also important in determining microbial productivity in heterogeneous environments such as the Salar de Huasco.
Collapse
Affiliation(s)
- Klaudia L Hernández
- Centro de Investigación Marina Quintay CIMARQ, Facultad de Ecología y Recursos Naturales, Universidad Andres BelloSantiago, Chile; Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de ChileValdivia, Chile
| | - Beatriz Yannicelli
- Centro de Estudios Avanzados en Zonas AridasLa Serena, Chile; Facultad de Ciencias del Mar, Universidad Católica del NorteCoquimbo, Chile; Ecology and Sustainable Management of Oceanic Islands, Universidad Católica del Norte, CoquimboCoquimbo, Chile; Centro Universitario de la Región Este, Universidad de la RepúblicaRocha, Uruguay
| | | | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional and Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de AntofagastaAntofagasta, Chile; Centro de Biotecnología y BioingenieríaSantiago, Chile
| | - Eduardo J Menschel
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de ChileValdivia, Chile; Programa de Postgrado en Oceanografía, Departamento de Oceanografía, Universidad de ConcepciónConcepción, Chile; Centro de Investigación Dinámica de Ecosistemas Marinos de Altas Latitudes (FONDAP-IDEAL), Universidad Austral de ChileValdivia-Punta Arenas, Chile
| | - Verónica Molina
- Departamento de Biología, Observatorio de Ecología Microbiana, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha Valparaíso, Chile
| | - Francisco Remonsellez
- Laboratorio de Microbiología Aplicada y Extremófilos, Departamento de Ingeniería Química, Universidad Católica del Norte Antofagasta, Chile
| | - Martha B Hengst
- Centro de Biotecnología y BioingenieríaSantiago, Chile; Departamento de Ciencias Farmacéuticas, Facultad de Ciencias, Universidad Católica del NorteAntofagasta, Chile
| | - Wade H Jeffrey
- Center for Environmental Diagnostics and Bioremediation, University of West Florida, Pensacola FL, USA
| |
Collapse
|
31
|
Fernandez AB, Rasuk MC, Visscher PT, Contreras M, Novoa F, Poire DG, Patterson MM, Ventosa A, Farias ME. Microbial Diversity in Sediment Ecosystems (Evaporites Domes, Microbial Mats, and Crusts) of Hypersaline Laguna Tebenquiche, Salar de Atacama, Chile. Front Microbiol 2016; 7:1284. [PMID: 27597845 PMCID: PMC4992683 DOI: 10.3389/fmicb.2016.01284] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 08/04/2016] [Indexed: 02/01/2023] Open
Abstract
We combined nucleic acid-based molecular methods, biogeochemical measurements, and physicochemical characteristics to investigate microbial sedimentary ecosystems of Laguna Tebenquiche, Atacama Desert, Chile. Molecular diversity, and biogeochemistry of hypersaline microbial mats, rhizome-associated concretions, and an endoevaporite were compared with: The V4 hypervariable region of the 16S rRNA gene was amplified by pyrosequencing to analyze the total microbial diversity (i.e., bacteria and archaea) in bulk samples, and in addition, in detail on a millimeter scale in one microbial mat and in one evaporite. Archaea were more abundant than bacteria. Euryarchaeota was one of the most abundant phyla in all samples, and particularly dominant (97% of total diversity) in the most lithified ecosystem, the evaporite. Most of the euryarchaeal OTUs could be assigned to the class Halobacteria or anaerobic and methanogenic archaea. Planctomycetes potentially also play a key role in mats and rhizome-associated concretions, notably the aerobic organoheterotroph members of the class Phycisphaerae. In addition to cyanobacteria, members of Chromatiales and possibly the candidate family Chlorotrichaceae contributed to photosynthetic carbon fixation. Other abundant uncultured taxa such as the candidate division MSBL1, the uncultured MBGB, and the phylum Acetothermia potentially play an important metabolic role in these ecosystems. Lithifying microbial mats contained calcium carbonate precipitates, whereas endoevoporites consisted of gypsum, and halite. Biogeochemical measurements revealed that based on depth profiles of O2 and sulfide, metabolic activities were much higher in the non-lithifying mat (peaking in the least lithified systems) than in lithifying mats with the lowest activity in endoevaporites. This trend in decreasing microbial activity reflects the increase in salinity, which may play an important role in the biodiversity.
Collapse
Affiliation(s)
- Ana B Fernandez
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas, Planta Piloto de Procesos Industriales Microbiológicos, Centro Científico Tecnológico, CONICET Tucumán, Argentina
| | - Maria C Rasuk
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas, Planta Piloto de Procesos Industriales Microbiológicos, Centro Científico Tecnológico, CONICET Tucumán, Argentina
| | - Pieter T Visscher
- Department of Marine Sciences, University of ConnecticutGroton, CT, USA; Australian Centre for Astrobiology, University of New South WalesSydney, NSW, Australia
| | | | | | - Daniel G Poire
- Centro de Investigaciones Geológicas, Universidad Nacional de La Plata-Conicet La Plata, Argentina
| | - Molly M Patterson
- Department of Marine Sciences, University of Connecticut Groton, CT, USA
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla Sevilla, Spain
| | - Maria E Farias
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas, Planta Piloto de Procesos Industriales Microbiológicos, Centro Científico Tecnológico, CONICET Tucumán, Argentina
| |
Collapse
|
32
|
Aguilar P, Acosta E, Dorador C, Sommaruga R. Large Differences in Bacterial Community Composition among Three Nearby Extreme Waterbodies of the High Andean Plateau. Front Microbiol 2016; 7:976. [PMID: 27446017 PMCID: PMC4914511 DOI: 10.3389/fmicb.2016.00976] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 06/06/2016] [Indexed: 11/30/2022] Open
Abstract
The high Andean plateau or Altiplano contains different waterbodies that are subjected to extreme fluctuations in abiotic conditions on a daily and an annual scale. The bacterial diversity and community composition of those shallow waterbodies is largely unexplored, particularly, of the ponds embedded within the peatland landscape (i.e., Bofedales). Here we compare the small-scale spatial variability (<1 m) in bacterial diversity and community composition between two of those ponds with contrasting apparent color, using 454 pyrosequencing of the 16S rRNA gene. Further, we compared the results with the nearest (80 m) main lagoon in the system to elucidate the importance of different environmental factors such as salinity and the importance of these ponds as a source of shared diversity. Bacterial diversity was higher in both ponds than in the lagoon and community composition was largely different among them and characterized by very low operational taxonomic unit sharing. Whereas the “green” pond with relatively low dissolved organic carbon (DOC) concentration (33.5 mg L-1) was dominated by Proteobacteria and Bacteroidetes, the one with extreme DOC concentration (424.1 mg L-1) and red hue was dominated by Cyanobacteria. By contrast, the lagoon was largely dominated by Proteobacteria, particularly by Gammaproteobacteria. A large percentage (47%) of all reads was unclassified suggesting the existence of large undiscovered bacterial diversity. Our results suggest that even at the very small-scale spatial range considered, local environmental factors are important in explaining differences in bacterial community composition in those systems. Further, our study highlights that Altiplano peatland ponds represent a hitherto unknown source of microbial diversity.
Collapse
Affiliation(s)
- Pablo Aguilar
- Lake and Glacier Ecology Research Group, Institute of Ecology, University of InnsbruckInnsbruck, Austria; Laboratory of Microbial Complexity and Functional Ecology, Antofagasta Institute, University of AntofagastaAntofagasta, Chile; Centre for Biotechnology and Bioengineering, Universidad de ChileSantiago, Chile
| | - Eduardo Acosta
- Laboratory of Microbial Complexity and Functional Ecology, Antofagasta Institute, University of AntofagastaAntofagasta, Chile; Centre for Biotechnology and Bioengineering, Universidad de ChileSantiago, Chile
| | - Cristina Dorador
- Laboratory of Microbial Complexity and Functional Ecology, Antofagasta Institute, University of AntofagastaAntofagasta, Chile; Centre for Biotechnology and Bioengineering, Universidad de ChileSantiago, Chile
| | - Ruben Sommaruga
- Lake and Glacier Ecology Research Group, Institute of Ecology, University of Innsbruck Innsbruck, Austria
| |
Collapse
|
33
|
Aszalós JM, Krett G, Anda D, Márialigeti K, Nagy B, Borsodi AK. Diversity of extremophilic bacteria in the sediment of high-altitude lakes located in the mountain desert of Ojos del Salado volcano, Dry-Andes. Extremophiles 2016; 20:603-20. [PMID: 27315168 DOI: 10.1007/s00792-016-0849-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 05/31/2016] [Indexed: 11/26/2022]
Abstract
Ojos del Salado, the highest volcano on Earth is surrounded by a special mountain desert with extreme aridity, great daily temperature range, intense solar radiation, and permafrost from 5000 meters above sea level. Several saline lakes and permafrost derived high-altitude lakes can be found in this area, often surrounded by fumaroles and hot springs. The aim of this study was to gain information about the bacterial communities inhabiting the sediment of high-altitude lakes of the Ojos del Salado region located between 3770 and 6500 m. Altogether 11 sediment samples from 4 different altitudes were examined with 16S rRNA gene based denaturing gradient gel electrophoresis and clone libraries. Members of 17 phyla or candidate divisions were detected with the dominance of Proteobacteria, Acidobacteria, Actinobacteria and Bacteroidetes. The bacterial community composition was determined mainly by the altitude of the sampling sites; nevertheless, the extreme aridity and the active volcanism had a strong influence on it. Most of the sequences showed the highest relation to bacterial species or uncultured clones from similar extreme environments.
Collapse
Affiliation(s)
- Júlia Margit Aszalós
- Department of Microbiology, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117, Budapest, Hungary
| | - Gergely Krett
- Department of Microbiology, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117, Budapest, Hungary
| | - Dóra Anda
- Department of Microbiology, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117, Budapest, Hungary
| | - Károly Márialigeti
- Department of Microbiology, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117, Budapest, Hungary
| | - Balázs Nagy
- Department of Physical Geography, Eötvös Loránd University, Pázmány P. sétány 1/C, 1117, Budapest, Hungary
| | - Andrea K Borsodi
- Department of Microbiology, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117, Budapest, Hungary.
| |
Collapse
|
34
|
Albarracín VH, Gärtner W, Farias ME. Forged Under the Sun: Life and Art of Extremophiles from Andean Lakes. Photochem Photobiol 2015; 92:14-28. [PMID: 26647770 DOI: 10.1111/php.12555] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 10/09/2015] [Accepted: 11/05/2015] [Indexed: 12/25/2022]
Abstract
High-altitude Andean lakes (HAAL) are a treasure chest for microbiological research in South America. Their indigenous microbial communities are exposed to extremely high UV irradiation and to multiple chemical extremes (Arsenic, high salt content, alkalinity). Microbes are found both, free-living or associated into microbial mats with different degrees of mineralization and lithification, including unique modern stromatolites located at 3570 m above sea level. Characterization of these polyextremophilic microbes began only recently, employing morphological and phylogenetic methods as well as high-throughput sequencing and proteomics approach. Aside from providing a general overview on microbial communities, special attention is given to various survival strategies; HAAL's microbes present a complex system of shared genetic and physiological mechanisms (UV-resistome) based on UV photoreceptors and stress sensors with their corresponding response regulators, UV avoidance and protection strategies, damage tolerance and UV damage repair. Molecular information will be provided for what is, so far the most studied HAAL molecule, a CPD-Class I photolyase from Acinetobacter Ver3 (Laguna Verde, 4400 m). This work further proposes some strategies that make an appeal for the preservation of HAAL, a highly fragile environment that offers promising and ample research possibilities.
Collapse
Affiliation(s)
- Virginia Helena Albarracín
- Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI), CCT, CONICET, Tucumán, Argentina.,Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, Tucumán, Argentina
| | - Wolfgang Gärtner
- Max-Planck-Institute for Chemical Energy Conversion, Mülheim, Germany
| | - María Eugenia Farias
- Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI), CCT, CONICET, Tucumán, Argentina
| |
Collapse
|
35
|
Albarracín VH, Kurth D, Ordoñez OF, Belfiore C, Luccini E, Salum GM, Piacentini RD, Farías ME. High-Up: A Remote Reservoir of Microbial Extremophiles in Central Andean Wetlands. Front Microbiol 2015; 6:1404. [PMID: 26733008 PMCID: PMC4679917 DOI: 10.3389/fmicb.2015.01404] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Accepted: 11/25/2015] [Indexed: 11/18/2022] Open
Abstract
The Central Andes region displays unexplored ecosystems of shallow lakes and salt flats at mean altitudes of 3700 m. Being isolated and hostile, these so-called "High-Altitude Andean Lakes" (HAAL) are pristine and have been exposed to little human influence. HAAL proved to be a rich source of microbes showing interesting adaptations to life in extreme settings (poly-extremophiles) such as alkalinity, high concentrations of arsenic and dissolved salts, intense dryness, large daily ambient thermal amplitude, and extreme solar radiation levels. This work reviews HAAL microbiodiversity, taking into account different microbial niches, such as plankton, benthos, microbial mats and microbialites. The modern stromatolites and other microbialites discovered recently at HAAL are highlighted, as they provide unique modern-though quite imperfect-analogs of environments proxy for an earlier time in Earth's history (volcanic setting and profuse hydrothermal activity, low atmospheric O2 pressure, thin ozone layer and high UV exposure). Likewise, we stress the importance of HAAL microbes as model poly-extremophiles in the study of the molecular mechanisms underlying their resistance ability against UV and toxic or deleterious chemicals using genome mining and functional genomics. In future research directions, it will be necessary to exploit the full potential of HAAL poly-extremophiles in terms of their biotechnological applications. Current projects heading this way have yielded detailed molecular information and functional proof on novel extremoenzymes: i.e., DNA repair enzymes and arsenic efflux pumps for which medical and bioremediation applications, respectively, are envisaged. But still, much effort is required to unravel novel functions for this and other molecules that dwell in a unique biological treasure despite its being hidden high up, in the remote Andes.
Collapse
Affiliation(s)
- Virginia H. Albarracín
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas, Planta Piloto de Procesos Industriales y Microbiológicos, Centro Científico Tecnológico, CONICETTucumán, Argentina
- Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de TucumánTucumán, Argentina
- Centro Integral de Microscopía Electrónica, Universidad Nacional de Tucumán, Centro Científico Tecnológico, CONICETTucumán, Argentina
| | - Daniel Kurth
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas, Planta Piloto de Procesos Industriales y Microbiológicos, Centro Científico Tecnológico, CONICETTucumán, Argentina
| | - Omar F. Ordoñez
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas, Planta Piloto de Procesos Industriales y Microbiológicos, Centro Científico Tecnológico, CONICETTucumán, Argentina
| | - Carolina Belfiore
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas, Planta Piloto de Procesos Industriales y Microbiológicos, Centro Científico Tecnológico, CONICETTucumán, Argentina
| | - Eduardo Luccini
- CONICET Centro de Excelencia en Productos y Procesos de la Provincia de CórdobaCórdoba, Argentina
- Facultad de Química e Ingeniería, Pontificia Universidad Católica ArgentinaRosario, Argentina
| | - Graciela M. Salum
- Instituto de Física Rosario, CONICET Universidad Nacional de RosarioRosario, Argentina
- Facultad Regional Concepción del Uruguay, Universidad Tecnológica NacionalConcepción del Uruguay, Argentina
| | - Ruben D. Piacentini
- Facultad Regional Concepción del Uruguay, Universidad Tecnológica NacionalConcepción del Uruguay, Argentina
- Facultad de Ciencias Exactas, Ingeniería y Agrimensura, Universidad Nacional de RosarioRosario, Argentina
| | - María E. Farías
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas, Planta Piloto de Procesos Industriales y Microbiológicos, Centro Científico Tecnológico, CONICETTucumán, Argentina
| |
Collapse
|
36
|
Fernández-Zenoff MV, Estévez MC, Farías ME. Diurnal variation in bacterioplankton composition and DNA damage in the microbial community from an Andean oligotrophic lake. Rev Argent Microbiol 2015; 46:358-62. [PMID: 25576421 DOI: 10.1016/s0325-7541(14)70095-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 10/02/2014] [Indexed: 10/24/2022] Open
Abstract
Laguna Azul is an oligotrophic lake situated at 4,560 m above sea level and subject to a high level of solar radiation. Bacterioplankton community composition (BCC) was analysed by denaturing gradient gel electrophoresis and the impact of solar ultraviolet radiation was assessed by measuring cyclobutane pyrimidine dimers (CPD). Furthermore, pure cultures of Acinetobacter johnsonii A2 and Rhodococcus sp. A5 were exposed simultaneously and CPD accumulation was studied. Gel analyses generated a total of 7 sequences belonging to Alpha-proteobacteria (1 band), Beta-proteobacteria (1 band), Bacteroidetes (2 bands), Actinobacteria (1 band), and Firmicutes (1 band). DGGE profiles showed minimal changes in BCC and no CPD was detected even though a high level of damage was found in biodosimeters. A. johnsonii A2 showed low level of DNA damage while Rhodococcus sp. A5 exhibited high resistance since no CPD were detected under natural UV-B exposure, suggesting that the bacterial community is well adapted to this highly solar irradiated environment.
Collapse
Affiliation(s)
- María V Fernández-Zenoff
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT, CONICET, Tucumán, Argentina; Instituto de Microbiología, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Tucumán, Argentina.
| | - María C Estévez
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT, CONICET, Tucumán, Argentina
| | - María E Farías
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT, CONICET, Tucumán, Argentina
| |
Collapse
|
37
|
Delgado-Serrano L, López G, Bohorquez LC, Bustos JR, Rubiano C, Osorio-Forero C, Junca H, Baena S, Zambrano MM. Neotropical Andes hot springs harbor diverse and distinct planktonic microbial communities. FEMS Microbiol Ecol 2014; 89:56-66. [DOI: 10.1111/1574-6941.12333] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 03/07/2014] [Accepted: 03/21/2014] [Indexed: 11/30/2022] Open
Affiliation(s)
- Luisa Delgado-Serrano
- Molecular Genetics & Microbial Ecology; Corporación CorpoGen; Bogotá DC Colombia
- Colombian Center for Genomics and Bioinformatics of Extreme Environments - GeBiX; Bogotá DC Colombia
| | - Gina López
- Colombian Center for Genomics and Bioinformatics of Extreme Environments - GeBiX; Bogotá DC Colombia
- Unidad de Saneamiento y Biotecnología Ambiental; Departamento de Biología; Pontificia Universidad Javeriana; Bogotá DC Colombia
| | - Laura C. Bohorquez
- Molecular Genetics & Microbial Ecology; Corporación CorpoGen; Bogotá DC Colombia
- Colombian Center for Genomics and Bioinformatics of Extreme Environments - GeBiX; Bogotá DC Colombia
| | - José R. Bustos
- Molecular Genetics & Microbial Ecology; Corporación CorpoGen; Bogotá DC Colombia
- Colombian Center for Genomics and Bioinformatics of Extreme Environments - GeBiX; Bogotá DC Colombia
| | - Carolina Rubiano
- Colombian Center for Genomics and Bioinformatics of Extreme Environments - GeBiX; Bogotá DC Colombia
- Unidad de Saneamiento y Biotecnología Ambiental; Departamento de Biología; Pontificia Universidad Javeriana; Bogotá DC Colombia
| | - César Osorio-Forero
- Molecular Genetics & Microbial Ecology; Corporación CorpoGen; Bogotá DC Colombia
- Colombian Center for Genomics and Bioinformatics of Extreme Environments - GeBiX; Bogotá DC Colombia
| | - Howard Junca
- Molecular Genetics & Microbial Ecology; Corporación CorpoGen; Bogotá DC Colombia
- Colombian Center for Genomics and Bioinformatics of Extreme Environments - GeBiX; Bogotá DC Colombia
| | - Sandra Baena
- Colombian Center for Genomics and Bioinformatics of Extreme Environments - GeBiX; Bogotá DC Colombia
- Unidad de Saneamiento y Biotecnología Ambiental; Departamento de Biología; Pontificia Universidad Javeriana; Bogotá DC Colombia
| | - María M. Zambrano
- Molecular Genetics & Microbial Ecology; Corporación CorpoGen; Bogotá DC Colombia
- Colombian Center for Genomics and Bioinformatics of Extreme Environments - GeBiX; Bogotá DC Colombia
| |
Collapse
|
38
|
Farías ME, Contreras M, Rasuk MC, Kurth D, Flores MR, Poiré DG, Novoa F, Visscher PT. Characterization of bacterial diversity associated with microbial mats, gypsum evaporites and carbonate microbialites in thalassic wetlands: Tebenquiche and La Brava, Salar de Atacama, Chile. Extremophiles 2014; 18:311-29. [DOI: 10.1007/s00792-013-0617-6] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 12/05/2013] [Indexed: 02/01/2023]
|