1
|
Bonacolta AM, Visscher PT, Del Campo J, White Iii RA. The eukaryome of modern microbialites reveals distinct colonization across aquatic ecosystems. NPJ Biofilms Microbiomes 2024; 10:78. [PMID: 39227595 PMCID: PMC11372052 DOI: 10.1038/s41522-024-00547-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 08/12/2024] [Indexed: 09/05/2024] Open
Abstract
Protists are less studied for their role and diversity in ecosystems. Notably, protists have played and still play an important role in microbialites. Microbialites, or lithified microbial mats, represent the oldest evidence of fossil biofilms (~3.5 Gyr). Modern microbialites may offer a unique proxy to study the potential role of protists within a geological context. We examined protist diversity in freshwater (Kelly and Pavilion Lake in British Columbia, Canada) and marine (Highborne Cay, Bahamas) to hypersaline (Shark Bay, Australia) microbialites to decipher their geomicrobiological role. The freshwater microbialite communities were clearly distinct from their marine and hypersaline counterparts. Chlorophytes had higher numerical abundance in freshwater microbialites; whereas pennate diatoms dominated numerically in marine microbialites. Despite the differences, protists across ecosystems may have adopted similar roles and functions. We suggest a consistent biogeochemical role of protists across microbialites globally; but that salinity may shape protist composition and evolution in these ecosystems.
Collapse
Affiliation(s)
- Anthony M Bonacolta
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, USA
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
| | - Pieter T Visscher
- Department of Marine Sciences and Earth Sciences, University of Connecticut, Storrs, CT, USA
- Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW, Australia
| | - Javier Del Campo
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, USA.
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain.
| | - Richard Allen White Iii
- Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW, Australia.
- North Carolina Research Center (NCRC), Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Kannapolis, NC, USA.
- Computational Intelligence to Predict Health and Environmental Risks (CIPHER), Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC, USA.
| |
Collapse
|
2
|
Saona LA, Villafañe PG, Carrizo D, Cónsole Gonella C, Néspolo RF, Farías ME. Geomicrobiological characterization of the evaporitic ecosystem in the hypersaline lake Laguna Verde (Andean Puna, Northwestern Argentina). Ecol Evol 2024; 14:e10931. [PMID: 38348017 PMCID: PMC10859677 DOI: 10.1002/ece3.10931] [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: 09/04/2023] [Revised: 12/04/2023] [Accepted: 01/02/2024] [Indexed: 02/15/2024] Open
Abstract
Laguna Verde's dome-shaped structures are distinctive formations within the Central Andes, displaying unique geomicrobiological features. This study represents a pioneering investigation into these structures, assessing their formation, associated taxa, and ecological significance. Through a multifaceted approach that includes chemical analysis of the water body, multiscale characterization of the domes, and analysis of the associated microorganisms, we reveal the complex interplay between geology and biology in this extreme environment. The lake's alkaline waters that are rich in dissolved cations and anions such as chloride, sodium sulfate, and potassium, coupled with its location at the margin of the Antofalla salt flat, fed by alluvial fans and hydrothermal input, provide favorable conditions for mineral precipitation and support for the microorganism's activity. Laguna Verde's dome-shaped structures are mainly composed of gypsum and halite, displaying an internal heterogeneous mesostructure consisting of three zones: microcrystalline, organic (orange and green layers), and crystalline. The green layer of the organic zone is predominantly composed of Proteobacteria, Bacteroidetes, and Cyanobacteria, while the orange layer is mostly inhabited by Cyanobacteria. The results of the study suggest that oxygenic photosynthesis performed by Cyanobacteria is the main carbon fixation pathway in the microbial community, supported by carbon isotopic ratios of specific biomarkers. This finding highlights the important role played by Cyanobacteria in this ecosystem.
Collapse
Affiliation(s)
- L. A. Saona
- Facultad de Química y BiologíaUniversidad de Santiago de Chile (USACH)SantiagoChile
- Millennium Nucleus of Patagonian Limit of Life (LiLi)ValdiviaChile
- Millennium Institute for Integrative Biology (iBio)SantiagoChile
| | - P. G. Villafañe
- Instituto Superior de Correlación Geológica (INSUGEO), CONICET‐UNTTucumánArgentina
- GIUV2016‐303, Department of Botany and GeologyUniversitat de ValènciaValènciaEspaña
| | - D. Carrizo
- Centro de AstrobiologíaInstituto Nacional de Técnica AeroespacialMadridEspaña
| | - C. Cónsole Gonella
- Instituto Superior de Correlación Geológica (INSUGEO), CONICET‐UNTTucumánArgentina
| | - R. F. Néspolo
- Millennium Nucleus of Patagonian Limit of Life (LiLi)ValdiviaChile
- Millennium Institute for Integrative Biology (iBio)SantiagoChile
- Instituto de Ciencias Ambientales y EvolutivasUniversidad Austral de ChileValdiviaChile
| | | |
Collapse
|
3
|
Gorriti MF, Bamann C, Alonso-Reyes DG, Wood P, Bamberg E, Farías ME, Gärtner W, Albarracín VH. Functional characterization of xanthorhodopsin in Salinivibrio socompensis, a novel halophile isolated from modern stromatolites. Photochem Photobiol Sci 2023; 22:1809-1823. [PMID: 37036621 DOI: 10.1007/s43630-023-00412-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/21/2023] [Indexed: 04/11/2023]
Abstract
A putative xanthorhodopsin-encoding gene, XR34, was found in the genome of the moderately halophilic gammaproteobacterium Salinivibrio socompensis S34, isolated from modern stromatolites found on the shore of Laguna Socompa (3570 m), Argentina Puna. XR-encoding genes were clustered together with genes encoding X-carotene, retinal (vitamin-A aldehyde), and carotenoid biosynthesis enzymes while the carotene ketolase gene critical for the salinixanthin antenna compound was absent. To identify its functional behavior, we herein overexpressed and characterized this intriguing microbial rhodopsin. Recombinant XR34 showed all the salient features of canonical microbial rhodopsin and covalently bound retinal as a functional chromophore with λmax = 561 nm (εmax ca. 60,000 M-1 cm-1). Two canonical counterions with pK values of around 6 and 3 were identified by pH titration of the recombinant protein. With a recovery time of approximately half an hour in the dark, XR34 shows light-dark adaptation shifting the absorption maximum from 551 to 561 nm. Laser-flash induced photochemistry at pH 9 (deprotonated primary counterion) identified a photocycle starting with a K-like intermediate, followed by an M-state (λmax ca. 400 nm, deprotonated Schiff base), and a final long wavelength-absorbing N- or O-like intermediate before returning to the parental 561 nm-state. Initiating the photocycle at pH 5 (protonated counterion) yields only bathochromic intermediates, due to the lacking capacity of the counterion to accept the Schiff base proton. Illumination of the membrane-embedded protein yielded a capacitive transport current. The presence of the M-intermediate under these conditions was demonstrated by a blue light-induced shunt process.
Collapse
Affiliation(s)
- Marta F Gorriti
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI), CCT, CONICET, Av. Belgrano y Pje. Caseros, San Miguel de Tucumán, 4000, Tucumán, Argentina
| | - Christian Bamann
- Max-Planck-Institute for Biophysics, Max-von-Laue-Straße 3, Frankfurt am Main, 60438, Germany
| | - Daniel Gonzalo Alonso-Reyes
- Laboratorio de Microbiología Ultraestructural y Molecular, Centro Integral de Microscopía Electrónica (CIME, CONICET, UNT) CCT, CONICET, Facultad de Agronomía, Zootecnia y Veterinaria, Finca El Manantial, UNT, Camino de Sirga s/n (4107), Yerba Buena, Tucumán, Argentina
- Institute for Analytical Chemistry, University of Leipzig, Johannisallee 29, Leipzig, 04103, Germany
| | - Phillip Wood
- Max-Planck-Institute for Biophysics, Max-von-Laue-Straße 3, Frankfurt am Main, 60438, Germany
| | - Ernst Bamberg
- Max-Planck-Institute for Biophysics, Max-von-Laue-Straße 3, Frankfurt am Main, 60438, Germany
| | - María Eugenia Farías
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI), CCT, CONICET, Av. Belgrano y Pje. Caseros, San Miguel de Tucumán, 4000, Tucumán, Argentina
| | - Wolfgang Gärtner
- Institute for Analytical Chemistry, University of Leipzig, Johannisallee 29, Leipzig, 04103, Germany
| | - Virginia Helena Albarracín
- Laboratorio de Microbiología Ultraestructural y Molecular, Centro Integral de Microscopía Electrónica (CIME, CONICET, UNT) CCT, CONICET, Facultad de Agronomía, Zootecnia y Veterinaria, Finca El Manantial, UNT, Camino de Sirga s/n (4107), Yerba Buena, Tucumán, Argentina.
- Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, Miguel Lillo 205, San Miguel de Tucumán, 4000, Tucumán, Argentina.
- Facultad de Agronomía, Zootecnia y Veterinaria, Universidad Nacional de Tucumán, Centro Universitario Ing. R. Herrera (Ex Quinta Agronómica), Avda. Pte. N. Kirchner 1900., San Miguel de Tucumán, 4000, Tucumán, Argentina.
| |
Collapse
|
4
|
Della Vedova M, Villafañe PG, Cónsole‐Gonella C, Bahniuk Rumbelsperger A, Fadel Cury L, Horta LR, Farías ME. Disentangling microstructure and environmental conditions in high-altitude Andean microbialite systems (Catamarca, Argentine Puna). ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:92-108. [PMID: 36192831 PMCID: PMC10103866 DOI: 10.1111/1758-2229.13128] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 09/16/2022] [Indexed: 05/20/2023]
Abstract
The study of microbialites development is a key tool to understand environmental pathways during deposition. We provide a detailed analysis of modern Central Andean microbialites from high-altitude lakes. The stratigraphic record of Turquesa Lake shows a significant short-term recolonization by microbialite-producing microorganisms during environmental stress. Far from a crisis paradigm, the coasts and paleocoasts of Turquesa lake exhibit three microbialitic buildups formed along different stages, providing a good study case of biological resilience of these systems in harsh environments. The MI and MII microbialite buildups occupied two paleocoasts. Both are composed of oncoids with micritic to microsparitic textures. Morphological, textural and mineralogical similarities between the two buildups suggest that they were formed at different times, but under very similar environmental conditions. The microorganisms that produced the microbialitic buildup MIII are currently colonizing the coast of this lake. The previous oncoid morphology change to a parallel micritic-spartic lamination. This remarkable changes in the microstructure can be explained by an important environmental change caused by the isolation of the Peinado Lake, and a subsequently microorganism adaptation. This microbialite structures can be proposed as an interesting modern analogue for environmental changes along the geological record.
Collapse
Affiliation(s)
- Micaela Della Vedova
- Laboratorio de Investigaciones Microbiológicas en Lagunas Andinas (LIMLA)Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CONICETSan Miguel de TucumánTucumánArgentina
- Instituto Superior de Correlación Geológica (INSUGEO), CONICET‐ UNTYerba BuenaTucumánArgentina
| | - Patricio G. Villafañe
- Laboratorio de Investigaciones Microbiológicas en Lagunas Andinas (LIMLA)Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CONICETSan Miguel de TucumánTucumánArgentina
- Instituto Superior de Correlación Geológica (INSUGEO), CONICET‐ UNTYerba BuenaTucumánArgentina
| | - Carlos Cónsole‐Gonella
- Instituto Superior de Correlación Geológica (INSUGEO), CONICET‐ UNTYerba BuenaTucumánArgentina
| | | | | | - Luis R. Horta
- Instituto Superior de Correlación Geológica (INSUGEO), CONICET‐ UNTYerba BuenaTucumánArgentina
| | - María E. Farías
- Laboratorio de Investigaciones Microbiológicas en Lagunas Andinas (LIMLA)Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CONICETSan Miguel de TucumánTucumánArgentina
| |
Collapse
|
5
|
Teece BL, Havig JR, George SC, Hamilton TL, Baumgartner RJ, Hartz J, Van Kranendonk MJ. Biogeochemistry of Recently Fossilized Siliceous Hot Spring Sinters from Yellowstone, USA. ASTROBIOLOGY 2023; 23:155-171. [PMID: 36413376 DOI: 10.1089/ast.2022.0012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Active hot springs are dynamic geobiologically active environments. Heat- and element-enriched fluids form hot spring sinter deposits that are inhabited by microbial and macroscopic eukaryotic communities, but it is unclear how variable heat, fluid circulation, and mineralization within hot spring systems affect the preservation of organic matter in sinters. We present geological, petrographic, and organic geochemical data from fossilized hot spring sinters (<13 Ka) from three distinct hot spring fields of Yellowstone National Park. The aims of this study were to examine the preservation of hydrocarbons and discern whether the hydrocarbons in these samples were derived from in situ communities or transported by hydrothermal fluids. Organic geochemistry reveals the presence of n-alkanes, methylalkanes, hopanes, and other terpanes, and the distribution of methylheptadecanes is compared to published observations of community composition in extant hot springs with similar geochemistry. Unexpectedly, hopanes have a thermally mature signal, and Raman spectroscopy confirms that the kerogen in some samples has nearly reached the oil window, despite never having been buried. Our results suggest that organic matter maturation occurred through below-surface processes in the hotter, deeper parts of the hydrothermal system and that this exogenous material was then transported and emplaced within the sinter.
Collapse
Affiliation(s)
- Bronwyn L Teece
- Australian Centre for Astrobiology (ACA), School of Biological, Earth and Environmental Sciences, University of New South Wales Sydney, Sydney, Australia
- Earth and Sustainability Science Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales Sydney, Sydney, Australia
| | - Jeff R Havig
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, Minnesota, USA
| | - Simon C George
- School of Natural Sciences, Macquarie University, Sydney, Australia
| | - Trinity L Hamilton
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
| | - Raphael J Baumgartner
- Australian Centre for Astrobiology (ACA), School of Biological, Earth and Environmental Sciences, University of New South Wales Sydney, Sydney, Australia
- Earth and Sustainability Science Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales Sydney, Sydney, Australia
- CSIRO Mineral Resources, Kensington, Australia
| | - Julie Hartz
- School of Natural Sciences, Macquarie University, Sydney, Australia
| | - Martin J Van Kranendonk
- Australian Centre for Astrobiology (ACA), School of Biological, Earth and Environmental Sciences, University of New South Wales Sydney, Sydney, Australia
- Earth and Sustainability Science Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales Sydney, Sydney, Australia
| |
Collapse
|
6
|
Alonso-Reyes DG, Galván FS, Irazoqui JM, Amadio A, Tschoeke D, Thompson F, Albarracín VH, Farias ME. Dissecting Light Sensing and Metabolic Pathways on the Millimeter Scale in High-Altitude Modern Stromatolites. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02112-7. [PMID: 36161499 DOI: 10.1007/s00248-022-02112-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
Modern non-lithifying stromatolites on the shore of the volcanic lake Socompa (SST) in the Puna are affected by several extreme conditions. The present study assesses for the first time light utilization and functional metabolic stratification of SST on a millimeter scale through shotgun metagenomics. In addition, a scanning-electron-microscopy approach was used to explore the community. The analysis on SST unveiled the profile of a photosynthetic mat, with cyanobacteria not directly exposed to light, but placed just below a high-UV-resistant community. Calvin-Benson and 3-hydroxypropinate cycles for carbon fixation were abundant in upper, oxic layers, while the Wood-Ljungdahl pathway was dominant in the deeper anoxic strata. The high abundance of genes for UV-screening and oxidant-quenching pigments and CPF (photoreactivation) in the UV-stressed layers could indicate that the zone itself works as a UV shield. There is a remarkable density of sequences associated with photoreceptors in the first two layers. Also, genetic evidence of photosynthesis split in eukaryotic (layer 1) and prokaryotic (layer 2). Photoheterotrophic bacteria, aerobic photoautotrophic bacteria, and anaerobic photoautotrophic bacteria coexist by selectively absorbing different parts of the light spectrum (blue, red, and IR respectively) at different positions of the mat. Genes for oxygen, nitrogen, and sulfur metabolism account for the microelectrode chemical data and pigment measurements performed in previous publications. We also provide here an explanation for the vertical microbial mobility within the SST described previously. Finally, our study points to SST as ideal modern analogues of ancient ST.
Collapse
Affiliation(s)
- Daniel Gonzalo Alonso-Reyes
- Laboratorio de Microbiología Ultraestructural Y Molecular, Centro Integral de Microscopía Electrónica (CIME,), CONICET-Universidad Nacional de Tucumán, Camino de Sirga s/n, Finca El Manantial, Yerba Buena (4107), San Miguel de Tucumán, Tucumán, Argentina
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI), CCT, CONICET, Tucumán, Argentina
| | - Fátima Silvina Galván
- Laboratorio de Microbiología Ultraestructural Y Molecular, Centro Integral de Microscopía Electrónica (CIME,), CONICET-Universidad Nacional de Tucumán, Camino de Sirga s/n, Finca El Manantial, Yerba Buena (4107), San Miguel de Tucumán, Tucumán, Argentina
| | - José Matías Irazoqui
- Instituto de Investigación de La Cadena Láctea (INTA-CONICET), Rafaela, Argentina
| | - Ariel Amadio
- Instituto de Investigación de La Cadena Láctea (INTA-CONICET), Rafaela, Argentina
| | - Diogo Tschoeke
- Institute of Biology and Coppe, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fabiano Thompson
- Institute of Biology and Coppe, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Virginia Helena Albarracín
- Laboratorio de Microbiología Ultraestructural Y Molecular, Centro Integral de Microscopía Electrónica (CIME,), CONICET-Universidad Nacional de Tucumán, Camino de Sirga s/n, Finca El Manantial, Yerba Buena (4107), San Miguel de Tucumán, Tucumán, Argentina.
- Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, Tucumán, Argentina.
| | - María Eugenia Farias
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI), CCT, CONICET, Tucumán, Argentina
| |
Collapse
|
7
|
Community Vertical Composition of the Laguna Negra Hypersaline Microbial Mat, Puna Region (Argentinean Andes). BIOLOGY 2022; 11:biology11060831. [PMID: 35741352 PMCID: PMC9220024 DOI: 10.3390/biology11060831] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 05/20/2022] [Accepted: 05/27/2022] [Indexed: 11/17/2022]
Abstract
The Altiplano-Puna region is a high-altitude plateau in South America characterized by extreme conditions, including the highest UV incidence on Earth. The Laguna Negra is a hypersaline lake located in the Catamarca Province, northwestern Argentina, where stromatolites and other microbialites are found, and where life is mostly restricted to microbial mats. In this study, a particular microbial mat that covers the shore of the lake was explored, to unravel its layer-by-layer vertical structure in response to the environmental stressors therein. Microbial community composition was assessed by high-throughput 16S rRNA gene sequencing and pigment content analyses, complemented with microscopy tools to characterize its spatial arrangement within the mat. The top layer of the mat has a remarkable UV-tolerance feature, characterized by the presence of Deinococcus-Thermus and deinoxanthin, which might reflect a shielding strategy to cope with high UV radiation. Chloroflexi and Deltaproteobacteria were abundant in the second and third underlying layers, respectively. The bottom layer harbors copious Halanaerobiaeota. Subspherical aggregates composed of calcite, extracellular polymeric substances, abundant diatoms, and other microorganisms were observed all along the mat as the main structural component. This detailed study provides insights into the strategies of microbial communities to thrive under high UV radiation and hypersalinity in high-altitude lakes in the Altiplano-Puna region.
Collapse
|
8
|
Carrizo D, Vignale FA, Sánchez-García L, Farías ME. Ecological variability based on lipid biomarkers in astrobiologically interesting wetlands from the Argentinian central Andes. FEMS Microbiol Ecol 2022; 98:6575537. [PMID: 35482603 DOI: 10.1093/femsec/fiac049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/01/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Andean wetlands hold extremophilic communities adapted to live in harsh conditions. Here, we investigated the microbial ecology of three high-altitude hypersaline ponds from La Puna region (Argentina) showing an increasing extent of desiccation by analyzing their lipid sedimentary record. We recreated the microbial community structure and the carbon metabolisms in each lacustrine system based on the molecular distribution of lipid biomarkers and their compound-specific carbon and hydrogen isotopic signatures. We detected lipid compounds considered to be biomarkers of cyanobacteria, sulfate-reducing bacteria, purple sulfur bacteria, and archaea in the three Andean ponds, as well as diatoms in the intermediate salinity system. The relative abundance of purple sulfur and sulfate-reducing bacteria decreased with salinity, whereas cyanobacteria and archaea decreased their relative abundance in the mid-saline pond to increase it again and became both prevailing at the highest salinity. Carbon fixation in the three ponds was driven by a combination of the reductive tricarboxylic acid cycle, the reductive pentose phosphate cycle, and the reductive acetyl-CoA pathway. This work is the first to describe molecular and isotopic lipid fingerprints in wetlands from the central Andean Puna, and serves as a basis for further biogeochemical studies in the area.
Collapse
Affiliation(s)
- Daniel Carrizo
- Centro de Astrobiología (CSIC-INTA), Department of Planetology and Habitability, Madrid, Spain
| | - 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, T4001MVB, Argentina.,Laboratorio de Bioinformática Estructural, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN)-CONICET, Universidad de Buenos Aires (UBA), Buenos Aires, C1428EHA, Argentina
| | - Laura Sánchez-García
- Centro de Astrobiología (CSIC-INTA), Department of Molecular Evolution, Madrid, Spain
| | - 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, T4001MVB, Argentina
| |
Collapse
|
9
|
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
|
10
|
Kindler GS, Wong HL, Larkum AWD, Johnson M, MacLeod FI, Burns BP. Genome-resolved metagenomics provides insights into the functional complexity of microbial mats in Blue Holes, Shark Bay. FEMS Microbiol Ecol 2021; 98:6448473. [PMID: 34865013 DOI: 10.1093/femsec/fiab158] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 11/30/2021] [Indexed: 11/13/2022] Open
Abstract
The present study describes for the first time the community composition and functional potential of the microbial mats found in the supratidal, gypsum-rich, and hypersaline region of Blue Holes, Shark Bay. This was achieved via high throughput metagenomic sequencing of total mat community DNA and complementary analyses using hyperspectral confocal microscopy. Mat communities were dominated by Proteobacteria (29%), followed by Bacteroidetes/Chlorobi Group (11%), and Planctomycetes (10%). These mats were found to also harbor a diverse community of potentially novel microorganisms including members from the DPANN, Asgard archaea, and Candidate Phyla Radiation, with highest diversity found in the lower regions (∼14-20 mm depth) of the mat. In addition to pathways for major metabolic cycles, a range of putative rhodopsins with previously uncharacterized motifs and functions were identified along with heliorhodopsins and putative schizorhodopsins. Critical microbial interactions were also inferred, and from 117 medium-to-high quality metagenome-assembled genomes (MAGs), viral defense mechanisms (CRISPR, BREX, and DISARM), elemental transport, osmoprotection, heavy metal and UV resistance were also detected. These analyses have provided a greater understanding of these distinct mat systems in Shark Bay, including key insights into adaptive responses and proposing that photoheterotrophy may be an important lifestyle in Blue Holes.
Collapse
Affiliation(s)
- Gareth S Kindler
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Hon Lun Wong
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic.,Australian Centre for Astrobiology, University of New South Wales Sydney, Sydney, NSW, Australia
| | - Anthony W D Larkum
- Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - Michael Johnson
- Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - Fraser I MacLeod
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia.,Australian Centre for Astrobiology, University of New South Wales Sydney, Sydney, NSW, Australia
| | - Brendan P Burns
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia.,Australian Centre for Astrobiology, University of New South Wales Sydney, Sydney, NSW, Australia
| |
Collapse
|
11
|
Vignale FA, Kurth D, Lencina AI, Poiré DG, Chihuailaf E, Muñoz-Herrera NC, Novoa F, Contreras M, Turjanski AG, Farías ME. Geobiology of Andean Microbial Ecosystems Discovered in Salar de Atacama, Chile. Front Microbiol 2021; 12:762076. [PMID: 34777316 PMCID: PMC8581658 DOI: 10.3389/fmicb.2021.762076] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 09/28/2021] [Indexed: 11/23/2022] Open
Abstract
The Salar de Atacama in the Chilean Central Andes harbors unique microbial ecosystems due to extreme environmental conditions, such as high altitude, low oxygen pressure, high solar radiation, and high salinity. Combining X-ray diffraction analyses, scanning electron microscopy and molecular diversity studies, we have characterized twenty previously unexplored Andean microbial ecosystems in eight different lakes and wetlands from the middle-east and south-east regions of this salt flat. The mats and microbialites studied are mainly formed by calcium carbonate (aragonite and calcite) and halite, whereas the endoevaporites are composed predominantly of gypsum and halite. The carbonate-rich mats and microbialites are dominated by Bacteroidetes and Proteobacteria phyla. Within the phylum Proteobacteria, the most abundant classes are Alphaproteobacteria, Gammaproteobacteria and Deltaproteobacteria. While in the phylum Bacteroidetes, the most abundant classes are Bacteroidia and Rhodothermia. Cyanobacteria, Chloroflexi, Planctomycetes, and Verrucomicrobia phyla are also well-represented in the majority of these systems. Gypsum endoevaporites, on the contrary, are dominated by Proteobacteria, Bacteroidetes, and Euryarchaeota phyla. The Cyanobacteria phylum is also abundant in these systems, but it is less represented in comparison to mats and microbialites. Regarding the eukaryotic taxa, diatoms are key structural components in most of the microbial ecosystems studied. The genera of diatoms identified were Achnanthes, Fallacia, Halamphora, Mastogloia, Navicula, Nitzschia, and Surirella. Normally, in the mats and microbialites, diatoms form nano-globular carbonate aggregates with filamentous cyanobacteria and other prokaryotic cells, suggesting their participation in the mineral precipitation process. This work expands our knowledge of the microbial ecosystems inhabiting the extreme environments from the Central Andes region, which is important to ensure their protection and conservation.
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, Argentina
- Laboratorio de Bioinformática Estructural, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN)-CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Daniel Kurth
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT, CONICET, San Miguel de Tucumán, 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, Argentina
| | - Daniel G. Poiré
- Centro de Investigaciones Geológicas (CIG), Universidad Nacional de La Plata (UNLP)-CONICET, La Plata, Argentina
| | | | | | | | | | - Adrián G. Turjanski
- Laboratorio de Bioinformática Estructural, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN)-CONICET, Universidad de Buenos Aires, Buenos Aires, 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, Argentina
| |
Collapse
|
12
|
Villafañe PG, Cónsole-Gonella C, Cury LF, Farías ME. Short-term microbialite resurgence as indicator of ecological resilience against crises (Catamarca, Argentine Puna). ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:659-667. [PMID: 34089237 DOI: 10.1111/1758-2229.12977] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 05/10/2021] [Accepted: 05/13/2021] [Indexed: 06/12/2023]
Abstract
Microbialite-producing microorganisms that inhabit the Puna lakes are traditionally considered constituents of fragile microsystems, unable to resist important environmental variations. Nevertheless, this region has experienced significant climatic fluctuations during the Holocene, raising the unsolved issue on how microbialite-forming systems have been able to resist these changes. Turquesa lake, located within Quaternary Peinado lake-basin (Puna), faces a hydric crisis in the last decades, which modified their physicochemical conditions. However, there has been a rapid re-establishment of the microbialite systems once the main parameters were stabilized, which allowed the establishment of three new microbialite levels in the coast and paleo-coastline. The aim of this contribution is to report for the first time microbialite levels in Turquesa lake, providing a multiscale analysis, besides an accurate study of the physico-chemical context of the lake. This new record provided us the opportunity to demonstrate the short-term resilience capacity of these microbialite-producing microorganisms to climatic changes, offering a key approach to understand analogue processes throughout Earth history.
Collapse
Affiliation(s)
- Patricio Guillermo Villafañe
- Laboratorio de Investigaciones Microbiológicas en Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CONICET, Av. Belgrano y Psje. Caseros S/N, San Miguel de Tucumán, Tucumán, Argentina
- Instituto Superior de Correlación Geológica (INSUGEO), CONICET- UNT, Av Perón s/n, Yerba Buena, Tucumán, Argentina
| | - Carlos Cónsole-Gonella
- Instituto Superior de Correlación Geológica (INSUGEO), CONICET- UNT, Av Perón s/n, Yerba Buena, Tucumán, Argentina
- Institute of Paleontology, Hebei GEO University, 136 East Huai' an Rd, Shijiazhuang, Hebei, China
| | - Leonardo Fadel Cury
- LAMIR Institute, Universidad Federal do Paraná (UFPR), Av. Cel. Francisco H. dos Santos 100, Curitiba, Paraná, Brazil
| | - María Eugenia Farías
- Laboratorio de Investigaciones Microbiológicas en Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CONICET, Av. Belgrano y Psje. Caseros S/N, San Miguel de Tucumán, Tucumán, Argentina
| |
Collapse
|
13
|
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
|
14
|
Saona LA, Soria M, Durán-Toro V, Wörmer L, Milucka J, Castro-Nallar E, Meneses C, Contreras M, Farías ME. Phosphate-Arsenic Interactions in Halophilic Microorganisms of the Microbial Mat from Laguna Tebenquiche: from the Microenvironment to the Genomes. MICROBIAL ECOLOGY 2021; 81:941-953. [PMID: 33388944 DOI: 10.1007/s00248-020-01673-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 12/22/2020] [Indexed: 06/12/2023]
Abstract
Arsenic (As) is a metalloid present in the earth's crust and widely distributed in the environment. Due to its high concentrations in the Andean valleys and its chemical similarity with phosphorus (P), its biological role in Andean Microbial Ecosystems (AMEs) has begun to be studied. The AMEs are home to extremophilic microbial communities that form microbial mats, evaporites, and microbialites inhabiting Andean lakes, puquios, or salt flats. In this work, we characterize the biological role of As and the effect of phosphate in AMEs from the Laguna Tebenquiche (Atacama Desert, Chile). Using micro X-ray fluorescence, the distribution of As in microbial mat samples was mapped. Taxonomic and inferred functional profiles were obtained from enriched cultures of microbial mats incubated under As stress and different phosphate conditions. Additionally, representative microorganisms highly resistant to As and able to grow under low phosphate concentration were isolated and studied physiologically. Finally, the genomes of the isolated Salicola sp. and Halorubrum sp. were sequenced to analyze genes related to both phosphate metabolism and As resistance. The results revealed As as a key component of the microbial mat ecosystem: (i) As was distributed across all sections of the microbial mat and represented a significant weight percentage of the mat (0.17 %) in comparison with P (0.40%); (ii) Low phosphate concentration drastically changed the microbial community in microbial mat samples incubated under high salinity and high As concentrations; (iii) Archaea and Bacteria isolated from the microbial mat were highly resistant to arsenate (up to 500 mM), even under low phosphate concentration; (iv) The genomes of the two isolates were predicted to contain key genes in As metabolism (aioAB and arsC/acr3) and the genes predicted to encode the phosphate-specific transport operon (pstSCAB-phoU) are next to the arsC gene, suggesting a functional relationship between these two elements.
Collapse
Affiliation(s)
- L 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.
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359, Bremen, Germany.
| | - M Soria
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT, CONICET, San Miguel de Tucumán, Tucumán, Argentina
| | - V Durán-Toro
- Hydrothermal Geomicrobiology Group, MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - L Wörmer
- Organic Geochemistry Group, MARUM-Center for Marine Environmental Sciences, University of Bremen, Leobener Str. 8, 28359, Bremen, Germany
| | - J Milucka
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359, Bremen, Germany
| | - E Castro-Nallar
- Facultad de Ciencias de la Vida, Center for Bioinformatics and Integrative Biology, Universidad Andres Bello, Santiago, Chile
| | - C Meneses
- Centro de Biotecnología Vegetal (CBV), FONDAP Center for Genome Regulation, Universidad Andres Bello, Santiago, Chile
| | - M Contreras
- Centro de Ecología Aplicada, Santiago, Chile
| | - M 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
|
15
|
Kurth D, Elias D, Rasuk MC, Contreras M, Farías ME. Carbon fixation and rhodopsin systems in microbial mats from hypersaline lakes Brava and Tebenquiche, Salar de Atacama, Chile. PLoS One 2021; 16:e0246656. [PMID: 33561170 PMCID: PMC7872239 DOI: 10.1371/journal.pone.0246656] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 01/25/2021] [Indexed: 01/08/2023] Open
Abstract
In this work, molecular diversity of two hypersaline microbial mats was compared by Whole Genome Shotgun (WGS) sequencing of environmental DNA from the mats. Brava and Tebenquiche are lakes in the Salar de Atacama, Chile, where microbial communities are growing in extreme conditions, including high salinity, high solar irradiance, and high levels of toxic metals and metaloids. Evaporation creates hypersaline conditions in these lakes and mineral precipitation is a characteristic geomicrobiological feature of these benthic ecosystems. The mat from Brava was more rich and diverse, with a higher number of different taxa and with species more evenly distributed. At the phylum level, Proteobacteria, Cyanobacteria, Chloroflexi, Bacteroidetes and Firmicutes were the most abundant, including ~75% of total sequences. At the genus level, the most abundant sequences were affilitated to anoxygenic phototropic and cyanobacterial genera. In Tebenquiche mats, Proteobacteria and Bacteroidetes covered ~70% of the sequences, and 13% of the sequences were affiliated to Salinibacter genus, thus addressing the lower diversity. Regardless of the differences at the taxonomic level, functionally the two mats were similar. Thus, similar roles could be fulfilled by different organisms. Carbon fixation through the Wood-Ljungdahl pathway was well represented in these datasets, and also in other mats from Andean lakes. In spite of presenting less taxonomic diversity, Tebenquiche mats showed increased abundance and variety of rhodopsin genes. Comparison with other metagenomes allowed identifying xantorhodopsins as hallmark genes not only from Brava and Tebenquiche mats, but also for other mats developing at high altitudes in similar environmental conditions.
Collapse
Affiliation(s)
- Daniel Kurth
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT, CONICET, Tucumán, Argentina
| | - Dario Elias
- Facultad de Ingeniería, Universidad Nacional de Entre Ríos, Oro Verde, Entre Ríos, Argentina
| | - María Cecilia Rasuk
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT, CONICET, Tucumán, Argentina
| | | | - María Eugenia Farías
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT, CONICET, Tucumán, Argentina
| |
Collapse
|
16
|
Iniesto M, Moreira D, Reboul G, Deschamps P, Benzerara K, Bertolino P, Saghaï A, Tavera R, López-García P. Core microbial communities of lacustrine microbialites sampled along an alkalinity gradient. Environ Microbiol 2020; 23:51-68. [PMID: 32985763 DOI: 10.1111/1462-2920.15252] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 08/26/2020] [Accepted: 09/23/2020] [Indexed: 11/28/2022]
Abstract
Microbialites are usually carbonate-rich sedimentary rocks formed by the interplay of phylogenetically and metabolically complex microbial communities with their physicochemical environment. Yet, the biotic and abiotic determinants of microbialite formation remain poorly constrained. Here, we analysed the structure of prokaryotic and eukaryotic communities associated with microbialites occurring in several crater lakes of the Trans-Mexican volcanic belt along an alkalinity gradient. Microbialite size and community structure correlated with lake physicochemical parameters, notably alkalinity. Although microbial community composition varied across lake microbialites, major taxa-associated functions appeared quite stable with both, oxygenic and anoxygenic photosynthesis and, to less extent, sulphate reduction, as major putative carbonatogenic processes. Despite interlake microbialite community differences, we identified a microbial core of 247 operational taxonomic units conserved across lake microbialites, suggesting a prominent ecological role in microbialite formation. This core mostly encompassed Cyanobacteria and their typical associated taxa (Bacteroidetes, Planctomycetes) and diverse anoxygenic photosynthetic bacteria, notably Chloroflexi, Alphaproteobacteria (Rhodobacteriales, Rhodospirilalles), Gammaproteobacteria (Chromatiaceae) and minor proportions of Chlorobi. The conserved core represented up to 40% (relative abundance) of the total community in lakes Alchichica and Atexcac, displaying the highest alkalinities and the most conspicuous microbialites. Core microbialite communities associated with carbonatogenesis might be relevant for inorganic carbon sequestration purposes.
Collapse
Affiliation(s)
- Miguel Iniesto
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - David Moreira
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Guillaume Reboul
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Philippe Deschamps
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Karim Benzerara
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, CNRS, Muséum National d'Histoire Naturelle, Sorbonne Université, Paris, France
| | - Paola Bertolino
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Aurélien Saghaï
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France.,Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Rosaluz Tavera
- Departamento de Ecología y Recursos Naturales, Universidad Nacional Autónoma de México, DF Mexico, Mexico
| | - Purificación López-García
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| |
Collapse
|
17
|
Sriaporn C, Campbell KA, Millan M, Ruff SW, Van Kranendonk MJ, Handley KM. Stromatolitic digitate sinters form under wide-ranging physicochemical conditions with diverse hot spring microbial communities. GEOBIOLOGY 2020; 18:619-640. [PMID: 32336004 DOI: 10.1111/gbi.12395] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 03/02/2020] [Accepted: 03/26/2020] [Indexed: 05/11/2023]
Abstract
Digitate siliceous hot spring deposits are a form of biomediated sinter that is relatively common in the Taupo Volcanic Zone (TVZ), New Zealand, and elsewhere on Earth. Such deposits have gained prominence recently because of their morphological similarity to opaline silica rocks of likely hot spring origin found by the Spirit rover on Mars and the consequent implications for potential biosignatures there. Here, we investigate the possible relationship between microbial community composition and morphological diversity among digitate structures from actively forming siliceous hot spring sinters depositing subaerially in shallow discharge channels and around pool rims at several physicochemically distinct geothermal fields in the TVZ. The TVZ digitate sinters range in morphologic subtype from knobby to spicular, and are shown to be microstromatolites that grow under varied pH ranges, temperatures, and water chemistries. Scanning electron microscopy and molecular analyses revealed that TVZ digitate sinters are intimately associated with a diverse array of bacterial, archaeal and eukaryotic micro-organisms, and for most digitate structures the diversity and quantity of prokaryotes was higher than that of eukaryotes. However, microbial community composition was not correlated with morphologic subtypes of digitate sinter, and observations provided limited evidence that pH (acidic versus alkali) affects morphology. Instead, results suggest hydrodynamics may be an important factor influencing variations in morphology, while water chemistry, pH, and temperature are strong drivers of microbial composition and diversity.
Collapse
Affiliation(s)
- Chanenath Sriaporn
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Kathleen A Campbell
- School of Environment & Te Ao Mārama - Centre for Fundamental Inquiry, The University of Auckland, Auckland, New Zealand
| | - Maeva Millan
- Department of Biology & NASA Goddard Space Flight Center, Georgetown University, Washington, DC, USA
| | - Steven W Ruff
- School of Earth and Space Exploration, Arizona State University, Tempe, AZ, USA
| | - Martin J Van Kranendonk
- Australian Centre for Astrobiology, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Kim M Handley
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| |
Collapse
|
18
|
Saona LA, Soria M, Villafañe PG, Lencina AI, Stepanenko T, Farías ME. Andean Microbial Ecosystems: Traces in Hypersaline Lakes About Life Origin. ACTA ACUST UNITED AC 2020. [DOI: 10.1007/978-3-030-46087-7_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
|
19
|
Tracking Organomineralization Processes from Living Microbial Mats to Fossil Microbialites. MINERALS 2020. [DOI: 10.3390/min10070605] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Geneses of microbialites and, more precisely, lithification of microbial mats have been studied in different settings to improve the recognition of biogenicity in the fossil record. Living microbial mats and fossil microbialites associated with older paleoshorelines have been studied in the continental Maquinchao Basin in southernmost South America. Here, we investigate carbonate crusts from a former pond where active mineralizing microbial mats have been previously studied. Petrographic observations revealed the presence of abundant erect and nonerect microfilaments and molds with diameters varying from 6 to 8 micrometers. Additionally, smaller pores and organic matter (OM) remains have been identified in areas containing less filaments and being dominated by carbonate. A Mg, Al and Si-rich phase has also been identified in the carbonate matrix associated with the dominant micritic calcite. Moreover, mineralized sheaths contain mixed carbonate (calcite) with Mg, Al and Si, where the latter elements are associated with authigenic clays. The presence of mineralized sheaths further attests to biologically induced processes during the uptake of CO2 by photosynthetic microorganisms. Additionally, the high density of the micritic phase supports the subsequent mineralization by nonphotosynthetic microorganisms and/or physicochemical processes, such as evaporation. Since the micritic filament microstructure of these recent crusts is very similar to that observed in fossil microbialites, they can be used to bridge the gap between living mats and fossil buildups.
Collapse
|
20
|
Perez MF, Kurth D, Farías ME, Soria MN, Castillo Villamizar GA, Poehlein A, Daniel R, Dib JR. First Report on the Plasmidome From a High-Altitude Lake of the Andean Puna. Front Microbiol 2020; 11:1343. [PMID: 32655530 PMCID: PMC7324554 DOI: 10.3389/fmicb.2020.01343] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 05/26/2020] [Indexed: 12/11/2022] Open
Abstract
Mobile genetic elements, including plasmids, drive the evolution of prokaryotic genomes through the horizontal transfer of genes allowing genetic exchange between bacteria. Moreover, plasmids carry accessory genes, which encode functions that may offer an advantage to the host. Thus, it is expected that in a certain ecological niche, plasmids are enriched in accessory functions, which are important for their hosts to proliferate in that niche. Puquio de Campo Naranja is a high-altitude lake from the Andean Puna exposed to multiple extreme conditions, including high UV radiation, alkalinity, high concentrations of arsenic, heavy metals, dissolved salts, high thermal amplitude and low O2 pressure. Microorganisms living in this lake need to develop efficient mechanisms and strategies to cope under these conditions. The aim of this study was to characterize the plasmidome of microbialites from Puquio de Campo Naranja, and identify potential hosts and encoded functions using a deep-sequencing approach. The potential ecological impact of the plasmidome, including plasmids from cultivable and non-cultivable microorganisms, is described for the first time in a lake representing an extreme environment of the Puna. This study showed that the recovered genetic information for the plasmidome was novel in comparison to the metagenome derived from the same environment. The study of the total plasmid population allowed the identification of genetic features typically encoded by plasmids, such as resistance and virulence factors. The resistance genes comprised resistances to heavy metals, antibiotics and stress factors. These results highlight the key role of plasmids for their hosts and impact of extrachromosomal elements to thrive in a certain ecological niche.
Collapse
Affiliation(s)
- María Florencia Perez
- Planta Piloto de Procesos Industriales Microbiológicos, Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucumán, Argentina
| | - Daniel Kurth
- Planta Piloto de Procesos Industriales Microbiológicos, Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucumán, Argentina
| | - María Eugenia Farías
- Planta Piloto de Procesos Industriales Microbiológicos, Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucumán, Argentina
| | - Mariana Noelia Soria
- Planta Piloto de Procesos Industriales Microbiológicos, Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucumán, Argentina
| | - Genis Andrés Castillo Villamizar
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany.,Línea Tecnológica Biocorrosión, Corporación para la Investigación de la Corrosión C.I.C., Piedecuesta, Colombia
| | - Anja Poehlein
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Julián Rafael Dib
- Planta Piloto de Procesos Industriales Microbiológicos, Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucumán, Argentina.,Facultad de Bioquímica, Química y Farmacia, Instituto de Microbiología, Universidad Nacional de Tucumán, San Miguel de Tucumán, Argentina
| |
Collapse
|
21
|
Popall RM, Bolhuis H, Muyzer G, Sánchez-Román M. Stromatolites as Biosignatures of Atmospheric Oxygenation: Carbonate Biomineralization and UV-C Resilience in a Geitlerinema sp. - Dominated Culture. Front Microbiol 2020; 11:948. [PMID: 32508777 PMCID: PMC7248245 DOI: 10.3389/fmicb.2020.00948] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 04/21/2020] [Indexed: 11/13/2022] Open
Abstract
Modern stromatolites are key to the record of past microbial activity preserved in fossil carbonate deposits. Mono-phototrophic cultures dominated by the cyanobacterium Geitlerinema sp. were obtained from a laboratory-maintained, low magnesium-calcite stromatolite originating from Lagoa Vermelha, Brazil. This lagoonal system has been described as a Precambrian analog, illustrating a period of photosynthetically induced atmospheric oxygenation, which created a global sanctuary from shortwave solar radiation and enabled the evolution of modern life on Earth. The enrichment cultures precipitate carbonates in minimal media, suggesting that cyanobacterial photosynthesis and extracellular polymeric substance production may be crucial in the mineralization of the studied stromatolite. We further show that Geitlerinema sp. can build and maintain filamentous mats under long-term UV-C exposure. Our results suggest that present day stromatolites dominated by cyanobacteria may be interpreted as biosignatures of atmospheric oxygenation and have implications for the search for putative biological traces on Mars.
Collapse
Affiliation(s)
- Rabja M. Popall
- Earth Sciences Department, Faculty of Science, Vrije Universiteit, Amsterdam, Netherlands
| | - Henk Bolhuis
- Marine Microbiology & Biogeochemistry Department, Royal Netherlands Institute for Sea Research, Utrecht University, Den Hoorn, Netherlands
| | - Gerard Muyzer
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Mónica Sánchez-Román
- Earth Sciences Department, Faculty of Science, Vrije Universiteit, Amsterdam, Netherlands
| |
Collapse
|
22
|
Unexpected Abundance and Diversity of Phototrophs in Mats from Morphologically Variable Microbialites in Great Salt Lake, Utah. Appl Environ Microbiol 2020; 86:AEM.00165-20. [PMID: 32198176 DOI: 10.1128/aem.00165-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 03/15/2020] [Indexed: 11/20/2022] Open
Abstract
Microbial mat communities are associated with extensive (∼700 km2) and morphologically variable carbonate structures, termed microbialites, in the hypersaline Great Salt Lake (GSL), Utah. However, whether the composition of GSL mat communities covaries with microbialite morphology and lake environment is unknown. Moreover, the potential adaptations that allow the establishment of these extensive mat communities at high salinity (14% to 17% total salts) are poorly understood. To address these questions, microbial mats were sampled from seven locations in the south arm of GSL representing different lake environments and microbialite morphologies. Despite the morphological differences, microbialite-associated mats were taxonomically similar and were dominated by the cyanobacterium Euhalothece and several heterotrophic bacteria. Metagenomic sequencing of a representative mat revealed Euhalothece and subdominant Thiohalocapsa populations that harbor the Calvin cycle and nitrogenase, suggesting they supply fixed carbon and nitrogen to heterotrophic bacteria. Fifteen of the next sixteen most abundant taxa are inferred to be aerobic heterotrophs and, surprisingly, harbor reaction center, rhodopsin, and/or bacteriochlorophyll biosynthesis proteins, suggesting aerobic photoheterotrophic (APH) capabilities. Importantly, proteins involved in APH are enriched in the GSL community relative to that in microbialite mat communities from lower salinity environments. These findings indicate that the ability to integrate light into energy metabolism is a key adaptation allowing for robust mat development in the hypersaline GSL.IMPORTANCE The earliest evidence of life on Earth is from organosedimentary structures, termed microbialites, preserved in 3.481-billion-year-old (Ga) rocks. Phototrophic microbial mats form in association with an ∼700-km2 expanse of morphologically diverse microbialites in the hypersaline Great Salt Lake (GSL), Utah. Here, we show taxonomically similar microbial mat communities are associated with morphologically diverse microbialites across the lake. Metagenomic sequencing reveals an abundance and diversity of autotrophic and heterotrophic taxa capable of harvesting light energy to drive metabolism. The unexpected abundance of and diversity in the mechanisms of harvesting light energy observed in GSL mat populations likely function to minimize niche overlap among coinhabiting taxa, provide a mechanism(s) to increase energy yield and osmotic balance during salt stress, and enhance fitness. Together, these physiological benefits promote the formation of robust mats that, in turn, influence the formation of morphologically diverse microbialite structures that can be imprinted in the rock record.
Collapse
|
23
|
Galisteo C, Sánchez-Porro C, de la Haba RR, López-Hermoso C, Fernández AB, Farias ME, Ventosa A. Characterization of Salinivibrio socompensis sp. nov., A New Halophilic Bacterium Isolated from the High-Altitude Hypersaline Lake Socompa, Argentina. Microorganisms 2019; 7:microorganisms7080241. [PMID: 31387286 PMCID: PMC6723482 DOI: 10.3390/microorganisms7080241] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 08/01/2019] [Accepted: 08/02/2019] [Indexed: 11/16/2022] Open
Abstract
The genus Salinivibrio belongs to the family Vibrionaceae and includes Gram-stain-negative, motile by a polar flagellum, and facultatively anaerobic curved rods. They are halophilic bacteria commonly found in hypersaline aquatic habitats and salted foods. This genus includes five species and two subspecies. A presumed novel species, strain S35T, was previously isolated from the high-altitude volcanic, alkaline, and saline lake Socompa (Argentinean Andes). In this study we carried out a complete taxonomic characterization of strain S35T, including the 16S rRNA gene sequence and core-genome analysis, the average nucleotide identity (ANIb, ANIm, and orthoANI), and in silico DNA-DNA hybridization (GGDC), as well as the phenotypic and chemotaxonomic characterization. It grew at 3%-20% (w/v) NaCl, pH 6-10, and 10-42 °C, with optimum growth at 7.0%-7.5% (w/v) NaCl, pH 8.0, and 37 °C, respectively. Strain S35T was oxidase- and catalase-positive, able to produce acid from D-glucose and other carbohydrates. Hydrolysis of DNA, methyl red test, and nitrate and nitrite reduction were positive. Its main fatty acids were C16:0, C16:1 ω7c and C16:1 ω6c, and C18:1 ω7c and/or C18:1 ω6c. ANI, GGDC, and core-genome analysis determined that strain S35T constitutes a novel species of the genus Salinivibrio, for which the name Salinivibrio socompensis sp. nov. is proposed. The type strain is S35T (= CECT 9634T = BNM 0535T).
Collapse
Affiliation(s)
- Cristina Galisteo
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain.
| | - Rafael R de la Haba
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Clara López-Hermoso
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Ana B Fernández
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas, Planta Piloto de Procesos Industriales Microbiológicos, Centro Científico Tecnológico, CONICET Tucumán T4000, Argentina
| | - María E Farias
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas, Planta Piloto de Procesos Industriales Microbiológicos, Centro Científico Tecnológico, CONICET Tucumán T4000, Argentina
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain.
| |
Collapse
|
24
|
Polyextremophilic Bacteria from High Altitude Andean Lakes: Arsenic Resistance Profiles and Biofilm Production. BIOMED RESEARCH INTERNATIONAL 2019; 2019:1231975. [PMID: 30915345 PMCID: PMC6409018 DOI: 10.1155/2019/1231975] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 01/01/2019] [Indexed: 11/23/2022]
Abstract
High levels of arsenic present in the High Altitude Andean Lakes (HAALs) ecosystems selected arsenic-resistant microbial communities which are of novel interest to study adaptations mechanisms potentially useful in bioremediation processes. We herein performed a detailed characterization of the arsenic tolerance profiles and the biofilm production of two HAAL polyextremophiles, Acinetobacter sp. Ver3 (Ver3) and Exiguobacterium sp. S17 (S17). Cellular adherence over glass and polypropylene surfaces were evaluated together with the effect of increasing doses and oxidative states of arsenic over the quality and quantity of their biofilm production. The arsenic tolerance outcomes showed that HAAL strains could tolerate higher arsenic concentrations than phylogenetic related strains belonging to the German collection of microorganisms and cell cultures (Deutsche Sammlung von Mikroorganismen und Zellkulturen, DSMZ), which suggest adaptations of HAAL strains to their original environment. On the other hand, the crystal violet method (CV) and SEM analysis showed that Ver3 and S17 were able to attach to solid surfaces and to form the biofilm. The quantification of biofilms production in 48 hours' cultures through CV shows that Ver3 yielded higher production in the treatment without arsenic cultured on a glass support, while S17 yield higher biofilm production under intermediate arsenic concentration on glass supports. Polypropylene supports had negative effects on the biofilm production of Ver3 and S17. SEM analysis shows that the highest biofilm yields could be associated with a larger number of attached cells as well as the development of more complex 3D multicellular structures.
Collapse
|
25
|
Changes of paradigms in agriculture soil microbiology and new challenges in microbial ecology. ACTA OECOLOGICA-INTERNATIONAL JOURNAL OF ECOLOGY 2019. [DOI: 10.1016/j.actao.2019.02.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
26
|
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
|
27
|
Flexer V, Baspineiro CF, Galli CI. Lithium recovery from brines: A vital raw material for green energies with a potential environmental impact in its mining and processing. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 639:1188-1204. [PMID: 29929287 DOI: 10.1016/j.scitotenv.2018.05.223] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 05/17/2018] [Accepted: 05/18/2018] [Indexed: 06/08/2023]
Abstract
The electrification of our world is driving a strong increase in demand for lithium. Energy storage is paramount in electric and hybrid vehicles, in green but intermittent energy sources, and in smart grids in general. Lithium is a vital raw material for the build-up of both currently available lithium-ion batteries, and prospective next generation batteries such as lithium-air and lithium sulphur. The continued availability of lithium can only rely on a strong increase of mining and ore processing. It would be an inconsistency if the increased production of lithium for a more sustainable society would be associated with non-sustainable mining practices. Currently 2/3 of the world production of lithium is extracted from brines, a practice that evaporates on average half a million litres of brine per ton of lithium carbonate. Furthermore, the extraction is chemical intensive, extremely slow, and delivers large volumes of waste. This technology is heavily dependent on the geological structure of the deposits, brine chemical composition and both climate and weather conditions. Therefore, it is difficult to adapt from one successful exploitation to new deposits. A few years of simulations and piloting are needed before large scale production is achieved. Consequently, this technology is struggling with the current surge in demand. At time of writing, only 5 industrial scale facilities are in operation worldwide, highlighting the shortcomings in this technology. Both mining companies and academics are intensively searching for new technologies for lithium recovery from brines. However, focus on the chemistry of brine processing has left unattended the analysis of the sustainability of the overall process. Here we review both the current available technology and new proposed methodologies. We make a special focus on an overall sustainability analysis, with particular emphasis to the geological characteristics of deposits and water usage in relation to mining processes.
Collapse
Affiliation(s)
- Victoria Flexer
- Centro de Investigación y Desarrollo en Materiales Avanzados y Almacenamiento de Energía de Jujuy (CONICET-Universidad Nacional de Jujuy), Centro de Desarrollo Tecnológico General Manuel Savio, Palpalá, Jujuy, Argentina.
| | - Celso Fernando Baspineiro
- Centro de Investigación y Desarrollo en Materiales Avanzados y Almacenamiento de Energía de Jujuy (CONICET-Universidad Nacional de Jujuy), Centro de Desarrollo Tecnológico General Manuel Savio, Palpalá, Jujuy, Argentina
| | - Claudia Inés Galli
- Instituto de Ecoregiones Andinas - INECOA-CONICET, Av. Bolivia 1661, S.S. de Jujuy, Argentina; Facultad de Ciencias Naturales, Universidad Nacional de Salta, Avenida Bolivia 5150, 4400 Salta, Argentina
| |
Collapse
|
28
|
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
|
29
|
Sirisena KA, Ramirez S, Steele A, Glamoclija M. Microbial Diversity of Hypersaline Sediments from Lake Lucero Playa in White Sands National Monument, New Mexico, USA. MICROBIAL ECOLOGY 2018; 76:404-418. [PMID: 29380029 DOI: 10.1007/s00248-018-1142-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Accepted: 01/02/2018] [Indexed: 06/07/2023]
Abstract
Lake Lucero is a gypsum-rich, hypersaline, ephemeral playa located on the southern part of the Alkali Flat at the White Sands National Monument (WSNM), New Mexico, USA. This modern playa setting provides a dynamic extreme environment that changes from a freshwater lake to a hypersaline dry desert during the year. We investigated the microbial diversity (bacteria, archaea, and microbial eukaryotes) of the Lake Lucero sediments using 16S- and 18S-based amplicon sequencing approach and explored the diversity patterns in different geochemical microenvironments. Our results indicated that similar microbial communities, in particular bacterial communities colonized, were remarkably consistent across our depth profiles. Therefore, these communities show a first-order relevance on the environmental conditions (moisture content, oxygen content, and mineral composition). We found that Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes, and Gemmatimonadetes were the major bacterial phyla, while Cyanobacteria were present in relatively low abundances and appeared only at the surface. Genus level assessment reflected that Truepera, Delftia, and Pseudomonas were the predominant bacterial genera across all samples. Euryarchaeota was the major archaeal phylum in all the samples, while Candidatus Halobonum and Candidatus Nitrososphaera were the main genera. Diatoms were the dominant eukaryotic group in surface samples and Fungi, Ciliophora, Metazoa, and Nematodes were the other major groups. As expected, metabolic inference indicated that aerobic microbial communities were near surface colonizers, with anaerobic communities dominating with increasing depth. We demonstrated that these microbial communities could be used to characterize unique geochemical microenvironments enabling us to extrapolate these results into other terrestrial and possibly extraterrestrial environments with comparable geochemical characteristics.
Collapse
Affiliation(s)
- Kosala Ayantha Sirisena
- Department of Earth and Environmental Sciences, Rutgers University, Newark, NJ, USA.
- Geophysical Laboratory, Carnegie Institution of Washington, Washington, DC, USA.
- Department of Zoology, University of Sri Jayewardenepura, Nugegoda, Sri Lanka.
| | - Steven Ramirez
- Department of Earth and Environmental Sciences, Rutgers University, Newark, NJ, USA
| | - Andrew Steele
- Geophysical Laboratory, Carnegie Institution of Washington, Washington, DC, USA
| | - Mihaela Glamoclija
- Department of Earth and Environmental Sciences, Rutgers University, Newark, NJ, USA
| |
Collapse
|
30
|
Babilonia J, Conesa A, Casaburi G, Pereira C, Louyakis AS, Reid RP, Foster JS. Comparative Metagenomics Provides Insight Into the Ecosystem Functioning of the Shark Bay Stromatolites, Western Australia. Front Microbiol 2018; 9:1359. [PMID: 29988640 PMCID: PMC6027182 DOI: 10.3389/fmicb.2018.01359] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 06/05/2018] [Indexed: 12/22/2022] Open
Abstract
Stromatolites are organosedimentary build-ups that have formed as a result of the sediment trapping, binding and precipitating activities of microbes. Today, extant systems provide an ideal platform for understanding the structure, composition, and interactions between stromatolite-forming microbial communities and their respective environments. In this study, we compared the metagenomes of three prevalent stromatolite-forming microbial mat types in the Spaven Province of Hamelin Pool, Shark Bay located in Western Australia. These stromatolite-forming mat types included an intertidal pustular mat as well as a smooth and colloform mat types located in the subtidal zone. Additionally, the metagenomes of an adjacent, non-lithifying mat located in the upper intertidal zone were also sequenced for comparative purposes. Taxonomic and functional gene analyses revealed distinctive differences between the lithifying and non-lithifying mat types, which strongly correlated with water depth. Three distinct populations emerged including the upper intertidal non-lithifying mats, the intertidal pustular mats associated with unlaminated carbonate build-ups, and the subtidal colloform and smooth mat types associated with laminated structures. Functional analysis of metagenomes revealed that amongst stromatolite-forming mats there was an enrichment of photosynthesis pathways in the pustular stromatolite-forming mats. In the colloform and smooth stromatolite-forming mats, however, there was an increase in the abundance of genes associated with those heterotrophic metabolisms typically associated with carbonate mineralization, such as sulfate reduction. The comparative metagenomic analyses suggest that stromatolites of Hamelin Pool may form by two distinctive processes that are highly dependent on water depth. These results provide key insight into the potential adaptive strategies and synergistic interactions between microbes and their environments that may lead to stromatolite formation and accretion.
Collapse
Affiliation(s)
- Joany Babilonia
- Space Life Science Lab, Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, United States
| | - Ana Conesa
- Department of Microbiology and Cell Science, Genetics Institute, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States.,Genomics of Gene Expression Laboratory, Prince Felipe Research Center, Valencia, Spain
| | - Giorgio Casaburi
- Space Life Science Lab, Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, United States
| | - Cecile Pereira
- Department of Microbiology and Cell Science, Genetics Institute, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States.,EURA NOVA, Marseille, France
| | - Artemis S Louyakis
- Space Life Science Lab, Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, United States
| | - R Pamela Reid
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States
| | - Jamie S Foster
- Space Life Science Lab, Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, United States
| |
Collapse
|
31
|
Mlewski EC, Pisapia C, Gomez F, Lecourt L, Soto Rueda E, Benzerara K, Ménez B, Borensztajn S, Jamme F, Réfrégiers M, Gérard E. Characterization of Pustular Mats and Related Rivularia-Rich Laminations in Oncoids From the Laguna Negra Lake (Argentina). Front Microbiol 2018; 9:996. [PMID: 29872427 PMCID: PMC5972317 DOI: 10.3389/fmicb.2018.00996] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 04/27/2018] [Indexed: 11/13/2022] Open
Abstract
Stromatolites are organo-sedimentary structures that represent some of the oldest records of the early biosphere on Earth. Cyanobacteria are considered as a main component of the microbial mats that are supposed to produce stromatolite-like structures. Understanding the role of cyanobacteria and associated microorganisms on the mineralization processes is critical to better understand what can be preserved in the laminated structure of stromatolites. Laguna Negra (Catamarca, Argentina), a high-altitude hypersaline lake where stromatolites are currently formed, is considered as an analog environment of early Earth. This study aimed at characterizing carbonate precipitation within microbial mats and associated oncoids in Laguna Negra. In particular, we focused on carbonated black pustular mats. By combining Confocal Laser Scanning Microscopy, Scanning Electron Microscopy, Laser Microdissection and Whole Genome Amplification, Cloning and Sanger sequencing, and Focused Ion Beam milling for Transmission Electron Microscopy, we showed that carbonate precipitation did not directly initiate on the sheaths of cyanobacterial Rivularia, which dominate in the mat. It occurred via organo-mineralization processes within a large EPS matrix excreted by the diverse microbial consortium associated with Rivularia where diatoms and anoxygenic phototrophic bacteria were particularly abundant. By structuring a large microbial consortium, Rivularia should then favor the formation of organic-rich laminations of carbonates that can be preserved in stromatolites. By using Fourier Transform Infrared spectroscopy and Synchrotron-based deep UV fluorescence imaging, we compared laminations rich in structures resembling Rivularia to putatively chemically-precipitated laminations in oncoids associated with the mats. We showed that they presented a different mineralogy jointly with a higher content in organic remnants, hence providing some criteria of biogenicity to be searched for in the fossil record.
Collapse
Affiliation(s)
- Estela C Mlewski
- Centro de Investigaciones en Ciencias de la Tierra (CICTERRA), Cordoba, Argentina
| | - Céline Pisapia
- Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Centre National de la Recherche Scientifique, Université Paris Diderot, Paris, France.,Synchrotron SOLEIL, DISCO Beamline, Saint Aubin, France
| | - Fernando Gomez
- Centro de Investigaciones en Ciencias de la Tierra (CICTERRA), Cordoba, Argentina
| | - Lena Lecourt
- Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Centre National de la Recherche Scientifique, Université Paris Diderot, Paris, France
| | - Eliana Soto Rueda
- Centro de Investigaciones en Ciencias de la Tierra (CICTERRA), Cordoba, Argentina
| | - Karim Benzerara
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, UMR Centre National de la Recherche Scientifique 7590, Sorbonne Université, Muséum National d'Histoire Naturelle, IRD UMR 206, Paris, France
| | - Bénédicte Ménez
- Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Centre National de la Recherche Scientifique, Université Paris Diderot, Paris, France
| | - Stephan Borensztajn
- Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Centre National de la Recherche Scientifique, Université Paris Diderot, Paris, France
| | | | | | - Emmanuelle Gérard
- Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Centre National de la Recherche Scientifique, Université Paris Diderot, Paris, France
| |
Collapse
|
32
|
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
|
33
|
Molina V, Eissler Y, Cornejo M, Galand PE, Dorador C, Hengst M, Fernandez C, Francois JP. Distribution of greenhouse gases in hyper-arid and arid areas of northern Chile and the contribution of the high altitude wetland microbiome (Salar de Huasco, Chile). Antonie van Leeuwenhoek 2018; 111:1421-1432. [PMID: 29626330 DOI: 10.1007/s10482-018-1078-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 03/31/2018] [Indexed: 01/25/2023]
Abstract
Northern Chile harbors different bioclimatic zones including hyper-arid and arid ecosystems and hotspots of microbial life, such as high altitude wetlands, which may contribute differentially to greenhouse gases (GHG) such as carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O). In this study, we explored ground level GHG distribution and the potential role of a wetland situated at 3800 m.a.s.l, and characterized by high solar radiation < 1600 W m-2, extreme temperature ranges (-12 to 24 °C) and wind stress (< 17 m s-1). The water source of the wetland is mainly groundwater springs, which generates streams and ponds surrounded by peatlands. These sites support a rich microbial aquatic life including diverse bacteria and archaea communities, which transiently form more complex structures, such as microbial mats. In this study, GHG were measured in the water and above ground level air at the wetland site and along an elevation gradient in different bioclimatic areas from arid to hyper-arid zones. The microbiome from the water and sediments was described by high-throughput sequencing 16S rRNA and rDNA genes. The results indicate that GHG at ground level were variable along the elevation gradient potentially associated with different bioclimatic zones, reaching high values at the high Andean steppe and variable but lower values in the Atacama Desert and at the wetland. The water areas of the wetland presented high concentrations of CH4 and CO2, particularly at the spring areas and in air bubbles below microbial mats. The microbial community was rich (> 40 phyla), including archaea and bacteria potentially active in the different matrices studied (water, sediments and mats). Functional microbial groups associated with GHG recycling were detected at low frequency, i.e., < 2.5% of total sequences. Our results indicate that hyper-arid and arid areas of northern Chile are sites of GHG exchange associated with various bioclimatic zones and particularly in aquatic areas of the wetland where this ecosystem could represent a net sink of N2O and a source for CH4 and CO2.
Collapse
Affiliation(s)
- Verónica Molina
- Programa de Biodiversidad y Departamento de Biología, Facultad de Ciencias Naturales y Exactas, Observatorio de Ecología Microbiana, Universidad de Playa Ancha, Valparaíso, Chile.
| | - Yoanna Eissler
- Centro de Investigación y Gestión de Recursos Naturales, Instituto de Química y Bioquímica, Universidad de Valparaíso, Valparaíso, Chile
| | - Marcela Cornejo
- Escuela de Ciencias del Mar e Instituto Milenio de Oceanografía Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Pierre E Galand
- Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Sorbonne Université, CNRS, Observatoire Océanologique de Banyuls, 66650, Banyuls/Mer, France
| | - 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, Antofagasta, Chile.,Centre for Biotechnology and Bioengineering, Santiago, Chile
| | - Martha Hengst
- Centre for Biotechnology and Bioengineering, Santiago, Chile.,Departamento de Ciencias Farmacéuticas, Facultad de Ciencias, Universidad Católica del Norte, Antofagasta, Chile
| | - Camila Fernandez
- Laboratoire d'Océanographie microbienne (LOMIC), Sorbonne Université, CNRS, Observatoire Océanologique de Banyuls, 66650, Banyuls/Mer, France.,FONDAP INCAR Center (15110027), PFB-31 COPAS Sur Austral, Departamento de Oceanografía, Universidad de Concepción, Concepción, Chile
| | | |
Collapse
|
34
|
Farias ME, Rasuk MC, Gallagher KL, Contreras M, Kurth D, Fernandez AB, Poiré D, Novoa F, Visscher PT. Prokaryotic diversity and biogeochemical characteristics of benthic microbial ecosystems at La Brava, a hypersaline lake at Salar de Atacama, Chile. PLoS One 2017; 12:e0186867. [PMID: 29140980 PMCID: PMC5687714 DOI: 10.1371/journal.pone.0186867] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 10/09/2017] [Indexed: 11/19/2022] Open
Abstract
Benthic microbial ecosystems of Laguna La Brava, Salar de Atacama, a high altitude hypersaline lake, were characterized in terms of bacterial and archaeal diversity, biogeochemistry, (including O2 and sulfide depth profiles and mineralogy), and physicochemical characteristics. La Brava is one of several lakes in the Salar de Atacama where microbial communities are growing in extreme conditions, including high salinity, high solar insolation, and high levels of metals such as lithium, arsenic, magnesium, and calcium. Evaporation creates hypersaline conditions in these lakes and mineral precipitation is a characteristic geomicrobiological feature of these benthic ecosystems. In this study, the La Brava non-lithifying microbial mats, microbialites, and rhizome-associated concretions were compared to each other and their diversity was related to their environmental conditions. All the ecosystems revealed an unusual community where Euryarchaeota, Crenarchaeota, Acetothermia, Firmicutes and Planctomycetes were the most abundant groups, and cyanobacteria, typically an important primary producer in microbial mats, were relatively insignificant or absent. This suggests that other microorganisms, and possibly novel pathways unique to this system, are responsible for carbon fixation. Depth profiles of O2 and sulfide showed active production and respiration. The mineralogy composition was calcium carbonate (as aragonite) and increased from mats to microbialites and rhizome-associated concretions. Halite was also present. Further analyses were performed on representative microbial mats and microbialites by layer. Different taxonomic compositions were observed in the upper layers, with Archaea dominating the non-lithifying mat, and Planctomycetes the microbialite. The bottom layers were similar, with Euryarchaeota, Crenarchaeota and Planctomycetes as dominant phyla. Sequences related to Cyanobacteria were very scarce. These systems may contain previously uncharacterized community metabolisms, some of which may be contributing to net mineral precipitation. Further work on these sites might reveal novel organisms and metabolisms of biotechnological interest.
Collapse
Affiliation(s)
- Maria Eugenia Farias
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT-Tucumán, CONICET, Tucumán, Argentina
- * E-mail:
| | - Maria Cecilia Rasuk
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT-Tucumán, CONICET, Tucumán, Argentina
| | - Kimberley L. Gallagher
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, United States of America
| | | | - Daniel Kurth
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT-Tucumán, CONICET, Tucumán, Argentina
| | - Ana Beatriz Fernandez
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT-Tucumán, CONICET, Tucumán, Argentina
| | - Daniel Poiré
- Centro de Investigaciones Geológicas, Universidad Nacional de La Plata-Conicet, La Plata, Argentina
| | - Fernando Novoa
- Centro de Ecología Aplicada (CEA), Ñuñoa, Santiago, Chile
| | - Pieter T. Visscher
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, United States of America
- Australian Centre for Astrobiology, University of New South Wales, Sydney, New South Wales, Australia
| |
Collapse
|
35
|
Proemse BC, Eberhard RS, Sharples C, Bowman JP, Richards K, Comfort M, Barmuta LA. Stromatolites on the rise in peat-bound karstic wetlands. Sci Rep 2017; 7:15384. [PMID: 29133809 PMCID: PMC5684344 DOI: 10.1038/s41598-017-15507-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 10/27/2017] [Indexed: 02/01/2023] Open
Abstract
Stromatolites are the oldest evidence for life on Earth, but modern living examples are rare and predominantly occur in shallow marine or (hyper-) saline lacustrine environments, subject to exotic physico-chemical conditions. Here we report the discovery of living freshwater stromatolites in cool-temperate karstic wetlands in the Giblin River catchment of the UNESCO-listed Tasmanian Wilderness World Heritage Area, Australia. These stromatolites colonize the slopes of karstic spring mounds which create mildly alkaline (pH of 7.0-7.9) enclaves within an otherwise uniformly acidic organosol terrain. The freshwater emerging from the springs is Ca-HCO3 dominated and water temperatures show no evidence of geothermal heating. Using 16 S rRNA gene clone library analysis we revealed that the bacterial community is dominated by Cyanobacteria, Alphaproteobacteria and an unusually high proportion of Chloroflexi, followed by Armatimonadetes and Planctomycetes, and is therefore unique compared to other living examples. Macroinvertebrates are sparse and snails in particular are disadvantaged by the development of debilitating accumulations of carbonate on their shells, corroborating evidence that stromatolites flourish under conditions where predation by metazoans is suppressed. Our findings constitute a novel habitat for stromatolites because cool-temperate freshwater wetlands are not a conventional stromatolite niche, suggesting that stromatolites may be more common than previously thought.
Collapse
Affiliation(s)
- Bernadette C Proemse
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania, 7001, Australia
- Australian Centre for Research on Separation Science, University of Tasmania, Tasmania, 7001, Australia
| | - Rolan S Eberhard
- Department of Primary Industries, Parks, Water & Environment, GPO Box 44, Hobart, Tasmania, 7001, Australia.
| | - Chris Sharples
- Geography and Spatial Science, University of Tasmania, Private Bag 76, Hobart, Tasmania, 7001, Australia
| | - John P Bowman
- Tasmanian Institute of Agriculture, University of Tasmania, Private Bag 98, Hobart, Tasmania, 7001, Australia
| | - Karen Richards
- Department of Primary Industries, Parks, Water & Environment, GPO Box 44, Hobart, Tasmania, 7001, Australia
| | - Michael Comfort
- Department of Primary Industries, Parks, Water & Environment, GPO Box 44, Hobart, Tasmania, 7001, Australia
| | - Leon A Barmuta
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania, 7001, Australia
| |
Collapse
|
36
|
Rasuk MC, Ferrer GM, Kurth D, Portero LR, Farías ME, Albarracín VH. UV-Resistant Actinobacteria from High-Altitude Andean Lakes: Isolation, Characterization and Antagonistic Activities. Photochem Photobiol 2017; 93:865-880. [DOI: 10.1111/php.12759] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 03/03/2017] [Indexed: 11/27/2022]
Affiliation(s)
- María Cecilia Rasuk
- Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI); CCT; CONICET; S. M. de Tucumán Argentina
| | - Gabriela Mónica Ferrer
- Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI); CCT; CONICET; S. M. de Tucumán Argentina
| | - Daniel Kurth
- Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI); CCT; CONICET; S. M. de Tucumán Argentina
| | - Luciano Raúl Portero
- Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI); CCT; CONICET; S. M. de Tucumán Argentina
| | - María Eugenia Farías
- Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI); CCT; CONICET; S. M. de Tucumán Argentina
| | - Virginia Helena Albarracín
- Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI); CCT; CONICET; S. M. de Tucumán Argentina
- Facultad de Ciencias Naturales e Instituto Miguel Lillo; Universidad Nacional de Tucumán; Tucumán Argentina
- Centro Integral de Microscopía Electrónica; CCT-Tucumán; CONICET; Universidad Nacional de Tucumán; Tucumán Argentina
| |
Collapse
|
37
|
Kurth D, Amadio A, Ordoñez OF, Albarracín VH, Gärtner W, Farías ME. Arsenic metabolism in high altitude modern stromatolites revealed by metagenomic analysis. Sci Rep 2017; 7:1024. [PMID: 28432307 PMCID: PMC5430908 DOI: 10.1038/s41598-017-00896-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 03/16/2017] [Indexed: 11/09/2022] Open
Abstract
Modern stromatolites thrive only in selected locations in the world. Socompa Lake, located in the Andean plateau at 3570 masl, is one of the numerous extreme Andean microbial ecosystems described over recent years. Extreme environmental conditions include hypersalinity, high UV incidence, and high arsenic content, among others. After Socompa's stromatolite microbial communities were analysed by metagenomic DNA sequencing, taxonomic classification showed dominance of Proteobacteria, Bacteroidetes and Firmicutes, and a remarkably high number of unclassified sequences. A functional analysis indicated that carbon fixation might occur not only by the Calvin-Benson cycle, but also through alternative pathways such as the reverse TCA cycle, and the reductive acetyl-CoA pathway. Deltaproteobacteria were involved both in sulfate reduction and nitrogen fixation. Significant differences were found when comparing the Socompa stromatolite metagenome to the Shark Bay (Australia) smooth mat metagenome: namely, those involving stress related processes, particularly, arsenic resistance. An in-depth analysis revealed a surprisingly diverse metabolism comprising all known types of As resistance and energy generating pathways. While the ars operon was the main mechanism, an important abundance of arsM genes was observed in selected phyla. The data resulting from this work will prove a cornerstone for further studies on this rare microbial community.
Collapse
Affiliation(s)
- Daniel Kurth
- Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI), CCT Tucumán, CONICET, San Miguel de Tucumán, Argentina
| | - Ariel Amadio
- E.E.A. Rafaela, Instituto Nacional de Tecnología Agropecuaria (INTA), CCT Santa Fe, CONICET, Rafaela, Argentina
| | - Omar F Ordoñez
- Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI), CCT Tucumán, CONICET, San Miguel de Tucumán, Argentina
| | - Virginia H Albarracín
- Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI), CCT Tucumán, CONICET, San Miguel de Tucumán, Argentina
- Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, San Miguel de Tucumán, Argentina
| | - Wolfgang Gärtner
- Max-Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany
| | - María E Farías
- Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI), CCT Tucumán, CONICET, San Miguel de Tucumán, Argentina.
| |
Collapse
|
38
|
Toneatti DM, Albarracín VH, Flores MR, Polerecky L, Farías ME. Stratified Bacterial Diversity along Physico-chemical Gradients in High-Altitude Modern Stromatolites. Front Microbiol 2017; 8:646. [PMID: 28446906 PMCID: PMC5388776 DOI: 10.3389/fmicb.2017.00646] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 03/29/2017] [Indexed: 11/13/2022] Open
Abstract
At an altitude of 3,570 m, the volcanic lake Socompa in the Argentinean Andes is presently the highest site where actively forming stromatolite-like structures have been reported. Interestingly, pigment and microsensor analyses performed through the different layers of the stromatolites (50 mm-deep) showed steep vertical gradients of light and oxygen, hydrogen sulfide and pH in the porewater. Given the relatively good characterization of these physico-chemical gradients, the aim of this follow-up work was to specifically address how the bacterial diversity stratified along the top six layers of the stromatolites which seems the most metabolically important and diversified zone of the whole microbial community. We herein discussed how, in only 7 mm, a drastic succession of metabolic adaptations occurred: i.e., microbial communities shift from a UV-high/oxic world to an IR-low/anoxic/high H2S environment which force stratification and metabolic specialization of the bacterial community, thus, modulating the chemical faces of the Socompa stromatolites. The oxic zone was dominated by Deinococcus sp. at top surface (0.3 mm), followed by a second layer of Coleofasciculus sp. (0.3 to ∼2 mm). Sequences from anoxygenic phototrophic Alphaproteobacteria, along with an increasing diversity of phyla including Bacteroidetes, Spirochaetes were found at middle layers 3 and 4. Deeper layers (5–7 mm) were mostly occupied by sulfate reducers of Deltaproteobacteria, Bacteroidetes and Firmicutes, next to a high diversity and equitable community of rare, unclassified and candidate phyla. This analysis showed how microbial communities stratified in a physicochemical vertical profile and according to the light source. It also gives an insight of which bacterial metabolic capabilities might operate and produce a microbial cooperative strategy to thrive in one of the most extreme environments on Earth.
Collapse
Affiliation(s)
- Diego M Toneatti
- Planta Piloto de Procesos Industriales y Microbiológicos, Centro Científico Tecnológico - Consejo Nacional de Investigaciones Científicas y TécnicasSan Miguel de Tucumán, Argentina
| | - Virginia H Albarracín
- Planta Piloto de Procesos Industriales y Microbiológicos, Centro Científico Tecnológico - Consejo Nacional de Investigaciones Científicas y TécnicasSan Miguel de Tucumán, Argentina.,Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de TucumánSan Miguel de Tucumán, Argentina.,Centro Integral de Microscopía Electrónica, Centro Científico Tecnológico - Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de TucumánSan Miguel de Tucumán, Argentina
| | - Maria R Flores
- Department of Earth Sciences - Geochemistry, Utrecht UniversityUtrecht, Netherlands
| | - Lubos Polerecky
- Department of Earth Sciences - Geochemistry, Utrecht UniversityUtrecht, Netherlands
| | - María E Farías
- Planta Piloto de Procesos Industriales y Microbiológicos, Centro Científico Tecnológico - Consejo Nacional de Investigaciones Científicas y TécnicasSan Miguel de Tucumán, Argentina
| |
Collapse
|
39
|
Castro-Severyn J, Remonsellez F, Valenzuela SL, Salinas C, Fortt J, Aguilar P, Pardo-Esté C, Dorador C, Quatrini R, Molina F, Aguayo D, Castro-Nallar E, Saavedra CP. Comparative Genomics Analysis of a New Exiguobacterium Strain from Salar de Huasco Reveals a Repertoire of Stress-Related Genes and Arsenic Resistance. Front Microbiol 2017; 8:456. [PMID: 28377753 PMCID: PMC5360010 DOI: 10.3389/fmicb.2017.00456] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 03/06/2017] [Indexed: 11/13/2022] Open
Abstract
The Atacama Desert hosts diverse ecosystems including salt flats and shallow Andean lakes. Several heavy metals are found in the Atacama Desert, and microorganisms growing in this environment show varying levels of resistance/tolerance to copper, tellurium, and arsenic, among others. Herein, we report the genome sequence and comparative genomic analysis of a new Exiguobacterium strain, sp. SH31, isolated from an altiplanic shallow athalassohaline lake. Exiguobacterium sp. SH31 belongs to the phylogenetic Group II and its closest relative is Exiguobacterium sp. S17, isolated from the Argentinian Altiplano (95% average nucleotide identity). Strain SH31 encodes a wide repertoire of proteins required for cadmium, copper, mercury, tellurium, chromium, and arsenic resistance. Of the 34 Exiguobacterium genomes that were inspected, only isolates SH31 and S17 encode the arsenic efflux pump Acr3. Strain SH31 was able to grow in up to 10 mM arsenite and 100 mM arsenate, indicating that it is arsenic resistant. Further, expression of the ars operon and acr3 was strongly induced in response to both toxics, suggesting that the arsenic efflux pump Acr3 mediates arsenic resistance in Exiguobacterium sp. SH31.
Collapse
Affiliation(s)
- Juan Castro-Severyn
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andres BelloSantiago, Chile; Centro de Bioinformática y Biología Integrativa, Facultad de Ciencias Biológicas, Universidad Andrés BelloSantiago, Chile
| | - Francisco Remonsellez
- Laboratorio de Tecnologías de Membranas, Biotecnología y Medio Ambiente, Departamento de Ingeniería Química, Facultad de Ingeniería y Ciencias Geológicas, Universidad Católica del Norte Antofagasta, Chile
| | - Sandro L Valenzuela
- Centro de Bioinformática y Biología Integrativa, Facultad de Ciencias Biológicas, Universidad Andrés Bello Santiago, Chile
| | - Cesar Salinas
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andres Bello Santiago, Chile
| | - Jonathan Fortt
- Laboratorio de Tecnologías de Membranas, Biotecnología y Medio Ambiente, Departamento de Ingeniería Química, Facultad de Ingeniería y Ciencias Geológicas, Universidad Católica del Norte Antofagasta, Chile
| | - Pablo Aguilar
- Laboratorio de Tecnologías de Membranas, Biotecnología y Medio Ambiente, Departamento de Ingeniería Química, Facultad de Ingeniería y Ciencias Geológicas, Universidad Católica del NorteAntofagasta, Chile; Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta and Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de AntofagastaAntofagasta, Chile
| | - Coral Pardo-Esté
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andres Bello Santiago, Chile
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta and Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de AntofagastaAntofagasta, Chile; Centre for Biotechnology and BioengineeringAntofagasta, Chile
| | - Raquel Quatrini
- Laboratorio de Ecofisiología Microbiana, Fundación Ciencia and Vida Santiago, Chile
| | | | - Daniel Aguayo
- Centro de Bioinformática y Biología Integrativa, Facultad de Ciencias Biológicas, Universidad Andrés BelloSantiago, Chile; Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de ValparaísoValparaíso, Chile
| | - Eduardo Castro-Nallar
- Centro de Bioinformática y Biología Integrativa, Facultad de Ciencias Biológicas, Universidad Andrés Bello Santiago, Chile
| | - Claudia P Saavedra
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andres Bello Santiago, Chile
| |
Collapse
|
40
|
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
|
41
|
Sforna MC, Daye M, Philippot P, Somogyi A, van Zuilen MA, Medjoubi K, Gérard E, Jamme F, Dupraz C, Braissant O, Glunk C, Visscher PT. Patterns of metal distribution in hypersaline microbialites during early diagenesis: Implications for the fossil record. GEOBIOLOGY 2017; 15:259-279. [PMID: 27935656 DOI: 10.1111/gbi.12218] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 09/28/2016] [Indexed: 06/06/2023]
Abstract
The use of metals as biosignatures in the fossil stromatolite record requires understanding of the processes controlling the initial metal(loid) incorporation and diagenetic preservation in living microbialites. Here, we report the distribution of metals and the organic fraction within the lithifying microbialite of the hypersaline Big Pond Lake (Bahamas). Using synchrotron-based X-ray microfluorescence, confocal, and biphoton microscopies at different scales (cm-μm) in combination with traditional geochemical analyses, we show that the initial cation sorption at the surface of an active microbialite is governed by passive binding to the organic matrix, resulting in a homogeneous metal distribution. During early diagenesis, the metabolic activity in deeper microbialite layers slows down and the distribution of the metals becomes progressively heterogeneous, resulting from remobilization and concentration as metal(loid)-enriched sulfides, which are aligned with the lamination of the microbialite. In addition, we were able to identify globules containing significant Mn, Cu, Zn, and As enrichments potentially produced through microbial activity. The similarity of the metal(loid) distributions observed in the Big Pond microbialite to those observed in the Archean stromatolites of Tumbiana provides the foundation for a conceptual model of the evolution of the metal distribution through initial growth, early diagenesis, and fossilization of a microbialite, with a potential application to the fossil record.
Collapse
Affiliation(s)
- M C Sforna
- Geobiosphère Actuelle & Primitive, Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Université Paris Diderot, CNRS, Paris, France
- Dipartimento di Scienze Chimiche e Geologiche, Università di Modena e Reggio Emilia, Modena, Italy
| | - M Daye
- Geobiosphère Actuelle & Primitive, Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Université Paris Diderot, CNRS, Paris, France
- Synchrotron Soleil, Gif-sur-Yvette, France
| | - P Philippot
- Geobiosphère Actuelle & Primitive, Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Université Paris Diderot, CNRS, Paris, France
| | - A Somogyi
- Synchrotron Soleil, Gif-sur-Yvette, France
| | - M A van Zuilen
- Geomicrobiologie, Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Université Paris Diderot, CNRS, Paris, France
| | - K Medjoubi
- Synchrotron Soleil, Gif-sur-Yvette, France
| | - E Gérard
- Geomicrobiologie, Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Université Paris Diderot, CNRS, Paris, France
| | - F Jamme
- Synchrotron Soleil, Gif-sur-Yvette, France
| | - C Dupraz
- Department of Geological Sciences, Stockholms Universitet, Stockholm, Sweden
| | - O Braissant
- Center for Biomechanics and Biocalorimetry, University of Basel, Basel, Switzerland
| | - C Glunk
- Societe Suisse des Explosifs SA, Brig, Switzerland
| | - P T Visscher
- Department of Marine Sciences, University of Connecticut, Groton, CT, USA
| |
Collapse
|
42
|
Saghaï A, Zivanovic Y, Moreira D, Benzerara K, Bertolino P, Ragon M, Tavera R, López-Archilla AI, López-García P. Comparative metagenomics unveils functions and genome features of microbialite-associated communities along a depth gradient. Environ Microbiol 2016; 18:4990-5004. [PMID: 27422734 PMCID: PMC5477898 DOI: 10.1111/1462-2920.13456] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 07/13/2016] [Indexed: 12/15/2022]
Abstract
Modern microbialites are often used as analogs of Precambrian stromatolites; therefore, studying the metabolic interplay within their associated microbial communities can help formulating hypotheses on their formation and long-term preservation within the fossil record. We performed a comparative metagenomic analysis of microbialite samples collected at two sites and along a depth gradient in Lake Alchichica (Mexico). The community structure inferred from single-copy gene family identification and long-contig (>10 kb) assignation, consistently with previous rRNA gene surveys, showed a wide prokaryotic diversity dominated by Alphaproteobacteria, Gammaproteobacteria, Cyanobacteria, and Bacteroidetes, while eukaryotes were largely dominated by green algae or diatoms. Functional analyses based on RefSeq, COG and SEED assignations revealed the importance of housekeeping functions, with an overrepresentation of genes involved in carbohydrate metabolism, as compared with other metabolic capacities. The search for genes diagnostic of specific metabolic functions revealed the important involvement of Alphaproteobacteria in anoxygenic photosynthesis and sulfide oxidation, and Cyanobacteria in oxygenic photosynthesis and nitrogen fixation. Surprisingly, sulfate reduction appeared negligible. Comparative analyses suggested functional similarities among various microbial mat and microbialite metagenomes as compared with soil or oceans, but showed differences in microbial processes among microbialite types linked to local environmental conditions.
Collapse
Affiliation(s)
- Aurélien Saghaï
- Ecologie Systématique Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Yvan Zivanovic
- Institut de Biologie Intégrative de la Cellule, CNRS, Université Paris-Sud Orsay, Université Paris-Saclay, France
| | - David Moreira
- Ecologie Systématique Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Karim Benzerara
- Institut de Minéralogie et de Physique des Matériaux et de Cosmochimie, CNRS, Muséum National d'Histoire Naturelle, Université Pierre et Marie Curie, Sorbonne Universités, Paris, France
| | - Paola Bertolino
- Ecologie Systématique Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Marie Ragon
- Ecologie Systématique Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Rosaluz Tavera
- Departamento de Ecología y Recursos Naturales, Universidad Nacional Autónoma de México, DF Mexico, Mexico
| | | | - Purificación López-García
- Ecologie Systématique Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, Orsay, France
| |
Collapse
|
43
|
Molina V, Hernández K, Dorador C, Eissler Y, Hengst M, Pérez V, Harrod C. Bacterial Active Community Cycling in Response to Solar Radiation and Their Influence on Nutrient Changes in a High-Altitude Wetland. Front Microbiol 2016; 7:1823. [PMID: 27909430 PMCID: PMC5112256 DOI: 10.3389/fmicb.2016.01823] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 10/31/2016] [Indexed: 01/08/2023] Open
Abstract
Microbial communities inhabiting high-altitude spring ecosystems are subjected to extreme changes in solar irradiance and temperature throughout the diel cycle. Here, using 16S rRNA gene tag pyrosequencing (cDNA) we determined the composition of actively transcribing bacteria from spring waters experimentally exposed through the day (morning, noon, and afternoon) to variable levels of solar radiation and light quality, and evaluated their influence on nutrient recycling. Solar irradiance, temperature, and changes in nutrient dynamics were associated with changes in the active bacterial community structure, predominantly by Cyanobacteria, Verrucomicrobia, Proteobacteria, and 35 other Phyla, including the recently described Candidate Phyla Radiation (e.g., Parcubacteria, Gracilibacteria, OP3, TM6, SR1). Diversity increased at noon, when the highest irradiances were measured (3.3-3.9 H', 1125 W m-2) compared to morning and afternoon (0.6-2.8 H'). This shift was associated with a decrease in the contribution to pyrolibraries by Cyanobacteria and an increase of Proteobacteria and other initially low frequently and rare bacteria phyla (< 0.5%) in the pyrolibraries. A potential increase in the activity of Cyanobacteria and other phototrophic groups, e.g., Rhodobacterales, was observed and associated with UVR, suggesting the presence of photo-activated repair mechanisms to resist high levels of solar radiation. In addition, the percentage contribution of cyanobacterial sequences in the afternoon was similar to those recorded in the morning. The shifts in the contribution by Cyanobacteria also influenced the rate of change in nitrate, nitrite, and phosphate, highlighted by a high level of nitrate accumulation during hours of high radiation and temperature associated with nitrifying bacteria activity. We did not detect ammonia or nitrite oxidizing bacteria in situ, but both functional groups (Nitrosomona and Nitrospira) appeared mainly in pyrolibraries generated from dark incubations. In total, our results reveal that both the structure and the diversity of the active bacteria community was extremely dynamic through the day, and showed marked shifts in composition that influenced nutrient recycling, highlighting how abiotic variation affects potential ecosystem functioning.
Collapse
Affiliation(s)
- Verónica Molina
- Programa de Biodiversidad and Departamento de Biología, Facultad de Ciencias Naturales y Exactas, Observatorio de Ecología Microbiana, Universidad de Playa AnchaValparaíso, Chile
| | - Klaudia Hernández
- Centro de Investigación Marina Quintay, Facultad de Ecología y Recursos Naturales, Universidad Andres BelloValparaíso, Chile
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional and Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, AntofagastaChile
- Centre for Biotechnology and BioengineeringSantiago, Chile
| | - Yoanna Eissler
- Centro de Investigación y Gestión de Recursos Naturales, Instituto de Química y Bioquímica, Facultad de Ciencias, Universidad de ValparaísoValparaíso, Chile
| | - Martha Hengst
- Centre for Biotechnology and BioengineeringSantiago, Chile
- Departamento de Ciencias Farmacéuticas, Facultad de Ciencias, Universidad Católica del NorteAntofagasta, Chile
| | - Vilma Pérez
- Laboratorio de Complejidad Microbiana y Ecología Funcional and Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, AntofagastaChile
- Centre for Biotechnology and BioengineeringSantiago, Chile
| | - 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 AntofagastaAntofagasta, Chile
| |
Collapse
|
44
|
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
|
45
|
Aanderud ZT, Vert JC, Lennon JT, Magnusson TW, Breakwell DP, Harker AR. Bacterial Dormancy Is More Prevalent in Freshwater than Hypersaline Lakes. Front Microbiol 2016; 7:853. [PMID: 27375575 PMCID: PMC4899617 DOI: 10.3389/fmicb.2016.00853] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 05/23/2016] [Indexed: 11/21/2022] Open
Abstract
Bacteria employ a diverse array of strategies to survive under extreme environmental conditions but maintaining these adaptations comes at an energetic cost. If energy reserves drop too low, extremophiles may enter a dormant state to persist. We estimated bacterial dormancy and identified the environmental variables influencing our activity proxy in 10 hypersaline and freshwater lakes across the Western United States. Using ribosomal RNA:DNA ratios as an indicator for bacterial activity, we found that the proportion of the community exhibiting dormancy was 16% lower in hypersaline than freshwater lakes. Based on our indicator variable multiple regression results, saltier conditions in both freshwater and hypersaline lakes increased activity, suggesting that salinity was a robust environmental filter structuring bacterial activity in lake ecosystems. To a lesser degree, higher total phosphorus concentrations reduced dormancy in all lakes. Thus, even under extreme conditions, the competition for resources exerted pressure on activity. Within the compositionally distinct and less diverse hypersaline communities, abundant taxa were disproportionately active and localized in families Microbacteriaceae (Actinobacteria), Nitriliruptoraceae (Actinobacteria), and Rhodobacteraceae (Alphaproteobacteria). Our results are consistent with the view that hypersaline communities are able to capitalize on a seemingly more extreme, yet highly selective, set of conditions and finds that extremophiles may need dormancy less often to thrive and survive.
Collapse
Affiliation(s)
- Zachary T Aanderud
- Department of Plant and Wildlife Sciences, Brigham Young University Provo, UT, USA
| | - Joshua C Vert
- Department of Microbiology and Molecular Biology, Brigham Young University Provo, UT, USA
| | - Jay T Lennon
- Department of Biology, Indiana University Bloomington, IN, USA
| | - Tylan W Magnusson
- Department of Microbiology and Molecular Biology, Brigham Young University Provo, UT, USA
| | - Donald P Breakwell
- Department of Microbiology and Molecular Biology, Brigham Young University Provo, UT, USA
| | - Alan R Harker
- Department of Microbiology and Molecular Biology, Brigham Young University Provo, UT, USA
| |
Collapse
|
46
|
Albarracín VH, Kraiselburd I, Bamann C, Wood PG, Bamberg E, Farias ME, Gärtner W. Functional Green-Tuned Proteorhodopsin from Modern Stromatolites. PLoS One 2016; 11:e0154962. [PMID: 27187791 PMCID: PMC4871484 DOI: 10.1371/journal.pone.0154962] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 04/21/2016] [Indexed: 11/18/2022] Open
Abstract
The sequenced genome of the poly-extremophile Exiguobacterium sp. S17, isolated from modern stromatolites at Laguna Socompa (3,570 m), a High-Altitude Andean Lake (HAAL) in Argentinean Puna revealed a putative proteorhodopsin-encoding gene. The HAAL area is exposed to the highest UV irradiation on Earth, making the microbial community living in the stromatolites test cases for survival strategies under extreme conditions. The heterologous expressed protein E17R from Exiguobacterium (248 amino acids, 85% sequence identity to its ortholog ESR from E. sibiricum) was assembled with retinal displaying an absorbance maximum at 524 nm, which makes it a member of the green-absorbing PR-subfamily. Titration down to low pH values (eventually causing partial protein denaturation) indicated a pK value between two and three. Global fitting of data from laser flash-induced absorption changes gave evidence for an early red-shifted intermediate (its formation being below the experimental resolution) that decayed (τ1 = 3.5 μs) into another red-shifted intermediate. This species decayed in a two-step process (τ2 = 84 μs, τ3 = 11 ms), to which the initial state of E17-PR was reformed with a kinetics of 2 ms. Proton transport capability of the HAAL protein was determined by BLM measurements. Additional blue light irradiation reduced the proton current, clearly identifying a blue light absorbing, M-like intermediate. The apparent absence of this intermediate is explained by closely matching formation and decay kinetics.
Collapse
Affiliation(s)
- Virginia Helena Albarracín
- Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI), CCT, CONICET. Av. Belgrano y Pasaje Caseros. 4000- S. M. de Tucumán, Argentina
- Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, 4000, S. M. de Tucumán, Argentina
- * E-mail: (VHA); (WG)
| | - Ivana Kraiselburd
- Instituto de Biología Molecular y Celular de Rosario (IBR - CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas (FBIOYF - UNR), Suipacha 590, 2000, Rosario, Santa Fe, Argentina
| | - Christian Bamann
- Max-Planck-Institute for Biophysics, Max-von-Laue-Straße 3, D-60438 Frankfurt am Main, Germany
| | - Phillip G. Wood
- Max-Planck-Institute for Biophysics, Max-von-Laue-Straße 3, D-60438 Frankfurt am Main, Germany
| | - Ernst Bamberg
- Max-Planck-Institute for Biophysics, Max-von-Laue-Straße 3, D-60438 Frankfurt am Main, Germany
| | - María Eugenia Farias
- Max-Planck-Institute for Biophysics, Max-von-Laue-Straße 3, D-60438 Frankfurt am Main, Germany
| | - Wolfgang Gärtner
- Max-Planck-Institute for Chemical Energy Conversion, Stiftstrasse 34–36, D-45470 Mülheim, Germany
- * E-mail: (VHA); (WG)
| |
Collapse
|
47
|
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
|
48
|
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
|
49
|
Casaburi G, Duscher AA, Reid RP, Foster JS. Characterization of the stromatolite microbiome from Little Darby Island, The Bahamas using predictive and whole shotgun metagenomic analysis. Environ Microbiol 2015; 18:1452-69. [PMID: 26471001 DOI: 10.1111/1462-2920.13094] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Revised: 10/13/2015] [Accepted: 10/13/2015] [Indexed: 02/01/2023]
Abstract
Modern stromatolites represent ideal ecosystems to understand the biological processes required for the precipitation of carbonate due to their long evolutionary history and occurrence in a wide range of habitats. However, most of the prior molecular work on stromatolites has focused on understanding the taxonomic complexity and not fully elucidating the functional capabilities of these systems. Here, we begin to characterize the microbiome associated with stromatolites of Little Darby Island, The Bahamas using predictive metagenomics of the 16S rRNA gene coupled with direct whole shotgun sequencing. The metagenomic analysis of the Little Darby stromatolites revealed many shared taxa and core pathways associated with biologically induced carbonate precipitation, suggesting functional convergence within Bahamian stromatolites. A comparison of the Little Darby stromatolites with other lithifying microbial ecosystems also revealed that although factors, such as geographic location and salinity, do drive some differences within the population, there are extensive similarities within the microbial populations. These results suggest that for stromatolite formation, 'who' is in the community is not as critical as metabolic activities and environmental interactions. Together, these analyses help improve our understanding of the similarities among lithifying ecosystems and provide an important first step in characterizing the shared microbiome of modern stromatolites.
Collapse
Affiliation(s)
- Giorgio Casaburi
- Department of Microbiology and Cell Science, University of Florida, Space Life Science Lab, Merritt Island, FL, USA
| | - Alexandrea A Duscher
- Department of Microbiology and Cell Science, University of Florida, Space Life Science Lab, Merritt Island, FL, USA
| | - R Pamela Reid
- Rosenstiel School of Marine Sciences, University of Miami, Miami, FL, USA
| | - Jamie S Foster
- Department of Microbiology and Cell Science, University of Florida, Space Life Science Lab, Merritt Island, FL, USA
| |
Collapse
|
50
|
Saghaï A, Zivanovic Y, Zeyen N, Moreira D, Benzerara K, Deschamps P, Bertolino P, Ragon M, Tavera R, López-Archilla AI, López-García P. Metagenome-based diversity analyses suggest a significant contribution of non-cyanobacterial lineages to carbonate precipitation in modern microbialites. Front Microbiol 2015; 6:797. [PMID: 26300865 PMCID: PMC4525015 DOI: 10.3389/fmicb.2015.00797] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 07/22/2015] [Indexed: 11/13/2022] Open
Abstract
Cyanobacteria are thought to play a key role in carbonate formation due to their metabolic activity, but other organisms carrying out oxygenic photosynthesis (photosynthetic eukaryotes) or other metabolisms (e.g., anoxygenic photosynthesis, sulfate reduction), may also contribute to carbonate formation. To obtain more quantitative information than that provided by more classical PCR-dependent methods, we studied the microbial diversity of microbialites from the Alchichica crater lake (Mexico) by mining for 16S/18S rRNA genes in metagenomes obtained by direct sequencing of environmental DNA. We studied samples collected at the Western (AL-W) and Northern (AL-N) shores of the lake and, at the latter site, along a depth gradient (1, 5, 10, and 15 m depth). The associated microbial communities were mainly composed of bacteria, most of which seemed heterotrophic, whereas archaea were negligible. Eukaryotes composed a relatively minor fraction dominated by photosynthetic lineages, diatoms in AL-W, influenced by Si-rich seepage waters, and green algae in AL-N samples. Members of the Gammaproteobacteria and Alphaproteobacteria classes of Proteobacteria, Cyanobacteria, and Bacteroidetes were the most abundant bacterial taxa, followed by Planctomycetes, Deltaproteobacteria (Proteobacteria), Verrucomicrobia, Actinobacteria, Firmicutes, and Chloroflexi. Community composition varied among sites and with depth. Although cyanobacteria were the most important bacterial group contributing to the carbonate precipitation potential, photosynthetic eukaryotes, anoxygenic photosynthesizers and sulfate reducers were also very abundant. Cyanobacteria affiliated to Pleurocapsales largely increased with depth. Scanning electron microscopy (SEM) observations showed considerable areas of aragonite-encrusted Pleurocapsa-like cyanobacteria at microscale. Multivariate statistical analyses showed a strong positive correlation of Pleurocapsales and Chroococcales with aragonite formation at macroscale, and suggest a potential causal link. Despite the previous identification of intracellularly calcifying cyanobacteria in Alchichica microbialites, most carbonate precipitation seems extracellular in this system.
Collapse
Affiliation(s)
- Aurélien Saghaï
- Unité d’Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-SudOrsay, France
| | - Yvan Zivanovic
- Institut de Génétique et Microbiologie, CNRS UMR 8621, Université Paris-SudOrsay, France
| | - Nina Zeyen
- Institut de Minéralogie et de Physique des Matériaux et de Cosmochimie, CNRS UMR 7590, Université Pierre et Marie CurieParis, France
| | - David Moreira
- Unité d’Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-SudOrsay, France
| | - Karim Benzerara
- Institut de Minéralogie et de Physique des Matériaux et de Cosmochimie, CNRS UMR 7590, Université Pierre et Marie CurieParis, France
| | - Philippe Deschamps
- Unité d’Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-SudOrsay, France
| | - Paola Bertolino
- Unité d’Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-SudOrsay, France
| | - Marie Ragon
- Unité d’Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-SudOrsay, France
| | - Rosaluz Tavera
- Departamento de Ecología y Recursos Naturales, Universidad Nacional Autónoma de MéxicoMexico City, Mexico
| | | | | |
Collapse
|