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Virus and Potential Host Microbes from Viral-Enriched Metagenomic Characterization in the High-Altitude Wetland, Salar de Huasco, Chile. Microorganisms 2020; 8:microorganisms8071077. [PMID: 32698305 PMCID: PMC7409041 DOI: 10.3390/microorganisms8071077] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/02/2020] [Accepted: 07/03/2020] [Indexed: 12/18/2022] Open
Abstract
Salar de Huasco is a wetland in the Andes mountains, located 3800 m above sea level at the Chilean Altiplano. Here we present a study aimed at characterizing the viral fraction and the microbial communities through metagenomic analysis. Two ponds (H0 and H3) were examined in November 2015. Water samples were processed using tangential flow filtration to obtain metagenomes from which the DNA fraction of the sample was amplified and sequenced (HiSeq system, Illumina). The ponds were characterized by freshwater and the viral-like particles to picoplankton ratio was 12.1 and 2.3 for H0 and H3, respectively. A great number of unassigned viral sequences were found in H0 (55.8%) and H3 (32.8%), followed by the family Fuselloviridae 20.8% (H0) and other less relatively abundant groups such as Microviridae (H0, 11.7% and H3, 3.3%) and Inoviridae (H3, 2.7%). The dominant viral sequences in both metagenomes belong to the order Caudovirales, with Siphoviridae being the most important family, especially in H3 (32.7%). The most important bacteria phyla were Proteobacteria, Bacteroidetes and Firmicutes in both sites, followed by Cyanobacteria (H0). Genes encoding lysogenic and lytic enzymes (i.e., recombinases and integrases) were found in H0 and H3, indicating a potential for active viral replication at the time of sampling; this was supported by the presence of viral metabolic auxiliary genes at both sites (e.g., cysteine hydrolase). In total, our study indicates a great novelty of viral groups, differences in taxonomic diversity and replication pathways between sites, which contribute to a better understanding of how viruses balance the cycling of energy and matter in this extreme environment.
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Galachyants AD, Tomberg IV, Shtykova YR, Sukhanova EV, Suslova MY, Zimens EA, Blinov VV, Sakirko MV, Domysheva VM, Belykh OI. Bacterioneuston Abundance and Physicochemical Properties of the Surface Microlayer of Lake Baikal. BIOL BULL+ 2019. [DOI: 10.1134/s1062359019100108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Galachyants AD, Tomberg IV, Sukhanova EV, Shtykova YR, Suslova MY, Zimens EA, Blinov VV, Sakirko MV, Domysheva VM, Belykh OI. Bacterioneuston in Lake Baikal: Abundance, Spatial and Temporal Distribution. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:E2587. [PMID: 30463268 PMCID: PMC6266163 DOI: 10.3390/ijerph15112587] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 11/12/2018] [Accepted: 11/18/2018] [Indexed: 11/21/2022]
Abstract
An aquatic surface microlayer covers more than 70% of the world's surface. Our knowledge about the biology of the surface microlayer of Lake Baikal, the most ancient lake on Earth with a surface area of 31,500 km², is still scarce. The total bacterial abundance, the number of cultured heterotrophic temporal bacteria, and the spatial distribution of bacteria in the surface microlayer and underlying waters of Lake Baikal were studied. For the first time, the chemical composition of the surface microlayer of Lake Baikal was determined. There were significant differences and a direct relationship between the total bacterial abundance in the surface microlayer and underlying waters of Lake Baikal, as well as between the number of cultured heterotrophic bacteria in studied water layers in the period of summer stratification. In the surface microlayer, the share of cultured heterotrophic bacteria was higher than in the underlying waters. The surface microlayer was characterized by enrichment with PO₄3-, total organic carbon and suspended particulate matter compared to underlying waters. A direct relationship was found between the number of bacteria in the surface microlayer and environmental factors, including temperature, total organic carbon and suspended particulate matter concentration.
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Affiliation(s)
- Agnia D Galachyants
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, 3, Ulan-Batorskaya, Irkutsk 664033, Russia.
| | - Irina V Tomberg
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, 3, Ulan-Batorskaya, Irkutsk 664033, Russia.
| | - Elena V Sukhanova
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, 3, Ulan-Batorskaya, Irkutsk 664033, Russia.
| | - Yulia R Shtykova
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, 3, Ulan-Batorskaya, Irkutsk 664033, Russia.
| | - Maria Yu Suslova
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, 3, Ulan-Batorskaya, Irkutsk 664033, Russia.
| | - Ekaterina A Zimens
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, 3, Ulan-Batorskaya, Irkutsk 664033, Russia.
| | - Vadim V Blinov
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, 3, Ulan-Batorskaya, Irkutsk 664033, Russia.
| | - Maria V Sakirko
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, 3, Ulan-Batorskaya, Irkutsk 664033, Russia.
| | - Valentina M Domysheva
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, 3, Ulan-Batorskaya, Irkutsk 664033, Russia.
| | - Olga I Belykh
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, 3, Ulan-Batorskaya, Irkutsk 664033, Russia.
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Echeverría-Vega A, Chong G, Serrano AE, Guajardo M, Encalada O, Parro V, Blanco Y, Rivas L, Rose KC, Moreno-Paz M, Luque JA, Cabrol NA, Demergasso CS. Watershed-Induced Limnological and Microbial Status in Two Oligotrophic Andean Lakes Exposed to the Same Climatic Scenario. Front Microbiol 2018; 9:357. [PMID: 29556224 PMCID: PMC5844981 DOI: 10.3389/fmicb.2018.00357] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 02/14/2018] [Indexed: 12/04/2022] Open
Abstract
Laguna Negra and Lo Encañado are two oligotrophic Andean lakes forming part of the system fed by meltwater from distinct glacial tongues of the Echaurren glacier in central Chile, which is in a recession period. The recent increase in temperature and decline in precipitation have led to an increase of glacial meltwater and sediments entering these lakes. Although the lacustrine systems are also hydrogeologically connected, the limnology of the lakes is strongly controlled by the surface processes related to the respective sub-watersheds and hydrology. Watershed characteristics (area and length, slope, lithology, resistance to erosion, among others) affect the chemical and physical characteristics of both lakes (e.g., nutrient concentration and turbidity). We studied physical and chemical variables and performed 16S rRNA amplicon sequencing to determine the specific microbial signature of the lakes. The transparency, temperature, turbidity and concentrations of chlorophyll-a, dissolved organic matter, nutrients and the total number of cells, revealed the different status of both lakes at the time of sampling. The predominant bacterial groups in both lakes were Proteobacteria, Verrucomicrobia, and Bacteroidetes. Interestingly, the contribution of phototrophs was significantly higher in LN compared to LE (13 and 4% respectively) and the major fraction corresponded to Anoxygenic Phototrophs (AP) represented by Chloroflexi, Alpha, and Betaproteobacteria. Multivariate analyses showed that the nutrient levels and the light availability of both lakes, which finally depend on the hydrological characteristics of the respective watersheds, explain the differential community composition/function. The abundance of a diverse photoheterotrophic bacterioplankton community suggests that the ability to utilize solar energy along with organic and inorganic substrates is a key function in these oligotrophic mountain lakes.
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Affiliation(s)
| | - Guillermo Chong
- Departamento de Ciencias Geológicas, Universidad Católica de Norte, Antofagasta, Chile
| | - Antonio E Serrano
- Centro de Biotecnología, Universidad Católica del Norte, Antofagasta, Chile
| | - Mariela Guajardo
- Centro de Investigación Científica y Tecnológica para la Minería, Antofagasta, Chile
| | - Olga Encalada
- Centro de Biotecnología, Universidad Católica del Norte, Antofagasta, Chile
| | - Victor Parro
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | - Yolanda Blanco
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | - Luis Rivas
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | - Kevin C Rose
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Mercedes Moreno-Paz
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | - José A Luque
- Departamento de Ciencias Geológicas, Universidad Católica de Norte, Antofagasta, Chile.,Centro de Investigación Tecnológica del Agua en el Desierto (CEITSAZA), Universidad Católica del Norte, Antofagasta, Chile
| | - Nathalie A Cabrol
- Carl Sagan Center, SETI Institute, Mountain View, CA, United States.,Space Science Division, NASA Ames Research Center, Moffett Field, CA, United States
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Some Mixotrophic Flagellate Species Selectively Graze on Archaea. Appl Environ Microbiol 2016; 83:AEM.02317-16. [PMID: 27815273 DOI: 10.1128/aem.02317-16] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 10/31/2016] [Indexed: 11/20/2022] Open
Abstract
Many phototrophic flagellates ingest prokaryotes. This mixotrophic trait becomes a critical aspect of the microbial loop in planktonic food webs because of the typical high abundance of these flagellates. Our knowledge of their selective feeding upon different groups of prokaryotes, particularly under field conditions, is still quite limited. In this study, we investigated the feeding behavior of three species (Rhodomonas sp., Cryptomonas ovata, and Dinobryon cylindricum) via their food vacuole content in field populations of a high mountain lake. We used the catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) protocol with probes specific for the domain Archaea and three groups of Eubacteria: Betaproteobacteria, Actinobacteria, and Cytophaga-Flavobacteria of Bacteroidetes Our results provide field evidence that contrasting selective feeding exists between coexisting mixotrophic flagellates under the same environmental conditions and that some prokaryotic groups may be preferentially impacted by phagotrophic pressure in aquatic microbial food webs. In our study, Archaea were the preferred prey, chiefly in the case of Rhodomonas sp., which rarely fed on any other prokaryotic group. In general, prey selection did not relate to prey size among the grazed groups. However, Actinobacteria, which were clearly avoided, mostly showed a size of <0.5 μm, markedly smaller than cells from the other groups. IMPORTANCE That mixotrophic flagellates are not randomly feeding in the main prokaryotic groups under field conditions is a pioneer finding in species-specific behavior that paves the way for future studies according to this new paradigm. The particular case that Archaea were preferentially affected in the situation studied shows that phagotrophic pressure cannot be disregarded when considering the distribution of this group in freshwater oligotrophic systems.
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Hernández KL, Yannicelli B, Olsen LM, Dorador C, Menschel EJ, Molina V, Remonsellez F, Hengst MB, Jeffrey WH. Microbial Activity Response to Solar Radiation across Contrasting Environmental Conditions in Salar de Huasco, Northern Chilean Altiplano. Front Microbiol 2016; 7:1857. [PMID: 27920763 PMCID: PMC5118629 DOI: 10.3389/fmicb.2016.01857] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 11/04/2016] [Indexed: 11/13/2022] Open
Abstract
In high altitude environments, extreme levels of solar radiation and important differences of ionic concentrations over narrow spatial scales may modulate microbial activity. In Salar de Huasco, a high-altitude wetland in the Andean mountains, the high diversity of microbial communities has been characterized and associated with strong environmental variability. Communities that differed in light history and environmental conditions, such as nutrient concentrations and salinity from different spatial locations, were assessed for bacterial secondary production (BSP, 3H-leucine incorporation) response from short-term exposures to solar radiation. We sampled during austral spring seven stations categorized as: (a) source stations, with recently emerged groundwater (no-previous solar exposure); (b) stream running water stations; (c) stations connected to source waters but far downstream from source points; and (d) isolated ponds disconnected from ground sources or streams with a longer isolation and solar exposure history. Very high values of 0.25 μE m-2 s-1, 72 W m-2 and 12 W m-2 were measured for PAR, UVA, and UVB incident solar radiation, respectively. The environmental factors measured formed two groups of stations reflected by principal component analyses (near to groundwater sources and isolated systems) where isolated ponds had the highest BSP and microbial abundance (35 microalgae taxa, picoeukaryotes, nanoflagellates, and bacteria) plus higher salinities and PO43- concentrations. BSP short-term response (4 h) to solar radiation was measured by 3H-leucine incorporation under four different solar conditions: full sun, no UVB, PAR, and dark. Microbial communities established in waters with the longest surface exposure (e.g., isolated ponds) had the lowest BSP response to solar radiation treatments, and thus were likely best adapted to solar radiation exposure contrary to ground source waters. These results support our light history (solar exposure) hypothesis where the more isolated the community is from ground water sources, the better adapted it is to solar radiation. We suggest that factors other than solar radiation (e.g., salinity, PO43-, NO3-) are also important in determining microbial productivity in heterogeneous environments such as the Salar de Huasco.
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Affiliation(s)
- Klaudia L Hernández
- Centro de Investigación Marina Quintay CIMARQ, Facultad de Ecología y Recursos Naturales, Universidad Andres BelloSantiago, Chile; Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de ChileValdivia, Chile
| | - Beatriz Yannicelli
- Centro de Estudios Avanzados en Zonas AridasLa Serena, Chile; Facultad de Ciencias del Mar, Universidad Católica del NorteCoquimbo, Chile; Ecology and Sustainable Management of Oceanic Islands, Universidad Católica del Norte, CoquimboCoquimbo, Chile; Centro Universitario de la Región Este, Universidad de la RepúblicaRocha, Uruguay
| | | | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional and Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de AntofagastaAntofagasta, Chile; Centro de Biotecnología y BioingenieríaSantiago, Chile
| | - Eduardo J Menschel
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de ChileValdivia, Chile; Programa de Postgrado en Oceanografía, Departamento de Oceanografía, Universidad de ConcepciónConcepción, Chile; Centro de Investigación Dinámica de Ecosistemas Marinos de Altas Latitudes (FONDAP-IDEAL), Universidad Austral de ChileValdivia-Punta Arenas, Chile
| | - Verónica Molina
- Departamento de Biología, Observatorio de Ecología Microbiana, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha Valparaíso, Chile
| | - Francisco Remonsellez
- Laboratorio de Microbiología Aplicada y Extremófilos, Departamento de Ingeniería Química, Universidad Católica del Norte Antofagasta, Chile
| | - Martha B Hengst
- Centro de Biotecnología y BioingenieríaSantiago, Chile; Departamento de Ciencias Farmacéuticas, Facultad de Ciencias, Universidad Católica del NorteAntofagasta, Chile
| | - Wade H Jeffrey
- Center for Environmental Diagnostics and Bioremediation, University of West Florida, Pensacola FL, USA
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Logue JB, Findlay SEG, Comte J. Editorial: Microbial Responses to Environmental Changes. Front Microbiol 2015; 6:1364. [PMID: 26696977 PMCID: PMC4667068 DOI: 10.3389/fmicb.2015.01364] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 11/17/2015] [Indexed: 12/03/2022] Open
Affiliation(s)
- Jürg B Logue
- Aquatic Ecology, Department of Biology, Lund University Lund, Sweden ; Science for Life Laboratory Stockholm, Sweden
| | | | - Jérôme Comte
- Département de Biologie, Centre d'études Nordiques - Takuvik and Institut de Biologie Intégrative et des Systèmes, Université Laval Québec, QC, Canada
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Gasol JM, Morán XAG. Flow Cytometric Determination of Microbial Abundances and Its Use to Obtain Indices of Community Structure and Relative Activity. SPRINGER PROTOCOLS HANDBOOKS 2015. [DOI: 10.1007/8623_2015_139] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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