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Cubillos CF, Aguilar P, Moreira D, Bertolino P, Iniesto M, Dorador C, López-García P. Exploring the prokaryote-eukaryote interplay in microbial mats from an Andean athalassohaline wetland. Microbiol Spectr 2024; 12:e0007224. [PMID: 38456669 DOI: 10.1128/spectrum.00072-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 01/28/2024] [Indexed: 03/09/2024] Open
Abstract
Microbial community assembly results from the interaction between biotic and abiotic factors. However, environmental selection is thought to predominantly shape communities in extreme ecosystems. Salar de Huasco, situated in the high-altitude Andean Altiplano, represents a poly-extreme ecosystem displaying spatial gradients of physicochemical conditions. To disentangle the influence of abiotic and biotic factors, we studied prokaryotic and eukaryotic communities from microbial mats and underlying sediments across contrasting areas of this athalassohaline ecosystem. The prokaryotic communities were primarily composed of bacteria, notably including a significant proportion of photosynthetic organisms like Cyanobacteria and anoxygenic photosynthetic members of Alpha- and Gammaproteobacteria and Chloroflexi. Additionally, Bacteroidetes, Verrucomicrobia, and Deltaproteobacteria were abundantly represented. Among eukaryotes, photosynthetic organisms (Ochrophyta and Archaeplastida) were predominant, alongside relatively abundant ciliates, cercozoans, and flagellated fungi. Salinity emerged as a key driver for the assembly of prokaryotic communities. Collectively, abiotic factors influenced both prokaryotic and eukaryotic communities, particularly those of algae. However, prokaryotic communities strongly correlated with photosynthetic eukaryotes, suggesting a pivotal role of biotic interactions in shaping these communities. Co-occurrence networks suggested potential interactions between different organisms, such as diatoms with specific photosynthetic and heterotrophic bacteria or with protist predators, indicating influences beyond environmental selection. While some associations may be explained by environmental preferences, the robust biotic correlations, alongside insights from other ecosystems and experimental studies, suggest that symbiotic and trophic interactions significantly shape microbial mat and sediment microbial communities in this athalassohaline ecosystem.IMPORTANCEHow biotic and abiotic factors influence microbial community assembly is still poorly defined. Here, we explore their influence on prokaryotic and eukaryotic community assembly within microbial mats and sediments of an Andean high-altitude polyextreme wetland system. We show that, in addition to abiotic elements, mutual interactions exist between prokaryotic and eukaryotic communities. Notably, photosynthetic eukaryotes exhibit a strong correlation with prokaryotic communities, specifically diatoms with certain bacteria and other protists. Our findings underscore the significance of biotic interactions in community assembly and emphasize the necessity of considering the complete microbial community.
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Affiliation(s)
- Carolina F Cubillos
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Pablo Aguilar
- Laboratorio de Complejidad Microbiana, Instituto Antofagasta and Centro de Bioingeniería y Biotecnología (CeBiB), Universidad de Antofagasta, Antofagasta, Chile
- Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
- Millennium Nucleus of Austral Invasive Salmonids - INVASAL, Concepción, Chile
| | - David Moreira
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Paola Bertolino
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Miguel Iniesto
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana, Instituto Antofagasta and Centro de Bioingeniería y Biotecnología (CeBiB), Universidad de Antofagasta, Antofagasta, Chile
- Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
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Acosta E, Nitsche F, Dorador C, Arndt H. Protist communities of microbial mats from the extreme environments of five saline Andean lagoons at high altitudes in the Atacama Desert. Front Microbiol 2024; 15:1356977. [PMID: 38572231 PMCID: PMC10987879 DOI: 10.3389/fmicb.2024.1356977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 02/08/2024] [Indexed: 04/05/2024] Open
Abstract
Introduction Heterotrophic protists colonizing microbial mats have received little attention over the last few years, despite their importance in microbial food webs. A significant challenge originates from the fact that many protists remain uncultivable and their functions remain poorly understood. Methods Metabarcoding studies of protists in microbial mats across high-altitude lagoons of different salinities (4.3-34 practical salinity units) were carried out to provide insights into their vertical stratification at the millimeter scale. DNA and cDNA were analyzed for selected stations. Results Sequence variants classified as the amoeboid rhizarian Rhogostoma and the ciliate Euplotes were found to be common members of the heterotrophic protist communities. They were accompanied by diatoms and kinetoplastids. Correlation analyses point to the salinity of the water column as a main driver influencing the structure of the protist communities at the five studied microbial mats. The active part of the protist communities was detected to be higher at lower salinities (<20 practical salinity units). Discussion We found a restricted overlap of the protist community between the different microbial mats indicating the uniqueness of these different aquatic habitats. On the other hand, the dominating genotypes present in metabarcoding were similar and could be isolated and sequenced in comparative studies (Rhogostoma, Euplotes, Neobodo). Our results provide a snapshot of the unculturable protist diversity thriving the benthic zone of five athalossohaline lagoons across the Andean plateau.
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Affiliation(s)
- Eduardo Acosta
- Department of General Ecology, Institute of Zoology, University of Cologne, Cologne, Germany
| | - Frank Nitsche
- Department of General Ecology, Institute of Zoology, University of Cologne, Cologne, Germany
| | - Cristina Dorador
- Department of Biotechnology, Universidad de Antofagasta, Antofagasta, Chile
- Centre for Biotechnology and Bioengineering (CeBiB), Universidad de Antofagasta, Antofagasta, Chile
| | - Hartmut Arndt
- Department of General Ecology, Institute of Zoology, University of Cologne, Cologne, Germany
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Berg G, Dorador C, Egamberdieva D, Kostka JE, Ryu CM, Wassermann B. Shared governance in the plant holobiont and implications for one health. FEMS Microbiol Ecol 2024; 100:fiae004. [PMID: 38364305 PMCID: PMC10876113 DOI: 10.1093/femsec/fiae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/30/2023] [Accepted: 02/12/2024] [Indexed: 02/18/2024] Open
Abstract
The holobiont Holobiont theory is more than 80 years old, while the importance of microbial communities for plant holobionts was already identified by Lorenz Hiltner more than a century ago. Both concepts are strongly supported by results from the new field of microbiome research. Here, we present ecological and genetic features of the plant holobiont that underpin principles of a shared governance between hosts and microbes and summarize the relevance of plant holobionts in the context of global change. Moreover, we uncover knowledge gaps that arise when integrating plant holobionts in the broader perspective of the holobiome as well as one and planetary health concepts. Action is needed to consider interacting holobionts at the holobiome scale, for prediction and control of microbiome function to improve human and environmental health outcomes.
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Affiliation(s)
- Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, 8010 Graz, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Cristina Dorador
- Department of Biotechnology, Universidad de Antofagasta & Centre for Biotechnology and Bioengineering (CeBiB), Angamos 601, Antofagasta, Chile
| | - Dilfuza Egamberdieva
- Institute of Fundamental and Applied Research, National Research University, TIIAME, Kari Niyazi street 39, Tashkent 100000, Uzbekistan
- Medical School, Central Asian University, Milliy bog street 264, Tashkent 111221, Uzbekistan
| | - Joel E Kostka
- Schools of Biological Sciences and Earth & Atmospheric Sciences, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30332, United States
| | - Choong-Min Ryu
- Biosystems and Bioengineering, University of Science and Technology KRIBB School, 125 Gwahangro, Yuseong, Daejeon 34141, South Korea
- Molecular Phytobacteriology Laboratory, Infectious Disease Research Center, KRIBB, 125 Gwahangro, Yuseong, Daejeon 34141, South Korea
| | - Birgit Wassermann
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, 8010 Graz, Austria
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Arias D, Saldaña M, Botero YL, Dinamarca F, Paredes B, Salazar-Ardiles C, Andrade DC, Cisternas LA, Carrasco J, Santos C, Dorador C, Gómez-Silva B. Exploring the potential of the halotolerant bacterial strain Bacillus subtilis LN8B as an ecofriendly sulfide collector for seawater flotation. J Appl Microbiol 2024; 135:lxad313. [PMID: 38126104 DOI: 10.1093/jambio/lxad313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/12/2023] [Accepted: 12/19/2023] [Indexed: 12/23/2023]
Abstract
AIM To assess the effectiveness of Bacillus subtilis strain LN8B as a biocollector for recovering pyrite (Py) and chalcopyrite (CPy) in both seawater (Sw) and deionized water (Dw), and to explore the underlying adhesion mechanism in these bioflotation experiments. MATERIALS AND METHODS The bioflotation test utilized B. subtilis strain LN8B as the biocollector through microflotation experiments. Additionally, frother methyl isobutyl carbinol (MIBC) and conventional collector potassium amyl xanthate (PAX) were introduced in some experiments. The zeta potential (ZP) and Fourier-transform infrared spectroscopy (FTIR) was employed to explore the adhesion mechanism of Py and CPy interacting with the biocollector in Sw and Dw. The adaptability of the B. subtilis strain to different water types and salinities was assessed through growth curves measuring optical density. Finally, antibiotic susceptibility tests were conducted to evaluate potential risks of the biocollector. RESULTS Superior outcomes were observed in Sw where Py and CPy recovery was ∼39.3% ± 7.7% and 41.1% ± 5.8%, respectively, without microorganisms' presence. However, B. subtilis LN8B potentiate Py and CPy recovery, reaching 72.8% ± 4.9% and 84.6% ± 1.5%, respectively. When MIBC was added, only the Py recovery was improved (89.4% ± 3.6%), depicting an adverse effect for CPy (81.8% ± 1.1%). ZP measurements indicated increased mineral surface hydrophobicity when Py and CPy interacted with the biocollector in both Sw and Dw. FTIR revealed the presence of protein-related amide peaks, highlighting the hydrophobic nature of the bacterium. The adaptability of this strain to diverse water types and salinities was assessed, demonstrating remarkable growth versatility. Antibiotic susceptibility tests indicated that B. subtilis LN8B was susceptible to 23 of the 25 antibiotics examined, suggesting it poses minimal environmental risks. CONCLUSIONS The study substantiates the biotechnological promise of B. subtilis strain LN8B as an efficient sulfide collector for promoting cleaner mineral production. This effectiveness is attributed to its ability to induce mineral surface hydrophobicity, a result of the distinct characteristics of proteins within its cell wall.
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Affiliation(s)
- Dayana Arias
- Laboratory of Molecular Biology and Applied Microbiology, Research Center in High Altitude Medicine and Physiology, Biomedical Department, Faculty of Health Science, Universidad de Antofagasta, Av. Angamos 601, Antofagasta 1270300, Chile
| | - Manuel Saldaña
- Faculty of Engineering and Architecture, Arturo Prat University, Iquique 1110939, Chile
| | - Yesica L Botero
- Departamento de Ingeniería Química y Procesos de Minerales, Universidad de Antofagasta, Av. Angamos 601, Antofagasta 1270300, Chile
| | - Francisco Dinamarca
- Biochemistry Lab., Biomedical Dept., Health Sciences Faculty and Centre for Biotechnology and Bioengineering (CeBiB), Universidad de Antofagasta, Av. Angamos 601, Antofagasta 1270300, Chile
| | - Bernardo Paredes
- Biochemistry Lab., Biomedical Dept., Health Sciences Faculty and Centre for Biotechnology and Bioengineering (CeBiB), Universidad de Antofagasta, Av. Angamos 601, Antofagasta 1270300, Chile
| | - Camila Salazar-Ardiles
- Laboratory of Molecular Biology and Applied Microbiology, Research Center in High Altitude Medicine and Physiology, Biomedical Department, Faculty of Health Science, Universidad de Antofagasta, Av. Angamos 601, Antofagasta 1270300, Chile
| | - David C Andrade
- Exercise Applied Physiology Laboratory, Research Center in High Altitude Medicine and Physiology, Biomedical Department, Faculty of Health Science, Universidad de Antofagasta, Av. Angamos 601, Antofagasta 1270300, Chile
| | - Luis A Cisternas
- Departamento de Ingeniería Química y Procesos de Minerales, Universidad de Antofagasta, Av. Angamos 601, Antofagasta 1270300, Chile
| | - Jorge Carrasco
- Departamento de Ingeniería en Minas, Facultad de Ingeniería, Universidad de Antofagasta, Av. Angamos 601, Antofagasta 1270300, Chile
| | - Carlos Santos
- Departamento de Ingeniería en Minas, Facultad de Ingeniería, Universidad de Antofagasta, Av. Angamos 601, Antofagasta 1270300, Chile
| | - Cristina Dorador
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources and Centre for Biotechnology and Bioengineering (CeBiB), Universidad de Antofagasta, Av. Angamos 601, Antofagasta 1270300, Chile
| | - Benito Gómez-Silva
- Biochemistry Lab., Biomedical Dept., Health Sciences Faculty and Centre for Biotechnology and Bioengineering (CeBiB), Universidad de Antofagasta, Av. Angamos 601, Antofagasta 1270300, Chile
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Nitsche F, Carduck S, von Ameln J, Mach N, Dorador C, Predel R, Rueckert S, Arndt H. Gregarines from darkling beetles of the Atacama Desert, Atacamagregarina paposa gen. et sp. nov. from Scotobius and Xiphocephalus ovatus sp. nov. from Psectrascelis (Coleoptera, Tenebrionidae). Eur J Protistol 2023; 90:126008. [PMID: 37536234 DOI: 10.1016/j.ejop.2023.126008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 07/06/2023] [Accepted: 07/08/2023] [Indexed: 08/05/2023]
Abstract
Gregarine apicomplexans, a group of single celled organisms, inhabit the extracellular spaces of most invertebrate species. The nature of the gregarine-host interactions is not yet fully resolved, mutualistic, commensal and parasitic life forms have been recorded. In the extreme arid environment of the Atacama Desert, only a few groups of invertebrates hosting gregarines such as darkling beetles (Tenebrionidae) were able to adapt, providing an unparalleled opportunity to study co-evolutionary diversification. Here, we describe one novel gregarine genus comprising one species, Atacamagregarina paposa gen. et sp. nov., and a new species, Xiphocephalus ovatus sp. nov. (Apicomplexa: Eugregarinoridea, Stylocephalidae), found in the tenebrionid beetle genera Scotobius (Tenebrioninae, Scotobiini) and Psectrascelis intricaticollis ovata (Pimeliinae, Nycteliini), respectively. In the phylogenetic analysis based on SSU rDNA, Atacamgregarina paposa representing the new genus is basal, forming a separate clade with terrestrial gregarines specific for North American darkling beetles.
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Affiliation(s)
- Frank Nitsche
- Institute of Zoology, Biocenter Cologne, University of Cologne, Zuelpicher Strasse 47b, 50674 Cologne, Germany.
| | - Sarah Carduck
- Institute of Zoology, Biocenter Cologne, University of Cologne, Zuelpicher Strasse 47b, 50674 Cologne, Germany
| | - Joshua von Ameln
- Institute of Zoology, Biocenter Cologne, University of Cologne, Zuelpicher Strasse 47b, 50674 Cologne, Germany
| | - Niclas Mach
- Institute of Zoology, Biocenter Cologne, University of Cologne, Zuelpicher Strasse 47b, 50674 Cologne, Germany
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Universidad de Antofagasta, Avenida Angamos 601, Antofagasta, Chile
| | - Reinhard Predel
- Institute of Zoology, Biocenter Cologne, University of Cologne, Zuelpicher Strasse 47b, 50674 Cologne, Germany
| | - Sonja Rueckert
- School of Applied Sciences, Edinburgh Napier University, Sighthill Campus, Edinburgh EH11 4BN, Scotland, UK; Faculty of Biology, Eukaryotic Microbiology, University of Duisburg-Essen, 45141 Essen, Germany
| | - Hartmut Arndt
- Institute of Zoology, Biocenter Cologne, University of Cologne, Zuelpicher Strasse 47b, 50674 Cologne, Germany.
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Corona Ramirez A, Bregnard D, Junier T, Cailleau G, Dorador C, Bindschedler S, Junier P. Assessment of fungal spores and spore-like diversity in environmental samples by targeted lysis. BMC Microbiol 2023; 23:68. [PMID: 36918804 PMCID: PMC10015814 DOI: 10.1186/s12866-023-02809-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 03/01/2023] [Indexed: 03/15/2023] Open
Abstract
At particular stages during their life cycles, fungi use multiple strategies to form specialized structures to survive unfavorable environmental conditions. These strategies encompass sporulation, as well as cell-wall melanization, multicellular tissue formation or even dimorphism. The resulting structures are not only used to disperse to other environments, but also to survive long periods of time awaiting favorable growth conditions. As a result, these specialized fungal structures are part of the microbial seed bank, which is known to influence the microbial community composition and contribute to the maintenance of diversity. Despite the importance of the microbial seed bank in the environment, methods to study the diversity of fungal structures with improved resistance only target spores dispersing in the air, omitting the high diversity of these structures in terms of morphology and environmental distribution. In this study, we applied a separation method based on cell lysis to enrich lysis-resistant fungal structures (for instance, spores, sclerotia, melanized yeast) to obtain a proxy of the composition of the fungal seed bank. This approach was first evaluated in-vitro in selected species. The results obtained showed that DNA from fungal spores and from yeast was only obtained after the application of the enrichment method, while mycelium was always lysed. After validation, we compared the diversity of the total and lysis-resistant fractions in the polyextreme environment of the Salar de Huasco, a high-altitude athalassohaline wetland in the Chilean Altiplano. Environmental samples were collected from the salt flat and from microbial mats in small surrounding ponds. Both the lake sediments and microbial mats were dominated by Ascomycota and Basidiomycota, however, the diversity and composition of each environment differed at lower taxonomic ranks. Members of the phylum Chytridiomycota were enriched in the lysis-resistant fraction, while members of the phylum Rozellomycota were never detected in this fraction. Moreover, we show that the community composition of the lysis-resistant fraction reflects the diversity of life cycles and survival strategies developed by fungi in the environment. To the best of our knowledge this is the first time that the fungal diversity is explored in the Salar de Huasco. In addition, the method presented here provides a simple and culture independent approach to assess the diversity of fungal lysis-resistant cells in the environment.
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Affiliation(s)
- Andrea Corona Ramirez
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Danaé Bregnard
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Thomas Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
- Vital-IT Group, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Guillaume Cailleau
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Cristina Dorador
- Department of Biotechnology, University of Antofagasta, Antofagasta, Chile
| | - Saskia Bindschedler
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland.
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Arias D, Salazar-Ardiles C, Andrade DC, Rivas M, Panico A, Race M, Cisternas LA, Dorador C. The microbial world in copper sulfide flotation plants (CSFP): Novel insights into bacterial communities and their application as potential pyrite bioreagents. Environ Res 2023; 218:114904. [PMID: 36502904 DOI: 10.1016/j.envres.2022.114904] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/10/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Operations in copper sulfide flotation plants (CSFP) are complex and governed by several variables such as available technologies, reagents, and environmental conditions. However, few investigations are related to studying the microbial communities. These aspects provide a reason to compare the bacterial communities of two CSFP operated with freshwater (FwFlo) and seawater (SwFlo), and study whether indigenous bacteria could be used as pyrite bioreagents. Analyses were determined through next-generation sequencing by Illumina MiSeq System and conducted throughout the entire process: (i) minerals before and after grinding; (ii) final concentrate and concentrate thickener overflow; (iii) final tailings and tailings thickener overflow; and (iv) intake water. Bacterial strains from both plants were tested as potential bioreagents, given their tendency to adhere to pyrite after 5 min. In both CSFP, Proteobacteria (relative abundance from 45.48% to 79.22%), followed by Bacteroidetes (9.37%-44.7%), were the most abundant phyla. Regarding species, Algoriphagus olei (11.35%-43.52%) was present exclusively in FwFlo samples in contact with process water and absent in the mineral before grinding, where Cupriavidus metallidurans (16.05%) and Pseudomonas_uc (11.79%) predominated. In SwFlo samples, Marinobacter flavimaris (3.47%-41.1%), and GU061212-s (10.92%-27.63%), were the most abundant microorganisms. All of them were also detected in intake seawater. The strains with the highest adhesion rate (from 29.84% ± 0.14-100%) were phylogenetically identified as species of the genera Marinobacter, Pseudomonas, Idiomarina, Halomonas, Bacillus, Aerocuccus, and Peribacillus. Our results reveal that bacterial communities are critically dependent on process waters during mining activities, and our data depicted that indigenous bacteria could be used as potential pyrite bioreagents, evidenced by a high adhesion rate. It is thus possible to propose that different indigenous bacterial strains could be considered as new bioreagents to reduce the impact of conventional flotation reagents on health from an environment friendly perspective.
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Affiliation(s)
- Dayana Arias
- Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Av. Angamos 601, Antofagasta, Chile.
| | - Camila Salazar-Ardiles
- Departamento Tecnología Médica, Facultad de Ciencias de Salud, Universidad de Antofagasta, Av. Angamos 601, Antofagasta, Chile; Centro de Investigación en Fisiología y Medicina de Altura, Departamento Biomédico, Facultad de Ciencias de la Salud, Universidad de Antofagasta, Av. Angamos 601, Antofagasta, Chile
| | - David C Andrade
- Centro de Investigación en Fisiología y Medicina de Altura, Departamento Biomédico, Facultad de Ciencias de la Salud, Universidad de Antofagasta, Av. Angamos 601, Antofagasta, Chile
| | - Mariella Rivas
- Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Av. Angamos 601, Antofagasta, Chile
| | - Antonio Panico
- Department of Engineering, University of Campania L. Vanvitelli, 81031, Aversa, Italy
| | - Marco Race
- Department of Civil and Mechanical Engineering, University of Cassino and Southern Lazio, Via di Biasio 43, 03043, Cassino, Italy
| | - Luis A Cisternas
- Departamento de Ingeniería Química y Procesos de Minerales, Universidad de Antofagasta, Av. Angamos 601, Antofagasta, Chile
| | - Cristina Dorador
- Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Av. Angamos 601, Antofagasta, Chile
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Zárate A, Molina V, Valdés J, Icaza G, Vega SE, Castillo A, Ugalde JA, Dorador C. Spatial co-occurrence patterns of benthic microbial assemblage in response to trace metals in the Atacama Desert Coastline. Front Microbiol 2023; 13:1020491. [PMID: 36726571 PMCID: PMC9885135 DOI: 10.3389/fmicb.2022.1020491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 12/31/2022] [Indexed: 01/17/2023] Open
Abstract
Taxonomic and functional microbial communities may respond differently to anthropogenic coastal impacts, but ecological quality monitoring assessments using environmental DNA and RNA (eDNA/eRNA) in response to pollution are poorly understood. In the present study, we investigated the utility of the co-occurrence network approach's to comprehensively explore both structure and potential functions of benthic marine microbial communities and their responses to Cu and Fe fractioning from two sediment deposition coastal zones of northern Chile via 16S rRNA gene metabarcoding. The results revealed substantial differences in the microbial communities, with the predominance of two distinct module hubs based on study zone. This indicates that habitat influences microbial co-occurrence networks. Indeed, the discriminant analysis allowed us to identify keystone taxa with significant differences in eDNA and eRNA comparison between sampled zones, revealing that Beggiatoaceae, Carnobacteriaceae, and Nitrosococcaceae were the primary representatives from Off Loa, whereas Enterobacteriaceae, Corynebacteriaceae, Latescibacteraceae, and Clostridiaceae were the families responsible for the observed changes in Mejillones Bay. The quantitative evidence from the multivariate analyses supports that the benthic microbial assemblages' features were linked to specific environments associated with Cu and Fe fractions, mainly in the Bay. Furthermore, the predicted functional microbial structure suggested that transporters and DNA repair allow the communities to respond to metals and endure the interacting variable environmental factors like dissolved oxygen, temperature, and salinity. Moreover, some active taxa recovered are associated with anthropogenic impact, potentially harboring antibiotic resistance and other threats in the coastal zone. Overall, the method of scoping eRNA in parallel with eDNA applied here has the capacity to significantly enhance the spatial and functional understanding of real-time microbial assemblages and, in turn, would have the potential to increase the acuity of biomonitoring programs key to responding to immediate management needs for the marine environment.
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Affiliation(s)
- Ana Zárate
- Doctorado en Ciencias Aplicadas mención Sistemas Marinos Costeros, Universidad de Antofagasta, Antofagasta, Chile,Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta and Centro de Bioingeniería y Biotecnología (CeBiB), Universidad de Antofagasta, Antofagasta, Chile,Laboratorio de Biotecnología en Ambientes Extremos, Centro de Excelencia en Medicina Traslacional, Universidad de la Frontera, Temuco, Chile,*Correspondence: Ana Zárate, ✉
| | - Verónica Molina
- Departamento de Ciencias y Geografía, Facultad de Ciencias Naturales y Exactas y HUB Ambiental UPLA, Universidad de Playa Ancha, Valparaíso, Chile,Centro de Investigación Oceanográfica COPAS COASTAL, Universidad de Concepción, Concepción, Chile,Verónica Molina, ✉
| | - Jorge Valdés
- Laboratorio de Sedimentología y Paleoambientes, Facultad de Ciencias del Mar y de Recursos Biológicos, Instituto de Ciencias Naturales A. von Humboldt, Universidad de Antofagasta, Antofagasta, Chile
| | - Gonzalo Icaza
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta and Centro de Bioingeniería y Biotecnología (CeBiB), Universidad de Antofagasta, Antofagasta, Chile
| | | | - Alexis Castillo
- Centro de Investigación y Estudios Avanzados del Maule, Vicerrectoría de Investigación de Investigación y Posgrado, Universidad Católica del Maule, Campus San Miguel, Talca, Chile,J’EAI CHARISMA (IRD-France, UMNG-Colombia, UA-Chile, UCM-Chile, UCH-Chile, IGP-Peru, UPCH-Peru) and Nucleo Milenio UPWELL, Concepción, Chile
| | - Juan A. Ugalde
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta and Centro de Bioingeniería y Biotecnología (CeBiB), Universidad de Antofagasta, Antofagasta, Chile,Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile,Cristina Dorador, ✉
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9
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Eissler Y, Castillo-Reyes A, Dorador C, Cornejo-D'Ottone M, Celis-Plá PSM, Aguilar P, Molina V. Virus-to-prokaryote ratio in the Salar de Huasco and different ecosystems of the Southern hemisphere and its relationship with physicochemical and biological parameters. Front Microbiol 2022; 13:938066. [PMID: 36060762 PMCID: PMC9434117 DOI: 10.3389/fmicb.2022.938066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/31/2022] [Indexed: 11/13/2022] Open
Abstract
The virus-to-prokaryote ratio (VPR) has been used in many ecosystems to study the relationship between viruses and their hosts. While high VPR values indicate a high rate of prokaryotes' cell lysis, low values are interpreted as a decrease in or absence of viral activity. Salar de Huasco is a high-altitude wetland characterized by a rich microbial diversity associated with aquatic sites like springs, ponds, streams and a lagoon with variable physicochemical conditions. Samples from two ponds, Poza Rosada (PR) and Poza Verde (PV), were analyzed by epifluorescence microscopy to determine variability of viral and prokaryotic abundance and to calculate the VPR in a dry season. In addition, to put Salar de Huasco results into perspective, a compilation of research articles on viral and prokaryotic abundance, VPR, and metadata from various Southern hemisphere ecosystems was revised. The ecosystems were grouped into six categories: high-altitude wetlands, Pacific, Atlantic, Indian, and Southern Oceans and Antarctic lakes. Salar de Huasco ponds recorded similar VPR values (an average of 7.4 and 1.7 at PR and PV, respectively), ranging from 3.22 to 15.99 in PR. The VPR variability was associated with VA and chlorophyll a, when considering all data available for this ecosystem. In general, high-altitude wetlands recorded the highest VPR average (53.22 ± 95.09), followed by the Oceans, Southern (21.91 ± 25.72), Atlantic (19.57 ± 15.77) and Indian (13.43 ± 16.12), then Antarctic lakes (11.37 ± 15.82) and the Pacific Ocean (6.34 ± 3.79). Physicochemical variables, i.e., temperature, conductivity, nutrients (nitrate, ammonium, and phosphate) and chlorophyll a as a biological variable, were found to drive the VPR in the ecosystems analyzed. Thus, the viral activity in the Wetland followed similar trends of previous reports based on larger sets of metadata analyses. In total, this study highlights the importance of including viruses as a biological variable to study microbial temporal dynamics in wetlands considering their crucial role in the carbon budgets of these understudied ecosystems in the southern hemisphere.
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Affiliation(s)
- Yoanna Eissler
- Instituto de Química y Bioquímica, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
- *Correspondence: Yoanna Eissler
| | - Alonso Castillo-Reyes
- Escuela de Biología Marina, Facultad de Ciencias del Mar y de Recursos Naturales, Universidad de Valparaíso, Viña del Mar, 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, Antofagasta, Chile
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Santiago, Chile
| | - Marcela Cornejo-D'Ottone
- Escuela de Ciencias del Mar e Instituto Milenio de Oceanografía, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Paula S. M. Celis-Plá
- Laboratory of Aquatic Environmental Research, Centro de Estudios Avanzados, Universidad de Playa Ancha, Viña del Mar, Chile
- HUB Ambiental UPLA, Universidad de Playa Ancha, Valparaíso, Chile
| | - Polette Aguilar
- HUB Ambiental UPLA, Universidad de Playa Ancha, Valparaíso, Chile
| | - Verónica Molina
- HUB Ambiental UPLA, Universidad de Playa Ancha, Valparaíso, Chile
- Departamento de Ciencias y Geografía, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Valparaíso, Chile
- Centro de Investigación Oceanográfica COPAS COASTAL, Universidad de Concepción, Concepción, Chile
- Verónica Molina
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10
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Zadjelovic V, Erni-Cassola G, Obrador-Viel T, Lester D, Eley Y, Gibson MI, Dorador C, Golyshin PN, Black S, Wellington EMH, Christie-Oleza JA. A mechanistic understanding of polyethylene biodegradation by the marine bacterium Alcanivorax. J Hazard Mater 2022; 436:129278. [PMID: 35739790 DOI: 10.1016/j.jhazmat.2022.129278] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 05/19/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Polyethylene (PE) is one of the most recalcitrant carbon-based synthetic materials produced and, currently, the most ubiquitous plastic pollutant found in nature. Over time, combined abiotic and biotic processes are thought to eventually breakdown PE. Despite limited evidence of biological PE degradation and speculation that hydrocarbon-degrading bacteria found within the plastisphere is an indication of biodegradation, there is no clear mechanistic understanding of the process. Here, using high-throughput proteomics, we investigated the molecular processes that take place in the hydrocarbon-degrading marine bacterium Alcanivorax sp. 24 when grown in the presence of low density PE (LDPE). As well as efficiently utilising and assimilating the leachate of weathered LDPE, the bacterium was able to reduce the molecular weight distribution (Mw from 122 to 83 kg/mol) and overall mass of pristine LDPE films (0.9 % after 34 days of incubation). Most interestingly, Alcanivorax acquired the isotopic signature of the pristine plastic and induced an extensive array of metabolic pathways for aliphatic compound degradation. Presumably, the primary biodegradation of LDPE by Alcanivorax sp. 24 is possible via the production of extracellular reactive oxygen species as observed both by the material's surface oxidation and the measurement of superoxide in the culture with LDPE. Our findings confirm that hydrocarbon-biodegrading bacteria within the plastisphere may in fact have a role in degrading PE.
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Affiliation(s)
- Vinko Zadjelovic
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK.
| | - Gabriel Erni-Cassola
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK; Program Man-Society-Environment (MGU), University of Basel, 4051 Basel, Switzerland
| | - Theo Obrador-Viel
- Department of Biology, University of the Balearic Islands, Palma 07122, Spain
| | - Daniel Lester
- Polymer Characterisation Research Technology Platform, University of Warwick, Coventry CV4 7AL, UK
| | - Yvette Eley
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston B15 2TT, UK
| | - Matthew I Gibson
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Chile; Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta Angamos 601, Antofagasta, Chile; Centre for Biotechnology & Bioengineering (CeBiB) Santiago, Chile
| | - Peter N Golyshin
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor LL57 2UW, UK
| | - Stuart Black
- Department of Geography and Environmental Science, University of Reading, UK
| | | | - Joseph A Christie-Oleza
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK; Department of Biology, University of the Balearic Islands, Palma 07122, Spain.
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11
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Corona Ramírez A, Cailleau G, Fatton M, Dorador C, Junier P. Diversity of Lysis-Resistant Bacteria and Archaea in the Polyextreme Environment of Salar de Huasco. Front Microbiol 2022; 13:826117. [PMID: 36687602 PMCID: PMC9847572 DOI: 10.3389/fmicb.2022.826117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/07/2022] [Indexed: 01/25/2023] Open
Abstract
The production of specialized resting cells is a remarkable strategy developed by several organisms to survive unfavorable environmental conditions. Spores are specialized resting cells that are characterized by low to absent metabolic activity and higher resistance. Spore-like cells are known from multiple groups of bacteria, which can form spores under suboptimal growth conditions (e.g., starvation). In contrast, little is known about the production of specialized resting cells in archaea. In this study, we applied a culture-independent method that uses physical and chemical lysis, to assess the diversity of lysis-resistant bacteria and archaea and compare it to the overall prokaryotic diversity (direct DNA extraction). The diversity of lysis-resistant cells was studied in the polyextreme environment of the Salar de Huasco. The Salar de Huasco is a high-altitude athalassohaline wetland in the Chilean Altiplano. Previous studies have shown a high diversity of bacteria and archaea in the Salar de Huasco, but the diversity of lysis-resistant microorganisms has never been investigated. The underlying hypothesis was that the combination of extreme abiotic conditions might favor the production of specialized resting cells. Samples were collected from sediment cores along a saline gradient and microbial mats were collected in small surrounding ponds. A significantly different diversity and composition were found in the sediment cores or microbial mats. Furthermore, our results show a high diversity of lysis-resistant cells not only in bacteria but also in archaea. The bacterial lysis-resistant fraction was distinct in comparison to the overall community. Also, the ability to survive the lysis-resistant treatment was restricted to a few groups, including known spore-forming phyla such as Firmicutes and Actinobacteria. In contrast to bacteria, lysis resistance was widely spread in archaea, hinting at a generalized resistance to lysis, which is at least comparable to the resistance of dormant cells in bacteria. The enrichment of Natrinema and Halarchaeum in the lysis-resistant fraction could hint at the production of cyst-like cells or other resistant cells. These results can guide future studies aiming to isolate and broaden the characterization of lysis-resistant archaea.
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Affiliation(s)
- Andrea Corona Ramírez
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Guillaume Cailleau
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Mathilda Fatton
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Cristina Dorador
- Department of Biotechnology, University of Antofagasta, Antofagasta, Chile
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland,*Correspondence: Pilar Junier,
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12
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Gutiérrez JS, Moore JN, Donnelly JP, Dorador C, Navedo JG, Senner NR. Climate change and lithium mining influence flamingo abundance in the Lithium Triangle. Proc Biol Sci 2022; 289:20212388. [PMID: 35259988 PMCID: PMC8905151 DOI: 10.1098/rspb.2021.2388] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The development of technologies to slow climate change has been identified as a global imperative. Nonetheless, such 'green' technologies can potentially have negative impacts on biodiversity. We explored how climate change and the mining of lithium for green technologies influence surface water availability, primary productivity and the abundance of three threatened and economically important flamingo species in the 'Lithium Triangle' of the Chilean Andes. We combined climate and primary productivity data with remotely sensed measures of surface water levels and a 30-year dataset on flamingo abundance using structural equation modelling. We found that, regionally, flamingo abundance fluctuated dramatically from year-to-year in response to variation in surface water levels and primary productivity but did not exhibit any temporal trends. Locally, in the Salar de Atacama-where lithium mining is focused-we found that mining was negatively correlated with the abundance of two of the three flamingo species. These results suggest continued increases in lithium mining and declines in surface water could soon have dramatic effects on flamingo abundance across their range. Efforts to slow the expansion of mining and the impacts of climate change are, therefore, urgently needed to benefit local biodiversity and the local human economy that depends on it.
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Affiliation(s)
- Jorge S Gutiérrez
- Conservation Biology Research Group, Department of Anatomy, Cell Biology and Zoology, University of Extremadura, Badajoz 06006, Spain.,Ecology in the Anthropocene, Associated Unit CSIC-UEx, Faculty of Sciences, University of Extremadura, Badajoz 06006, Spain
| | - Johnnie N Moore
- Group For Quantitative Study of Snow and Ice, Department of Geosciences, University of Montana, 32 Campus Drive, Missoula, MT 59812, USA
| | - J Patrick Donnelly
- Intermountain West Joint Venture, US Fish and Wildlife Service, 1001 S. Higgins Avenue, Missoula, MT 59801, USA
| | - Cristina Dorador
- Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Angamos 601, Antofagasta, Chile
| | - Juan G Navedo
- Ecology in the Anthropocene, Associated Unit CSIC-UEx, Faculty of Sciences, University of Extremadura, Badajoz 06006, Spain.,Bird Ecology Lab, Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Campus Isla Teja, Valdivia, Chile
| | - Nathan R Senner
- Department of Biological Sciences, University of South Carolina, 715 Sumter Street, Columbia, SC 29208, USA
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13
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Guzmán Salas S, Weber A, Malci A, Lin X, Herrera-Molina R, Cerpa W, Dorador C, Signorelli J, Zamorano P. The metabolite p-cresol impairs dendritic development, synaptogenesis and synapse function in hippocampal neurons: Implications for autism spectrum disorder. J Neurochem 2022; 161:335-349. [PMID: 35257373 DOI: 10.1111/jnc.15604] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 02/21/2022] [Accepted: 03/01/2022] [Indexed: 11/29/2022]
Abstract
Autism spectrum disorder (ASD) is a heterogenous neurodevelopment disorder resulting from different etiological factors, both genetic and/or environmental. These factors can lead to abnormal neuronal development on dendrite and synaptic function at the central nervous system. Recent studies have shown that a subset of ASD patients display increased circulation levels of the tyrosine metabolite, p-cresol, related to chronic intestinal disorders due to dysbiosis of the intestinal microbiota. In particular, abnormal presence of intestinal Clostridium sp. has been linked to high levels of p-cresol in ASD children younger than 8 years. However, the role of p-cresol during development of the central nervous system is unknown. Here, we evaluated in vitro the effect of p-cresol on neurite outgrowth in N2a and PC12 cell lines and dendritic morphology, synaptic density, neuronal activity, and calcium responses in primary rat hippocampal neurons. p-cresol inhibits neural differentiation and neurites outgrowth in N2a and PC12 neuronal cell lines. In hippocampal neuronal cultures, Sholl´s analysis shows a decrease in the dendritic arborization of neurons treated with p-cresol. Synaptic density analyzed with the synaptic markers Piccolo and Shank2 is diminished in hippocampal neurons treated with p-cresol. Electrically-evoked intracellular calcium rise was drastically, but reversely, blocked by p-cresol, whereas that spontaneous neuronal activity was severely affected by early addition of the metabolite. These findings show that p-cresol alters dendrite development, synaptogenesis and synapse function of neurons in culture, therefore, neuronal alterations occurring in ASD children may be related to this metabolite and dysbiosis of the intestinal microbiota.
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Affiliation(s)
- Sheyla Guzmán Salas
- Departamento Biomédico, Universidad de Antofagasta, Antofagasta, Chile.,Centre for Biotechnology and Bioengineering CeBiB, Antofagasta
| | - André Weber
- Leibniz Institute for Neurobiology, Magdeburg, Germany
| | - Ayse Malci
- Leibniz Institute for Neurobiology, Magdeburg, Germany
| | - Xiao Lin
- Leibniz Institute for Neurobiology, Magdeburg, Germany
| | - Rodrigo Herrera-Molina
- Leibniz Institute for Neurobiology, Magdeburg, Germany.,Centro Integrativo de Biología y Química Aplicada, Universidad Bernardo O'Higgins, Santiago, Chile.,Center for Behavioral Brain Sciences and Medical Faculty, Otto von Guericke University, Magdeburg, Germany
| | - Waldo Cerpa
- Laboratorio de Función y Patología Neuronal; Departamento de Biología Celular y Molecular, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331150, Santiago, Chile.,Centro de Excelencia en Biomedicina de Magallanes (CEBIMA); Universidad de Magallanes, Punta Arenas, Chile.,Centro de Envejecimiento y Regeneración (CARE); Departamento de Biología Celular y Molecular, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Cristina Dorador
- Centre for Biotechnology and Bioengineering CeBiB, Antofagasta.,Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
| | | | - Pedro Zamorano
- Departamento Biomédico, Universidad de Antofagasta, Antofagasta, Chile.,Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
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14
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Villalobos AS, Wiese J, Borchert E, Rahn T, Slaby BM, Steiner LX, Künzel S, Dorador C, Imhoff JF. Micromonospora tarapacensis sp. nov., a bacterium isolated from a hypersaline lake. Int J Syst Evol Microbiol 2021; 71. [PMID: 34787539 DOI: 10.1099/ijsem.0.005109] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain Llam7T was isolated from microbial mat samples from the hypersaline lake Salar de Llamará, located in Taracapá region in the hyper-arid core of the Atacama Desert (Chile). Phenotypic, chemotaxonomic and genomic traits were studied. Phylogenetic analyses based on 16S rRNA gene sequences assigned the strain to the family Micromonosporaceae with affiliation to the genera Micromonospora and Salinispora. Major fatty acids were C17 : 1ω8c, iso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The cell walls contained meso-diaminopimelic acid and ll-2,6 diaminopimelic acid (ll-DAP), while major whole-cell sugars were glucose, mannose, xylose and ribose. The major menaquinones were MK-9(H4) and MK-9(H6). As polar lipids phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and several unidentified lipids, i.e. two glycolipids, one aminolipid, three phospholipids, one aminoglycolipid and one phosphoglycolipid, were detected. Genome sequencing revealed a genome size of 6.894 Mb and a DNA G+C content of 71.4 mol%. Phylogenetic analyses with complete genome sequences positioned strain Llam7T within the family Micromonosporaceae forming a distinct cluster with Micromonospora (former Xiangella) phaseoli DSM 45730T. This cluster is related to Micromonospora pelagivivens KJ-029T, Micromonospora craterilacus NA12T, and Micromonospora craniellae LHW63014T as well as to all members of the former genera Verrucosispora and Jishengella, which were re-classified as members of the genus Micromonospora, forming a clade distinct from the genus Salinispora. Pairwise whole genome average nucleotide identity (ANI) values, digital DNA-DNA hybridization (dDDH) values, the presence of the diamino acid ll-DAP, and the composition of whole sugars and polar lipids indicate that Llam7T represents a novel species, for which the name Micromonospora tarapacensis sp. nov. is proposed, with Llam7T (=DSM 109510T,=LMG 31023T) as the type strain.
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Affiliation(s)
- Alvaro S Villalobos
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Research Unit Marine Symbioses, Kiel, Germany.,Escuela de Ciencias del Mar, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Jutta Wiese
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Research Unit Marine Symbioses, Kiel, Germany
| | - Erik Borchert
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Research Unit Marine Symbioses, Kiel, Germany
| | - Tanja Rahn
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Research Unit Marine Symbioses, Kiel, Germany
| | - Beate M Slaby
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Research Unit Marine Symbioses, Kiel, Germany
| | - Leon X Steiner
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Research Unit Marine Symbioses, Kiel, Germany
| | - Sven Künzel
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional and Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos Universidad de Antofagasta, Antofagasta, Chile
| | - Johannes F Imhoff
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Research Unit Marine Symbioses, Kiel, Germany
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15
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Zárate A, Dorador C, Valdés J, Molina V, Icaza G, Pacheco AS, Castillo A. Benthic microbial diversity trends in response to heavy metals in an oxygen-deficient eutrophic bay of the Humboldt current system offshore the Atacama Desert. Environ Pollut 2021; 286:117281. [PMID: 33992902 DOI: 10.1016/j.envpol.2021.117281] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 03/25/2021] [Accepted: 04/27/2021] [Indexed: 06/12/2023]
Abstract
Mejillones Bay is a coastal ecosystem situated in an oxygen-deficient upwelling area impacted by mining activities in the coastal desert region of northern Chile, where conspicuous microbial life develops in the sediments. Herein, heavy metal (loid)s (HMs) such as Cu, Pb, As, Zn, Al, Fe, Cd, Mo, Ni and V as well as benthic microbial communities were studied using spectrometry and iTag-16 S rRNA sequencing. Samples were taken from two contrasting sedimentary localities in the Bay named Punta Rieles (PR) and Punta Chacaya (PC) within 10-50 m water-depth gradient. PR sediments were organic matter rich (21.1% of TOM at 50 m) and overlaid with low-oxygen waters (<0.06 ml O2/L bottom layer) compared with PC. In general, HMs like Al, Ni, Cd, As and Pb tended to increase in concentration with depth in PR, while the opposite pattern was observed in PC. In addition, PR presented a higher number of unique families (72) compared to PC (35). Among the top ten microbial families, Desulfobulbaceae (4.6% vs. 3.2%), Flavobacteriaceae (2.8% vs. 2.3%) and Anaerolineaceae (3.3% vs. 2.3%) dominated in PR, meanwhile Actinomarinales_Unclassified (8.1% vs. 4.2%) and Sandaracinaceae (4.4% vs. 2.0%) were more abundant in PC. Multivariate analyses confirmed that water depth-related variation was a good proxy for oxygen conditions and metal concentrations, explaining the structure of benthic microbial assemblages. Cd, Ni, As and Pb showed uniformly positive associations with communities that represented the keystone taxa in the co-occurrence network, including Anaerolineaceae, Thiotrichaceae, Desulfobulbaceae, Desulfarculaceae and Bacteroidales_unclassified communities. Collectively, these findings provide new insights for establishing the ecological interconnections of benthic microorganisms in response to metal contamination in a coastal upwelling environment.
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Affiliation(s)
- Ana Zárate
- Doctorado en Ciencias Aplicadas Mención Sistemas Marinos Costeros, Universidad de Antofagasta, Antofagasta, Chile; Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta & Centro de Bioingeniería y Biotecnología (CeBiB), Universidad de Antofagasta, Antofagasta, Chile; Humedales Del Caribe Colombiano, Universidad Del Atlántico, Barranquilla, Colombia.
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta & Centro de Bioingeniería y Biotecnología (CeBiB), Universidad de Antofagasta, Antofagasta, Chile; Departamento de Biotecnología, Facultad de Ciencias Del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Jorge Valdés
- Laboratorio de Sedimentología y Paleoambientes, Instituto de Ciencias Naturales A. von Humboldt, Facultad de Ciencias Del Mar y de Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Verónica Molina
- Departamento de Biología, Observatorio de Ecología Microbiana, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Valparaíso, Chile; HUB Ambiental UPLA, Universidad de Playa Ancha, Valparaíso, Chile
| | - Gonzalo Icaza
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta & Centro de Bioingeniería y Biotecnología (CeBiB), Universidad de Antofagasta, Antofagasta, Chile
| | - Aldo S Pacheco
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Alexis Castillo
- Centro de Investigación y Estudios Avanzados Del Maule. Vicerrectoría de Investigación de Investigación y Posgrado. Universidad Católica Del Maule, Campus San Miguel. Talca, Chile
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16
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Molina V, Eissler Y, Fernandez C, Cornejo-D'Ottone M, Dorador C, Bebout BM, Jeffrey WH, Romero C, Hengst M. Greenhouse gases and biogeochemical diel fluctuations in a high-altitude wetland. Sci Total Environ 2021; 768:144370. [PMID: 33454466 DOI: 10.1016/j.scitotenv.2020.144370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 12/02/2020] [Accepted: 12/04/2020] [Indexed: 06/12/2023]
Abstract
The landscapes of high-altitude wetland ecosystems are characterized by different kinds of aquatic sites, including ponds holding conspicuous microbial life. Here, we examined a representative pond of the wetland landscape for dynamics of greenhouse gases, and their association with other relevant biogeochemical conditions including diel shifts of microbial communities' structure and activity over two consecutive days. Satellite image analysis indicates that the area of ponds cover 238 of 381.3 Ha (i.e., 62.4%), representing a significant landscape in this wetland. Solar radiation, wind velocity and temperature varied daily and between the days sampled, influencing the biogeochemical dynamics in the pond, shifting the pond reservoir of inorganic versus dissolved organic nitrogen/phosphorus bioavailability, between day 1 and day 2. Day 2 was characterized by high dissolved organic nitrogen/phosphorus and N2O accumulation. CH4 presented a positive excess showing maxima at hours of high radiation during both days. The microbial community in the sediment was diverse and enriched in keystone active groups potentially related with GHG recycling including bacteria and archaea, such as Cyanobacteria, Verrucomicrobia, Rhodobacterales and Nanoarchaeaota (Woesearchaeia). Archaea account for the microbial community composition changes between both days and for the secondary productivity in the water measured during day 2. The results indicate that an intense recycling of organic matter occurs in the pond systems and that the activity of the microbial community is correlated with the availability of nutrients. Together, the above results indicate a net sink of CO2 and N2O, which has also been reported for other natural and artificial ponds. Overall, our two-day fluctuation study in a representative pond of a high-altitude wetland aquatic landscape indicates the need to explore in more detail the short-term besides the long-term biogeochemical variability in arid ecosystems of the Andes plateau, where wetlands are hotspots of life currently under high anthropogenic pressure.
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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 2340000, Chile; HUB Ambiental UPLA, Universidad de Playa Ancha, Avenida Leopoldo Carvallo 200, Playa Ancha, Valparaíso 2340000, Chile.
| | - Yoanna Eissler
- Instituto de Química y Bioquímica, Facultad de Ciencias, Universidad de Valparaíso, Gran Bretaña 1111, Playa Ancha, Valparaíso 2360102, Chile.
| | - Camila Fernandez
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique, de Banyuls sur Mer, F-6665 Banyuls/mer, France; Interdisciplinary Center for Aquaculture Research (INCAR), PIA CONICYT COPAS SUR-AUSTRAL Program, Barrio Universitario s/n, Universidad de Concepción, Concepción 4030000, Chile; Centro Fondap IDEAL, Universidad Austral de Chile, Independencia 631, Valdivia 5110566, Chile.
| | - Marcela Cornejo-D'Ottone
- Escuela de Ciencias del Mar e Instituto Milenio de Oceanografía, Pontificia Universidad Católica de Valparaíso, Altamirano 1480, Valparaíso 2360007, 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 1240000, Chile; Centre for Biotechnology and Bioengineering, Santiago 8320000, Chile.
| | - Brad M Bebout
- Exobiology Branch, Ames Research Center National Aeronautics and Space Administration, Moffett Field, CA 94035-0001, USA.
| | - Wade H Jeffrey
- Center for Environmental Diagnostics and Bioremediation, University of West Florida, Pensacola, FL 32514, USA.
| | - Carlos Romero
- Laboratorio de Teledetección Ambiental, Departamento de Ciencias Geográficas, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha. Avenida Leopoldo Carvallo 270, Playa Ancha, Valparaíso 2340000, Chile.
| | - Martha Hengst
- Centre for Biotechnology and Bioengineering, Santiago 8320000, Chile; Departamento de Ciencias Farmacéuticas, Facultad de Ciencias, Universidad Católica del Norte. Av Angamos 0610, Antofagasta 1270709, Chile.
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17
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Bonelli C, Dorador C. Endangered Salares: micro-disasters in Northern Chile. Tapuya: Latin American Science, Technology and Society 2021; 4:1968634. [PMID: 35252764 PMCID: PMC8887917 DOI: 10.1080/25729861.2021.1968634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
This article emerges from a transdisciplinary collaboration between a micro-biologist and an anthropologist deeply concerned with the protection of endangered salares (saltpans) in northern Chile. Our aim is to establish the concept of “micro-disaster” as a tool for examining how extractivism is disrupting salares and their “deep-time” microbial ecologies. These ecologies are key for understanding early events on Earth, as their evolution enabled the oxygenation of the planet 2.5 billion years ago and caused the biodiversity explosion. By considering how beinghuman involves beingmicroorganismal – and how human time is entangled with microorganismic time –, this article connects neoliberal extractivist history with geo-biological evolutionary history. “Micro-disasters” therefore affect us deeply as complex humans, and oblige us to develop further a planet-centered mode of collaborating, thinking, feeling, and acting. In the context of this special issue on extinction, we insist that concerns over extinction must be considered in continuity with deep-time ecologies. We propose to rethink humans as an “environmentally complex we” simultaneously entangled with historical experiential time and microbial “deep-time.”
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Affiliation(s)
| | - Cristina Dorador
- Department of Biotechnology, Universidad de Antofagasta, Antofagasta, Chile
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18
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Zárate A, Dorador C, Araya R, Guajardo M, Z Florez J, Icaza G, Cornejo D, Valdés J. Connectivity of bacterial assemblages along the Loa River in the Atacama Desert, Chile. PeerJ 2020; 8:e9927. [PMID: 33062423 PMCID: PMC7533063 DOI: 10.7717/peerj.9927] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 08/21/2020] [Indexed: 01/04/2023] Open
Abstract
The Loa River is the only perennial artery that crosses the Atacama Desert in northern Chile. It plays an important role in the ecological and economic development of the most water-stressed region, revealing the impact of the mining industry, which exacerbate regional water shortages for many organisms and ecological processes. Despite this, the river system has remained understudied. To our knowledge, this study provides the first effort to attempt to compare the microbial communities at spatial scale along the Loa River, as well as investigate the physicochemical factors that could modulate this important biological component that still remains largely unexplored. The analysis of the spatial bacterial distribution and their interconnections in the water column and sediment samples from eight sites located in three sections along the river catchment (upper, middle and lower) was conducted using 16S rRNA gene-based Illumina MiSeq sequencing. Among a total of 543 ASVs identified at the family level, over 40.5% were cosmopolitan in the river and distributed within a preference pattern by the sediment substrate with 162 unique ASVs, while only 87 were specific to the column water. Bacterial diversity gradually decreased from the headwaters, where the upper section had the largest number of unique families. Distinct groupings of bacterial communities often associated with anthropogenic disturbance, including Burkholderiaceae and Flavobacteriaceae families were predominant in the less-impacted upstream section. Members of the Arcobacteraceae and Marinomonadaceae were prominent in the agriculturally and mining-impacted middle sector while Rhodobacteraceae and Coxiellaceae were most abundant families in downstream sites. Such shifts in the community structure were also related to the influence of salinity, chlorophyll, dissolved oxygen and redox potential. Network analyses corroborated the strong connectivity and modular structure of bacterial communities across this desert river, shedding light on taxonomic relatedness of co-occurring species and highlighting the need for planning the integral conservation of this basin.
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Affiliation(s)
- Ana Zárate
- Doctorado en Ciencias Aplicadas mención Sistemas Marinos Costeros, Universidad de Antofagasta, Antofagasta, Chile.,Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta & Centro de Bioingeniería y Biotecnología (CeBiB), Universidad de Antofagasta, Antofagasta, Chile.,Humedales del Caribe colombiano, Universidad del Atlantico, Barranquilla, Colombia
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta & Centro de Bioingeniería y Biotecnología (CeBiB), Universidad de Antofagasta, Antofagasta, Chile.,Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Ruben Araya
- Laboratorio de Microbiología de Sedimentos, Departamento de Acuicultura, Facultad de Recursos del Mar, Universidad de Antofagasta, Antofagasta, Chile
| | - Mariela Guajardo
- Doctorado en Genómica Integrativa y Centro GEMA, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - July Z Florez
- Humedales del Caribe colombiano, Universidad del Atlantico, Barranquilla, Colombia.,Centro i mar and CeBiB, Universidad de Los Lagos, Puerto Montt, Chile.,Departamento de Ciencias Farmacéuticas, Universidad Católica del Norte, Antofagasta, Chile
| | - Gonzalo Icaza
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta & Centro de Bioingeniería y Biotecnología (CeBiB), Universidad de Antofagasta, Antofagasta, Chile
| | - Diego Cornejo
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta & Centro de Bioingeniería y Biotecnología (CeBiB), Universidad de Antofagasta, Antofagasta, Chile.,Chair of Technical Biochemistry, Technische Universitāt, Dresden Dresden, Germany
| | - Jorge Valdés
- Laboratorio de Sedimentología y Paleoambientes, Instituto de Ciencias Naturales A. von Humboldt, Facultad de Ciencias del Mar y de Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
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19
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Barahona S, Castro-Severyn J, Dorador C, Saavedra C, Remonsellez F. Determinants of Copper Resistance in Acidithiobacillus Ferrivorans ACH Isolated from the Chilean Altiplano. Genes (Basel) 2020; 11:genes11080844. [PMID: 32722087 PMCID: PMC7463520 DOI: 10.3390/genes11080844] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/22/2020] [Accepted: 07/22/2020] [Indexed: 11/16/2022] Open
Abstract
The use of microorganisms in mining processes is a technology widely employed around the world. Leaching bacteria are characterized by having resistance mechanisms for several metals found in their acidic environments, some of which have been partially described in the Acidithiobacillus genus (mainly on ferrooxidans species). However, the response to copper has not been studied in the psychrotolerant Acidithiobacillus ferrivorans strains. Therefore, we propose to elucidate the response mechanisms of A. ferrivorans ACH to high copper concentrations (0-800 mM), describing its genetic repertoire and transcriptional regulation. Our results show that A. ferrivorans ACH can grow in up to 400 mM of copper. Moreover, we found the presence of several copper-related makers, belonging to cop and cus systems, as well as rusticyanins and periplasmatic acop protein in the genome. Interestingly, the ACH strain is the only one in which we find three copies of copB and copZ genes. Moreover, transcriptional expression showed an up-regulation response (acop, copZ, cusA, rusA, and rusB) to high copper concentrations. Finally, our results support the important role of these genes in A. ferrivorans copper stress resistance, promoting the use of the ACH strain in industrial leaching under low temperatures, which could decrease the activation times of oxidation processes and the energy costs.
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Affiliation(s)
- Sergio Barahona
- Laboratorio de Microbiología Aplicada y Extremófilos, Departamento de Ingeniería Química, Universidad Católica del Norte, Antofagasta 1240000, Chile;
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Departamento de Biotecnología, Facultad de Ciencias del Mar y Recurso Biológicos, Universidad de Antofagasta, Antofagasta 1240000, Chile;
- Programa de Doctorado en Ingeniería de Procesos de Minerales, Facultad de Ingeniería, Universidad de Antofagasta, Antofagasta 1240000, Chile
- Correspondence: (S.B.); (F.R.)
| | - Juan Castro-Severyn
- Laboratorio de Microbiología Aplicada y Extremófilos, Departamento de Ingeniería Química, Universidad Católica del Norte, Antofagasta 1240000, Chile;
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Departamento de Biotecnología, Facultad de Ciencias del Mar y Recurso Biológicos, Universidad de Antofagasta, Antofagasta 1240000, Chile;
- Centro de Biotecnología y Bioingeniería (CeBiB), Universidad de Antofagasta, Antofagasta 1240000, Chile
| | - Claudia Saavedra
- Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8320000, Chile;
| | - Francisco Remonsellez
- Laboratorio de Microbiología Aplicada y Extremófilos, Departamento de Ingeniería Química, Universidad Católica del Norte, Antofagasta 1240000, Chile;
- Centro de Investigación Tecnológica del Agua en el Desierto (CEITSAZA), Universidad Católica del Norte, Antofagasta 1240000, Chile
- Correspondence: (S.B.); (F.R.)
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20
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Mark D, DeWald J, Dorador C, Tucker N, Herron P. Characterisation of anti-pseudomonad activity of hyper-arid Micromonospora species. Access Microbiol 2020. [DOI: 10.1099/acmi.ac2020.po0212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The opportunistic pathogen Pseudomonas aeruginosa is a major cause of nosocomial infections, and has been categorised by the World Health Organisation as a “Priority 1: Critical” target for research and development of novel antibiotics owing to its intrinsic multi-resistance and ability to acquire novel resistance mechanisms.
One strategy for discovering novel antibiotics is the identification and characterisation of metabolites with antimicrobial activity. Members of the bacterial phylum Actinobacteria are historic source of these metabolites, in particular the genus Streptomyces. However, other genera have not received this same level of interest despite sharing the capacity to biosynthesise a diverse array of metabolites. One such genus is Micromonospora, responsible for production of the broad-spectrum aminoglycoside antibiotic gentamicin (M. purpurea).
Here we present three Micromonospora species isolated from the Atacama Desert, Chile; that possess anti-pseudomonad bioactivity inducible by culture on International Streptomyces Project (ISP) Media. In addition, preliminary data indicates that this activity can be affected by the addition of P. aeruginosa conditioned media. In parallel, short-read Illumina sequencing was used to assemble draft genomes for these strains, enabling antiSMASH analysis of putative biosynthetic gene clusters. In addition to this, estimated Average Nucleotide Identity (ANI) as calculated by the autoMLST server indicates that these strains may all be novel Micromonospora species.
The results of this work serve to highlight the biosynthetic capacity of an understudied genus of bacteria, as well as the value of examining underexplored environments and habitats in the search for novel bioactive molecules.
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Affiliation(s)
- David Mark
- University of Strathclyde,Glasgow,United Kingdom
| | - Jan DeWald
- University of Strathclyde,Glasgow,United Kingdom
| | | | | | - Paul Herron
- University of Strathclyde,Glasgow,United Kingdom
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21
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Zadjelovic V, Chhun A, Quareshy M, Silvano E, Hernandez-Fernaud JR, Aguilo-Ferretjans MM, Bosch R, Dorador C, Gibson MI, Christie-Oleza JA. Beyond oil degradation: enzymatic potential of Alcanivorax to degrade natural and synthetic polyesters. Environ Microbiol 2020; 22:1356-1369. [PMID: 32079039 PMCID: PMC7187450 DOI: 10.1111/1462-2920.14947] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 02/18/2020] [Indexed: 12/31/2022]
Abstract
Pristine marine environments are highly oligotrophic ecosystems populated by well‐established specialized microbial communities. Nevertheless, during oil spills, low‐abundant hydrocarbonoclastic bacteria bloom and rapidly prevail over the marine microbiota. The genus Alcanivorax is one of the most abundant and well‐studied organisms for oil degradation. While highly successful under polluted conditions due to its specialized oil‐degrading metabolism, it is unknown how they persist in these environments during pristine conditions. Here, we show that part of the Alcanivorax genus, as well as oils, has an enormous potential for biodegrading aliphatic polyesters thanks to a unique and abundantly secreted alpha/beta hydrolase. The heterologous overexpression of this esterase proved a remarkable ability to hydrolyse both natural and synthetic polyesters. Our findings contribute to (i) better understand the ecology of Alcanivorax in its natural environment, where natural polyesters such as polyhydroxyalkanoates (PHA) are produced by a large fraction of the community and, hence, an accessible source of carbon and energy used by the organism in order to persist, (ii) highlight the potential of Alcanivorax to clear marine environments from polyester materials of anthropogenic origin as well as oils, and (iii) the discovery of a new versatile esterase with a high biotechnological potential.
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Affiliation(s)
| | - Audam Chhun
- School of Life Sciences, University of Warwick, Warwick, UK
| | - Mussa Quareshy
- School of Life Sciences, University of Warwick, Warwick, UK
| | | | - Juan R Hernandez-Fernaud
- School of Life Sciences, University of Warwick, Warwick, UK.,Unidad de investigación-HUC, La Laguna-Tenerife, Spain
| | - María M Aguilo-Ferretjans
- School of Life Sciences, University of Warwick, Warwick, UK.,Department of Biology, University of the Balearic Islands, Spain
| | - Rafael Bosch
- Department of Biology, University of the Balearic Islands, Spain.,IMEDEA (CSIC-UIB), Esporles, Spain
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Universidad de Antofagasta, Antofagasta, Chile.,Departamento de Biotecnología, Universidad de Antofagasta, Antofagasta, Chile.,Centre for Biotechnology & Bioengineering (CeBiB), Santiago, Chile
| | - Matthew I Gibson
- Department of Chemistry, University of Warwick, Warwick, UK.,Warwick Medical School, University of Warwick, Warwick, UK
| | - Joseph A Christie-Oleza
- School of Life Sciences, University of Warwick, Warwick, UK.,Department of Biology, University of the Balearic Islands, Spain.,IMEDEA (CSIC-UIB), Esporles, Spain
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22
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Pérez V, Cortés J, Marchant F, Dorador C, Molina V, Cornejo-D’Ottone M, Hernández K, Jeffrey W, Barahona S, Hengst MB. Aquatic Thermal Reservoirs of Microbial Life in a Remote and Extreme High Andean Hydrothermal System. Microorganisms 2020; 8:E208. [PMID: 32028722 PMCID: PMC7074759 DOI: 10.3390/microorganisms8020208] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/29/2020] [Accepted: 01/31/2020] [Indexed: 11/30/2022] Open
Abstract
Hydrothermal systems are ideal to understand how microbial communities cope with challenging conditions. Lirima, our study site, is a polyextreme, high-altitude, hydrothermal ecosystem located in the Chilean Andean highlands. Herein, we analyze the benthic communities of three nearby springs in a gradient of temperature (42-72 °C represented by stations P42, P53, and P72) and pH, and we characterize their microbial diversity by using bacteria 16S rRNA (V4) gene metabarcoding and 16S rRNA gene clone libraries (bacteria and archaea). Bacterial clone libraries of P42 and P53 springs showed that the community composition was mainly represented by phototrophic bacteria (Chlorobia, 3%, Cyanobacteria 3%, at P42; Chlorobia 5%, and Chloroflexi 5% at P53), Firmicutes (32% at P42 and 43% at P53) and Gammaproteobacteria (13% at P42 and 29% at P53). Furthermore, bacterial communities that were analyzed by 16S rRNA gene metabarcoding were characterized by an overall predominance of Chloroflexi in springs with lower temperatures (33% at P42), followed by Firmicutes in hotter springs (50% at P72). The archaeal diversity of P42 and P53 were represented by taxa belonging to Crenarchaeota, Diapherotrites, Nanoarchaeota, Hadesarchaeota, Thaumarchaeota, and Euryarchaeota. The microbial diversity of the Lirima hydrothermal system is represented by groups from deep branches of the tree of life, suggesting this ecosystem as a reservoir of primitive life and a key system to study the processes that shaped the evolution of the biosphere.
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Affiliation(s)
- Vilma Pérez
- Laboratorio de Ecologia Molecular y Microbiologia Aplicada, Departamento de Ciencias Farmacéuticas, Facultad de Ciencias, Universidad Católica del Norte, Antofagasta 1240000, Chile; (V.P.);
- Australian Centre for Ancient DNA (ACAD), University of Adelaide, Adelaide, SA 5005, Australia
| | - Johanna Cortés
- Laboratorio de Ecologia Molecular y Microbiologia Aplicada, Departamento de Ciencias Farmacéuticas, Facultad de Ciencias, Universidad Católica del Norte, Antofagasta 1240000, Chile; (V.P.);
- Centro de Biotecnología y Bioingeniería (CeBiB), Universidad de Chile, Santiago 8320000, Chile; (F.M.); (C.D.)
| | - Francisca Marchant
- Centro de Biotecnología y Bioingeniería (CeBiB), Universidad de Chile, Santiago 8320000, Chile; (F.M.); (C.D.)
| | - Cristina Dorador
- Centro de Biotecnología y Bioingeniería (CeBiB), Universidad de Chile, Santiago 8320000, Chile; (F.M.); (C.D.)
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta & Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta 1240000, Chile;
| | - Verónica Molina
- Observatorio de Ecología Microbiana, Departamento de Biología Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Valparaíso 2340000, Chile;
| | - Marcela Cornejo-D’Ottone
- Escuela de Ciencias del Mar & Instituto Milenio de Oceanografía, Pontificia Universidad Católica de Valparaíso, Valparaíso 2340000, Chile;
| | - Klaudia Hernández
- Centro de Investigación Marina Quintay CIMARQ, Facultad de Ecología y Recursos Naturales, Universidad Andrés Bello, Santiago 8320000, Chile;
| | - Wade Jeffrey
- Center for Environmental Diagnostics & Bioremediation, University of West Florida, Pensacola, FL 32514, USA;
| | - Sergio Barahona
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta & Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta 1240000, Chile;
- Laboratorio de Microbiología Aplicada y Extremófilos, Universidad Católica del Norte, Antofagasta 1240000, Chile
| | - Martha B. Hengst
- Laboratorio de Ecologia Molecular y Microbiologia Aplicada, Departamento de Ciencias Farmacéuticas, Facultad de Ciencias, Universidad Católica del Norte, Antofagasta 1240000, Chile; (V.P.);
- Centro de Biotecnología y Bioingeniería (CeBiB), Universidad de Chile, Santiago 8320000, Chile; (F.M.); (C.D.)
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23
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Ruginescu R, Purcărea C, Dorador C, Lavin P, Cojoc R, Neagu S, Lucaci I, Enache M. Exploring the hydrolytic potential of cultured halophilic bacteria isolated from the Atacama Desert. FEMS Microbiol Lett 2019; 366:5613365. [DOI: 10.1093/femsle/fnz224] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 10/31/2019] [Indexed: 01/23/2023] Open
Abstract
ABSTRACTConsidering that most industrial processes are carried out under harsh physicochemical conditions, which would inactivate enzymes from commonly isolated mesophilic organisms, current studies are geared toward the identification of extremophilic microorganisms producing enzymes resistant to extreme salt concentrations, temperature and pH. Among the extremophiles, halophilic microorganisms are an important source of salt-tolerant enzymes that can be used in varying biotechnological applications. In this context, the aim of the present work was to isolate and identify halophiles producing hydrolases from the Atacama Desert, one of the harshest environments on Earth. Isolates were recovered from halite samples and screened for the presence of seven different hydrolase activities (amylase, caseinase, gelatinase, lipase, pectinase, cellulase and inulinase) using agar plate-based assays. From a total of 23 halophilic bacterial isolates, most showed lipolytic (19 strains) and pectinolytic (11 strains) activities. The molecular identification of eight selected isolates showed a strong similarity to members of the Halomonas and Idiomarina genera. Therefore, the present study represents a preliminary, but essential, step to identify novel biological sources of extremozymes in an environment once thought to be devoid of life.
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Affiliation(s)
- Robert Ruginescu
- Department of Microbiology, Institute of Biology Bucharest of the Romanian Academy, 296 Splaiul Independentei, Bucharest, 060031, Romania
| | - Cristina Purcărea
- Department of Microbiology, Institute of Biology Bucharest of the Romanian Academy, 296 Splaiul Independentei, Bucharest, 060031, Romania
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, 601 Angamos Av., Antofagasta, 1240000, Chile
| | - Paris Lavin
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, 601 Angamos Av., Antofagasta, 1240000, Chile
| | - Roxana Cojoc
- Department of Microbiology, Institute of Biology Bucharest of the Romanian Academy, 296 Splaiul Independentei, Bucharest, 060031, Romania
| | - Simona Neagu
- Department of Microbiology, Institute of Biology Bucharest of the Romanian Academy, 296 Splaiul Independentei, Bucharest, 060031, Romania
| | - Ioana Lucaci
- Department of Microbiology, Institute of Biology Bucharest of the Romanian Academy, 296 Splaiul Independentei, Bucharest, 060031, Romania
| | - Mădălin Enache
- Department of Microbiology, Institute of Biology Bucharest of the Romanian Academy, 296 Splaiul Independentei, Bucharest, 060031, Romania
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Contador CA, Veas-Castillo L, Tapia E, Antipán M, Miranda N, Ruiz-Tagle B, García-Araya J, Andrews BA, Marin M, Dorador C, Asenjo JA. Atacama Database: a platform of the microbiome of the Atacama Desert. Antonie Van Leeuwenhoek 2019; 113:185-195. [PMID: 31535335 DOI: 10.1007/s10482-019-01328-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 09/07/2019] [Indexed: 11/30/2022]
Abstract
The Atacama Desert is one of the oldest and driest places on Earth. In the last decade, microbial richness and diversity has been acknowledged as an important biological resource of this region. Owing to the value of the microbial diversity apparent in potential biotechnology applications and conservation purposes, it is necessary to catalogue these microbial communities to promote research activities and help to preserve the wide range of ecological niches of the Atacama region. A prototype Atacama Database has been designed and it provides a description of the rich microbial diversity of the Atacama Desert, and helps to visualise available literature resources. Data has been collected, curated, and organised into several categories to generate a single record for each organism in the database that covers classification, isolation metadata, morphology, physiology, genome and metabolism information. The current version of Atacama Database contains 2302 microorganisms and includes cultured and uncultured organisms retrieved from different environments within the desert between 1984 and 2016. These organisms are distributed in bacterial, archaeal or eukaryotic domains, along with those that are unclassified taxonomically. The initial prototype of the Atacama Database includes a basic search and taxonomic and advanced search tools to allow identification and comparison of microbial populations, and space distribution within this biome. A geolocation search was implemented to visualise the microbial diversity of the ecological niches defined by sectors and extract general information of the sampling sites. This effort will aid understanding of the microbial ecology of the desert, microbial population dynamics, seasonal behaviour, impact of climate change over time, and reveal further biotechnological applications of these microorganisms. The Atacama Database is freely available at: https://www.atacamadb.cl.
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Affiliation(s)
- Carolina A Contador
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, 8370456, Santiago, Chile.
| | - Luis Veas-Castillo
- Centre for Biotechnology and Bioengineering (CeBiB), Departamento de Ingeniería Informática (DIINF), Universidad de Santiago de Chile, Santiago, Chile
| | - Emilio Tapia
- Centre for Biotechnology and Bioengineering (CeBiB), Departamento de Ingeniería Informática (DIINF), Universidad de Santiago de Chile, Santiago, Chile
| | - Marcela Antipán
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, 8370456, Santiago, Chile
| | - Noemi Miranda
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, 8370456, Santiago, Chile
| | - Benjamín Ruiz-Tagle
- Centre for Biotechnology and Bioengineering (CeBiB), Departamento de Ingeniería Informática (DIINF), Universidad de Santiago de Chile, Santiago, Chile
| | - Jonathan García-Araya
- Centre for Biotechnology and Bioengineering (CeBiB), Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta & Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Barbara A Andrews
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, 8370456, Santiago, Chile
| | - Mauricio Marin
- Centre for Biotechnology and Bioengineering (CeBiB), Departamento de Ingeniería Informática (DIINF), Universidad de Santiago de Chile, Santiago, Chile
| | - Cristina Dorador
- Centre for Biotechnology and Bioengineering (CeBiB), Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta & Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Juan A Asenjo
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, 8370456, Santiago, Chile
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Cortés-Albayay C, Dorador C, Schumann P, Andrews B, Asenjo J, Nouioui I. Streptomyces huasconensis sp. nov., an haloalkalitolerant actinobacterium isolated from a high altitude saline wetland at the Chilean Altiplano. Int J Syst Evol Microbiol 2019; 69:2315-2322. [DOI: 10.1099/ijsem.0.003468] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Carlos Cortés-Albayay
- 1School of Natural and Environmental Sciences, Newcastle University, Devonshire Building, Newcastle upon Tyne NE1 7RU, UK
- 2Centre for Biotechnology and Bioengineering, University of Chile, Beauchef 851, Santiago, Chile
| | - Cristina Dorador
- 3Laboratory of Microbial Complexity and Functional Ecology, Departamento de Biotecnología, Facultad de Ciencias del Mary Recursos Biológicos and Centre for Biotechnology and Bioengineering, Universidad de Antofagasta, Chile
| | - Peter Schumann
- 4Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Germany
| | - Barbara Andrews
- 2Centre for Biotechnology and Bioengineering, University of Chile, Beauchef 851, Santiago, Chile
| | - Juan Asenjo
- 2Centre for Biotechnology and Bioengineering, University of Chile, Beauchef 851, Santiago, Chile
| | - Imen Nouioui
- 1School of Natural and Environmental Sciences, Newcastle University, Devonshire Building, Newcastle upon Tyne NE1 7RU, UK
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Cubillos CF, Paredes A, Yáñez C, Palma J, Severino E, Vejar D, Grágeda M, Dorador C. Insights Into the Microbiology of the Chaotropic Brines of Salar de Atacama, Chile. Front Microbiol 2019; 10:1611. [PMID: 31354691 PMCID: PMC6637823 DOI: 10.3389/fmicb.2019.01611] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 06/27/2019] [Indexed: 02/02/2023] Open
Abstract
Microbial life inhabiting hypersaline environments belong to a limited group of extremophile or extremotolerant taxa. Natural or artificial hypersaline environments are not limited to high concentrations of NaCl, and under such conditions, specific adaptation mechanisms are necessary to permit microbial survival and growth. Argentina, Bolivia, and Chile include three large salars (salt flats) which globally, represent the largest lithium reserves, and are commonly referred to as the Lithium Triangle Zone. To date, a large amount of information has been generated regarding chemical, geological, meteorological and economical perspectives of these salars. However, there is a remarkable lack of information regarding the biology of these unique environments. Here, we report the presence of two bacterial strains (isolates LIBR002 and LIBR003) from one of the most hypersaline lithium-dominated man-made environments (total salinity 556 g/L; 11.7 M LiCl) reported to date. Both isolates were classified to the Bacillus genera, but displayed differences in 16S rRNA gene and fatty acid profiles. Our results also revealed that the isolates are lithium-tolerant and that they are phylogenetically differentiated from those Bacillus associated with high NaCl concentration environments, and form a new clade from the Lithium Triangle Zone. To determine osmoadaptation strategies in these microorganisms, both isolates were characterized using morphological, metabolic and physiological attributes. We suggest that our characterization of bacterial isolates from a highly lithium-enriched environment has revealed that even at such extreme salinities with high concentrations of chaotropic solutes, scope for microbial life exists. These conditions have previously been considered to limit the development of life, and our work extends the window of life beyond high concentrations of MgCl2, as previously reported, to LiCl. Our results can be used to further the understanding of salt tolerance, most especially for LiCl-dominated brines, and likely have value as models for the understanding of putative extra-terrestrial (e.g., Martian) life.
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Affiliation(s)
- Carolina F. Cubillos
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
- Department of Chemical Engineering and Mineral Process, Center for Advanced Study of Lithium and Industrial Minerals, Universidad de Antofagasta, Antofagasta, Chile
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Santiago, Chile
| | - Adrián Paredes
- Laboratorio Química Biológica, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
- Departamento de Química, Facultad de Ciencias Básicas, Universidad de Antofagasta, Antofagasta, Chile
| | - Carolina Yáñez
- Laboratorio Microbiología, Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Jenifer Palma
- Departamento de Ciencias de los Alimentos, Facultad de Ciencias de la Salud, Universidad de Antofagasta, Antofagasta, Chile
| | - Esteban Severino
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
| | - Drina Vejar
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Santiago, Chile
| | - Mario Grágeda
- Department of Chemical Engineering and Mineral Process, Center for Advanced Study of Lithium and Industrial Minerals, Universidad de Antofagasta, Antofagasta, Chile
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Santiago, Chile
- Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
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27
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Cortés-Albayay C, Dorador C, Schumann P, Schniete JK, Herron P, Andrews B, Asenjo J, Nouioui I. Streptomyces altiplanensis sp. nov., an alkalitolerant species isolated from Chilean Altiplano soil, and emended description of Streptomyces chryseus (Krasil'nikov et al. 1965) Pridham 1970. Int J Syst Evol Microbiol 2019; 69:2498-2505. [PMID: 31204968 DOI: 10.1099/ijsem.0.003525] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A polyphasic approach was used for evaluating the taxonomic status of strain HST21T isolated from Salar de Huasco in the Atacama Desert. The results of 16S rRNA gene and multilocus sequence phylogenetic analyses assigned strain HST21T to the genus Streptomyceswith Streptomyces albidochromogenes DSM 41800Tand Streptomyces flavidovirens DSM 40150T as its nearest neighbours. Digital DNA-DNA hydridization (dDDH) and average nucleotide identity (ANI) values between the genome sequences of strain HST21T and S. albidochromogenes DSM 41800T (35.6 and 88.2 %) and S. flavidovirens DSM 40105T (47.2 and 88.8 %) were below the thresholds of 70 and 95-96 % for prokaryotic conspecific assignation. Phenotypic, chemotaxonomic and genetic results distinguished strain HST21T from its closest neighbours. Strain HST21T is characterized by the presence of ll-diaminopimelic acid in its peptidoglycan layer; glucose and ribose as whole cell sugars; diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylinositol, glycophospholipids, unknown lipids and phospholipids as polar lipids; and anteiso-C15 : 0 (21.6 %) and anteiso-C17 : 0 (20.5 %) as major fatty acids (>15 %). Based on these results, strain HST21T merits recognition as a novel species, for which the name Streptomyces altiplanensis sp. nov. is proposed. The type strain is HST21T=DSM 107267T=CECT 9647T. While analysing the phylogenies of strain HST21T, Streptomyces chryseus DSM 40420T and Streptomyces helvaticus DSM 40431T were found to have 100 % 16S rRNA gene sequence similarity with digital DNA-DNA hydridization (dDDH) and average nucleotide identity (ANI) values of 95.3 and 99.4 %, respectively. Therefore, S. helvaticus is considered as a later heterotypic synonym of S. chryseus and, consequently, we emend the description of S. chryseus.
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Affiliation(s)
- Carlos Cortés-Albayay
- School of Natural and Environmental Sciences, Newcastle University, Devonshire Building, Newcastle upon Tyne NE1 7RU, UK
- Centre for Biotechnology and Bioengineering, University of Chile, Beauchef 851, Santiago, Chile
| | - Cristina Dorador
- Laboratory of Microbial Complexity and Functional Ecology, Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos & Centre for Biotechnology and Bioengineering, Universidad de Antofagasta, Chile
| | - Peter Schumann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Germany
| | - Jana K Schniete
- Department of Physics, University of Strathclyde, 107 Rottenrow, Glasgow G4 0NG, UK
| | - Paul Herron
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK
| | - Barbara Andrews
- Centre for Biotechnology and Bioengineering, University of Chile, Beauchef 851, Santiago, Chile
| | - Juan Asenjo
- Centre for Biotechnology and Bioengineering, University of Chile, Beauchef 851, Santiago, Chile
| | - Imen Nouioui
- School of Natural and Environmental Sciences, Newcastle University, Devonshire Building, Newcastle upon Tyne NE1 7RU, UK
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Paun VI, Icaza G, Lavin P, Marin C, Tudorache A, Perşoiu A, Dorador C, Purcarea C. Total and Potentially Active Bacterial Communities Entrapped in a Late Glacial Through Holocene Ice Core From Scarisoara Ice Cave, Romania. Front Microbiol 2019; 10:1193. [PMID: 31244788 PMCID: PMC6563852 DOI: 10.3389/fmicb.2019.01193] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 05/13/2019] [Indexed: 01/20/2023] Open
Abstract
Our understanding of the icy-habitat microbiome is likely limited by a lack of reliable data on microorganisms inhabiting underground ice that has accumulated inside caves. To characterize how environmental variation impacts cave ice microbial community structure, we determined the composition of total and potentially active bacterial communities along a 13,000-year-old ice core from Scarisoara cave (Romania) through 16S rRNA gene Illumina sequencing. An average of 2,546 prokaryotic gDNA operational taxonomic units (OTUs) and 585 cDNA OTUs were identified across the perennial cave ice block and analyzed in relation to the geochemical composition of ice layers. The total microbial community and the putative active fraction displayed dissimilar taxa profiles. The ice-contained microbiome was dominated by Actinobacteria with a variable representation of Proteobacteria, while the putative active microbial community was equally shared between Proteobacteria and Firmicutes. Accordingly, a major presence of Cryobacterium, Lysinomonas, Pedobacter, and Aeromicrobium phylotypes homologous to psychrotrophic and psychrophilic bacteria from various cold environments were noted in the total community, while the prevalent putative active bacteria belonged to Clostridium, Pseudomonas, Janthinobacterium, Stenotrophomonas, and Massilia genera. Variation in the microbial cell density of ice strata with the dissolved organic carbon (DOC) content and the strong correlation of DOC and silicon concentrations revealed a major impact of depositional processes on microbial abundance throughout the ice block. Post-depositional processes appeared to occur mostly during the 4,000–7,000 years BP interval. A major bacterial composition shift was observed in 4,500–5,000-year-old ice, leading to a high representation of Beta- and Deltaproteobacteria in the potentially active community in response to the increased concentrations of DOC and major chemical elements. Estimated metabolic rates suggested the presence of a viable microbial community within the cave ice block, characterized by a maintenance metabolism in most strata and growth capacity in those ice deposits with high microbial abundance and DOC content. This first survey of microbial distribution in perennial cave ice formed since the Last Glacial period revealed a complex potentially active community, highlighting major shifts in community composition associated with geochemical changes that took place during climatic events that occurred about 5,000 years ago, with putative formation of photosynthetic biofilms.
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Affiliation(s)
- Victoria I Paun
- Department of Microbiology, Institute of Biology, Bucharest, Romania
| | - Gonzalo Icaza
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile.,Centre for Biotechnology and Bioengineering, Universidad de Antofagasta, Antofagasta, Chile
| | - Paris Lavin
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile.,Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Constantin Marin
- Laboratory of Hydrogeochemistry, "Emil Racovita" Institute of Speleology, Bucharest, Romania
| | - Alin Tudorache
- Laboratory of Hydrogeochemistry, "Emil Racovita" Institute of Speleology, Bucharest, Romania
| | - Aurel Perşoiu
- Department of Microbiology, Institute of Biology, Bucharest, Romania.,"Emil Racovita" Institute of Speleology, Cluj-Napoca, Romania.,Stefan cel Mare University of Suceava, Suceava, Romania
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile.,Centre for Biotechnology and Bioengineering, Universidad de Antofagasta, Antofagasta, Chile.,Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Cristina Purcarea
- Department of Microbiology, Institute of Biology, Bucharest, Romania
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Villalobos AS, Wiese J, Imhoff JF, Dorador C, Keller A, Hentschel U. Systematic Affiliation and Genome Analysis of Subtercola vilae DB165 T with Particular Emphasis on Cold Adaptation of an Isolate from a High-Altitude Cold Volcano Lake. Microorganisms 2019; 7:microorganisms7040107. [PMID: 31018526 PMCID: PMC6518244 DOI: 10.3390/microorganisms7040107] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 04/17/2019] [Accepted: 04/18/2019] [Indexed: 11/16/2022] Open
Abstract
Among the Microbacteriaceae the species of Subtercola and Agreia form closely associated clusters. Phylogenetic analysis demonstrated three major phylogenetic branches of these species. One of these branches contains the two psychrophilic species Subtercola frigoramans and Subtercola vilae, together with a larger number of isolates from various cold environments. Genomic evidence supports the separation of Agreia and Subtercola species. In order to gain insight into the ability of S. vilae to adapt to life in this extreme environment, we analyzed the genome with a particular focus on properties related to possible adaptation to a cold environment. General properties of the genome are presented, including carbon and energy metabolism, as well as secondary metabolite production. The repertoire of genes in the genome of S. vilae DB165T linked to adaptations to the harsh conditions found in Llullaillaco Volcano Lake includes several mechanisms to transcribe proteins under low temperatures, such as a high number of tRNAs and cold shock proteins. In addition, S. vilae DB165T is capable of producing a number of proteins to cope with oxidative stress, which is of particular relevance at low temperature environments, in which reactive oxygen species are more abundant. Most important, it obtains capacities to produce cryo-protectants, and to combat against ice crystal formation, it produces ice-binding proteins. Two new ice-binding proteins were identified which are unique to S. vilae DB165T. These results indicate that S. vilae has the capacity to employ different mechanisms to live under the extreme and cold conditions prevalent in Llullaillaco Volcano Lake.
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Affiliation(s)
- Alvaro S Villalobos
- Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany.
| | - Jutta Wiese
- Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany.
| | - Johannes F Imhoff
- Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany.
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional and Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Av. Angamos 601, Antofagasta, Chile.
| | - Alexander Keller
- Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany.
| | - Ute Hentschel
- Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany.
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Aguilar P, Dorador C, Vila I, Sommaruga R. Bacterial Communities Associated With Spherical Nostoc Macrocolonies. Front Microbiol 2019; 10:483. [PMID: 30949138 PMCID: PMC6437075 DOI: 10.3389/fmicb.2019.00483] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 02/25/2019] [Indexed: 12/22/2022] Open
Abstract
Species of the genus Nostoc (Cyanobacteria) can form large colonies of up to several centimeters in diameter that may represent a unique habitat for bacteria in freshwaters. Bacteria inside the colony are probably segregated from the surrounding water and largely dependent on the metabolism of this primary producer. However, the existence of a specific bacterial community associated with free-living representatives of Nostoc from lakes and streams is unknown. Here, we studied large Nostoc spp. colonies (ca. 2-10 cm in diameter) from two adjacent, high altitude aquatic environments and assessed the diversity, and community composition of the bacterial community associated with the inner gelatinous matrix (GM). Further, we compared this community with that of the lake's littoral zone where the colonies live or with the outer layer (OL) of the colony in samples collected from a stream. Alpha bacterial diversity in the inner GM of the colonies from both sites was lower than in the littoral zone or than in the OL. Significant differences in community composition were found between the inner and the OL, as well as between the inner GM, and the littoral zone. Further, these differences were supported by the putative metabolic processes of the bacterial communities. Our results indicate the existence of a specific bacterial community inside macrocolonies of Nostoc spp. and also imply that the inner environment exerts a strong selection. Finally, these large colonies represent not only a unique habitat, but probably also a hotspot of bacterial activity in an otherwise oligotrophic environment.
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Affiliation(s)
- Pablo Aguilar
- Lake and Glacier Ecology Research Group, Department of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
- Centre for Biotechnology and Bioengineering (CeBiB), Antofagasta, Chile
| | - Irma Vila
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Ruben Sommaruga
- Lake and Glacier Ecology Research Group, Department of Ecology, University of Innsbruck, Innsbruck, Austria
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Aguilar P, Dorador C, Vila I, Sommaruga R. Bacterioplankton composition in tropical high-elevation lakes of the Andean plateau. FEMS Microbiol Ecol 2019; 94:4810748. [PMID: 29346530 PMCID: PMC6018938 DOI: 10.1093/femsec/fiy004] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 01/15/2018] [Indexed: 01/12/2023] Open
Abstract
High-elevation lakes in the tropics are subject to extreme environmental fluctuations and microbes may harbor a unique genomic repertoire, but their composition and diversity are largely unknown. Here, we compared the planktonic bacterial community composition (BCC) and diversity of three tropical lakes located in the high Andean plateau (≥4400 m above sea level) during the dry and wet season. Diversity in these lakes was higher in the cool and wet season than in the warm and dry one. Operational taxonomic units (OTUs) composition was significantly different among lakes and between seasons. Members of the class Opitutae, Spartobacteria, Burkholderiales and Actinobacteria were dominant, but only the hgcI clade (Actinobacteria) and the Comamonadaceae family (Burkholderiales) were shared between seasons among the three lakes. In general, a large percentage (up to 42%) of the rare OTUs was unclassified even at the family level. In one lake, a pycnocline and an anoxic water layer with high abundance of Thiocapsa sp. was found in the wet season indicating that the known polymictic thermal condition is not always given. Our study highlights the particular BCC of tropical high-elevation lakes and also how little is known about the variability in physico-chemical conditions of these ecosystems.
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Affiliation(s)
- Pablo Aguilar
- Lake and Glacier Ecology Research Group, Institute of Ecology, University of Innsbruck, Technikerstr 25, Innsbruck 6020, Austria
| | - Cristina Dorador
- Laboratory of Microbial Complexity and Functional Ecology, Instituto Antofagasta & Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Chile.,Centre for Biotechnology and Bioengineering (CeBiB), Beaucheff 851 Antofagasta, Chile
| | - Irma Vila
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Av. Libertador Bernardo O'Higgins 1058 Santiago, Chile
| | - Ruben Sommaruga
- Lake and Glacier Ecology Research Group, Institute of Ecology, University of Innsbruck, Technikerstr 25, Innsbruck 6020, Austria
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Filippidou S, Junier T, Wunderlin T, Kooli WM, Palmieri I, Al-Dourobi A, Molina V, Lienhard R, Spangenberg JE, Johnson SL, Chain PSG, Dorador C, Junier P. Adaptive Strategies in a Poly-Extreme Environment: Differentiation of Vegetative Cells in Serratia ureilytica and Resistance to Extreme Conditions. Front Microbiol 2019; 10:102. [PMID: 30804904 PMCID: PMC6370625 DOI: 10.3389/fmicb.2019.00102] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 01/17/2019] [Indexed: 11/13/2022] Open
Abstract
Poly-extreme terrestrial habitats are often used as analogs to extra-terrestrial environments. Understanding the adaptive strategies allowing bacteria to thrive and survive under these conditions could help in our quest for extra-terrestrial planets suitable for life and understanding how life evolved in the harsh early earth conditions. A prime example of such a survival strategy is the modification of vegetative cells into resistant resting structures. These differentiated cells are often observed in response to harsh environmental conditions. The environmental strain (strain Lr5/4) belonging to Serratia ureilytica was isolated from a geothermal spring in Lirima, Atacama Desert, Chile. The Atacama Desert is the driest habitat on Earth and furthermore, due to its high altitude, it is exposed to an increased amount of UV radiation. The geothermal spring from which the strain was isolated is oligotrophic and the temperature of 54°C exceeds mesophilic conditions (15 to 45°C). Although the vegetative cells were tolerant to various environmental insults (desiccation, extreme pH, glycerol), a modified cell type was formed in response to nutrient deprivation, UV radiation and thermal shock. Scanning (SEM) and Transmission Electron Microscopy (TEM) analyses of vegetative cells and the modified cell structures were performed. In SEM, a change toward a circular shape with reduced size was observed. These circular cells possessed what appears as extra coating layers under TEM. The resistance of the modified cells was also investigated, they were resistant to wet heat, UV radiation and desiccation, while vegetative cells did not withstand any of those conditions. A phylogenomic analysis was undertaken to investigate the presence of known genes involved in dormancy in other bacterial clades. Genes related to spore-formation in Myxococcus and Firmicutes were found in S. ureilytica Lr5/4 genome; however, these genes were not enough for a full sporulation pathway that resembles either group. Although, the molecular pathway of cell differentiation in S. ureilytica Lr5/4 is not fully defined, the identified genes may contribute to the modified phenotype in the Serratia genus. Here, we show that a modified cell structure can occur as a response to extremity in a species that was previously not known to deploy this strategy. This strategy may be widely spread in bacteria, but only expressed under poly-extreme environmental conditions.
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Affiliation(s)
- Sevasti Filippidou
- Laboratory of Microbiology, University of Neuchatel, Neuchatel, Switzerland
- Microbial Ecology Group, Centre for Ecology and Hydrology, Wallingford, United Kingdom
- Space Microbiology Research Group, Radiation Biology Department, Institute of Aerospace Medicine, German Aerospace Center (DLR e.V.), Cologne, Germany
| | - Thomas Junier
- Vital-IT Group, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Tina Wunderlin
- Laboratory of Microbiology, University of Neuchatel, Neuchatel, Switzerland
| | - Wafa M. Kooli
- Laboratory of Microbiology, University of Neuchatel, Neuchatel, Switzerland
| | - Ilona Palmieri
- Laboratory of Microbiology, University of Neuchatel, Neuchatel, Switzerland
| | - Andrej Al-Dourobi
- Laboratory of Microbiology, University of Neuchatel, Neuchatel, Switzerland
| | - Veronica Molina
- Departamento de Biología, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Valparaíso, Chile
| | | | - Jorge E. Spangenberg
- Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
| | | | | | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
- Centre for Biotechnology and Bioengineering, Antofagasta, Chile
| | - Pilar Junier
- Laboratory of Microbiology, University of Neuchatel, Neuchatel, Switzerland
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Solon AJ, Vimercati L, Darcy JL, Arán P, Porazinska D, Dorador C, Farías ME, Schmidt SK. Microbial Communities of High-Elevation Fumaroles, Penitentes, and Dry Tephra "Soils" of the Puna de Atacama Volcanic Zone. Microb Ecol 2018; 76:340-351. [PMID: 29305629 DOI: 10.1007/s00248-017-1129-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 12/12/2017] [Indexed: 06/07/2023]
Abstract
The aim of this study was to understand the spatial distribution of microbial communities (18S and 16S rRNA genes) across one of the harshest terrestrial landscapes on Earth. We carried out Illumina sequencing using samples from two expeditions to the high slopes (up to 6050 m.a.s.l.) of Volcán Socompa and Llullaillaco to describe the microbial communities associated with the extremely dry tephra compared to areas that receive water from fumaroles and ice fields made up of nieves penitentes. There were strong spatial patterns relative to these landscape features with the most diverse (alpha diversity) communities being associated with fumaroles. Penitentes did not significantly increase alpha diversity compared to dry tephra at the same elevation (5825 m.a.s.l.) on Volcán Socompa, but the structure of the 18S community (beta diversity) was significantly affected by the presence of penitentes on both Socompa and Llullaillaco. In addition, the 18S community was significantly different in tephra wetted by penitentes versus dry tephra sites across many elevations on Llullaillaco. Traditional phototrophs (algae and cyanobacteria) were abundant in wetter tephra associated with fumaroles, and algae (but not cyanobacteria) were common in tephra associated with penitentes. Dry tephra had neither algae nor cyanobacteria but did host potential phototrophs in the Rhodospirillales on Volcán Llullaillaco, but not on Socompa. These results provide new insights into the distribution of microbes across one of the most extreme terrestrial environments on Earth and provide the first ever glimpse of life associated with nieves penitentes, spire-shaped ice structures that are widespread across the mostly unexplored high-elevation Andean Central Volcanic Zone.
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Affiliation(s)
- Adam J Solon
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
| | - Lara Vimercati
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
| | - J L Darcy
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
| | - Pablo Arán
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta & Centre for Biotechnology and Bioengineering (CeBiB), Universidad de Antofagasta, Antofagasta, Chile
- Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Dorota Porazinska
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
| | - C Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta & Centre for Biotechnology and Bioengineering (CeBiB), Universidad de Antofagasta, Antofagasta, Chile
- Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - M E Farías
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas, PROIMI, Tucumán, Argentina
| | - S K Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA.
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Eissler Y, Gálvez MJ, Dorador C, Hengst M, Molina V. Active microbiome structure and its association with environmental factors and viruses at different aquatic sites of a high-altitude wetland. Microbiologyopen 2018; 8:e00667. [PMID: 30062777 PMCID: PMC6436485 DOI: 10.1002/mbo3.667] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 04/04/2018] [Accepted: 04/21/2018] [Indexed: 01/23/2023] Open
Abstract
Salar de Huasco is a high‐altitude wetland characterized by a highly diverse microbial life adapted to extreme climatic and environmental conditions. Our study aims to determine active microbial community structure changes within different aquatic sites and its relationship with environmental factors and viruses as potential drivers of diversification in different aquatic areas of this ecosystem. In this study, bacteria and archaea composition (16S rRNA subunit pyrolibraries) and picoplankton and viral abundance were determined at ponds, springs and lagoon sites of the wetland during wet and dry seasons (February and July 2012, respectively). In general, mixosaline waters (1,400–51,000 μS/cm) usually found in ponds and lagoon presented higher picoplanktonic abundances compared to freshwater (<800 μS/cm) spring sites, ranging from 1.07 × 105 to 1.83 × 107 cells/ml. Viral abundance and viral to picoplankton ratio (VPR) also presented greater values at ponds compared to spring sites, reaching up to 4.78 × 108 viruses‐like particles and up to 351 for VPR. In general, ponds hold a higher microbial diversity and complexity associated also with the presence of microbial mats compared with water sources or lagoon (Shannon index H′ 2.6–3.9 vs. <2.0). A greater richness of archaea was also detected in ponds characterized by functional groups such as known methanogens and ammonia oxidizers, and uncultured groups. In total, our results indicate that among the different aquatic sites of the wetland, ponds presented a great microbial community diversification associated to a higher top‐down control by viruses which may influence nutrient and greenhouse gases cycling.
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Affiliation(s)
- Yoanna Eissler
- Facultad de Ciencias, Centro de Investigación y Gestión de Recursos Naturales, Instituto de Química y Bioquímica, Universidad de Valparaíso, Valparaíso, Chile
| | - María-Jesús Gálvez
- Programa de Biodiversidad and Departamento de Biología, Facultad de Ciencias Naturales y Exactas, Observatorio de Ecología Microbiana, Universidad de Playa Ancha, Valparaíso, Chile
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, 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
| | - Verónica Molina
- Programa de Biodiversidad and Departamento de Biología, Facultad de Ciencias Naturales y Exactas, Observatorio de Ecología Microbiana, Universidad de Playa Ancha, Valparaíso, Chile
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Dorador C, Fink P, Hengst M, Icaza G, Villalobos AS, Vejar D, Meneses D, Zadjelovic V, Burmann L, Moelzner J, Harrod C. Microbial community composition and trophic role along a marked salinity gradient in Laguna Puilar, Salar de Atacama, Chile. Antonie Van Leeuwenhoek 2018; 111:1361-1374. [PMID: 29744693 DOI: 10.1007/s10482-018-1091-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 04/23/2018] [Indexed: 10/16/2022]
Abstract
The geological, hydrological and microbiological features of the Salar de Atacama, the most extensive evaporitic sedimentary basin in the Atacama Desert of northern Chile, have been extensively studied. In contrast, relatively little attention has been paid to the composition and roles of microbial communities in hypersaline lakes which are a unique feature in the Salar. In the present study biochemical, chemical and molecular biological tools were used to determine the composition and roles of microbial communities in water, microbial mats and sediments along a marked salinity gradient in Laguna Puilar which is located in the "Los Flamencos" National Reserve. The bacterial communities at the sampling sites were dominated by members of the phyla Bacteroidetes, Chloroflexi, Cyanobacteria and Proteobacteria. Stable isotope and fatty acid analyses revealed marked variability in the composition of microbial mats at different sampling sites both horizontally (at different sites) and vertically (in the different layers). The Laguna Puilar was shown to be a microbially dominated ecosystem in which more than 60% of the fatty acids at particular sites are of bacterial origin. Our pioneering studies also suggest that the energy budgets of avian consumers (three flamingo species) and dominant invertebrates (amphipods and gastropods) use minerals as a source of energy and nutrients. Overall, the results of this study support the view that the Salar de Atacama is a heterogeneous and fragile ecosystem where small changes in environmental conditions may alter the balance of microbial communities with possible consequences at different trophic levels.
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Affiliation(s)
- Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile. .,Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Angamos 601, Antofagasta, Chile. .,Centre for Biotechnology & Bioengineering (CeBiB), Santiago, Chile.
| | - Patrick Fink
- Workgroup Aquatic Chemical Ecology, University of Cologne, Cologne Biocenter, ZülpicherStraße 47b, 50674, Cologne, Germany
| | - Martha Hengst
- Centre for Biotechnology & Bioengineering (CeBiB), Santiago, Chile.,Laboratory of Molecular Ecology and Applied Microbiology, Departamento de Ciencias Farmacéuticas, Universidad Católica del Norte, Antofagasta, Chile
| | - Gonzalo Icaza
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile.,Centre for Biotechnology & Bioengineering (CeBiB), Santiago, Chile
| | - Alvaro S Villalobos
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile.,Marine Microbiology, GEOMAR Helmholtz, Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105, Kiel, Germany
| | - Drina Vejar
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile.,Centre for Biotechnology & Bioengineering (CeBiB), Santiago, Chile
| | - Daniela Meneses
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile.,Centre for Biotechnology & Bioengineering (CeBiB), Santiago, Chile
| | - Vinko Zadjelovic
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
| | - Lisa Burmann
- Workgroup Aquatic Chemical Ecology, University of Cologne, Cologne Biocenter, ZülpicherStraße 47b, 50674, Cologne, Germany
| | - Jana Moelzner
- Workgroup Aquatic Chemical Ecology, University of Cologne, Cologne Biocenter, ZülpicherStraße 47b, 50674, Cologne, Germany
| | - Chris Harrod
- Instituto de Ciencias Naturales Alexander von Humboldt, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile.,Núcleo Milenio INVASAL, Concepción, Chile
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Tapia JS, Valdés J, Orrego R, Tchernitchin A, Dorador C, Bolados A, Harrod C. Geologic and anthropogenic sources of contamination in settled dust of a historic mining port city in northern Chile: health risk implications. PeerJ 2018; 6:e4699. [PMID: 29707438 PMCID: PMC5922233 DOI: 10.7717/peerj.4699] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 04/12/2018] [Indexed: 11/20/2022] Open
Abstract
Chile is the leading producer of copper worldwide and its richest mineral deposits are found in the Antofagasta Region of northern Chile. Mining activities have significantly increased income and employment in the region; however, there has been little assessment of the resulting environmental impacts to residents. The port of Antofagasta, located 1,430 km north of Santiago, the capital of Chile, functioned as mineral stockpile until 1998 and has served as a copper concentrate stockpile since 2014. Samples were collected in 2014 and 2016 that show elevated concentrations of As, Cu, Pb, and Zn in street dust and in residents' blood (Pb) and urine (As) samples. To interpret and analyze the spatial variability and likely sources of contamination, existent data of basement rocks and soil geochemistry in the city as well as public-domain airborne dust were studied. Additionally, a bioaccessibility assay of airborne dust was conducted and the chemical daily intake and hazard index were calculated to provide a preliminary health risk assessment in the vicinity of the port. The main conclusions indicate that the concentrations of Ba, Co, Cr, Mn, Ni, and V recorded from Antofagasta dust likely originate from intrusive, volcanic, metamorphic rocks, dikes, or soil within the city. However, the elevated concentrations of As, Cd, Cu, Mo, Pb, and Zn do not originate from these geologic outcrops, and are thus considered anthropogenic contaminants. The average concentrations of As, Cu, and Zn are possibly the highest in recorded street dust worldwide at 239, 10,821, and 11,869 mg kg-1, respectively. Furthermore, the contaminants As, Pb, and Cu exhibit the highest bioaccessibilities and preliminary health risk indices show that As and Cu contribute to elevated health risks in exposed children and adults chronically exposed to dust in Antofagasta, whereas Pb is considered harmful at any concentration. Therefore, an increased environmental awareness and greater protective measures are necessary in Antofagasta and possibly other similar mining port cities in developing countries.
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Affiliation(s)
- Joseline S Tapia
- Instituto de Ciencias de la Tierra, Universidad Austral de Chile, Valdivia, Chile
| | - Jorge Valdés
- Instituto de Ciencias Naturales Alexander von Humboldt, Universidad de Antofagasta, Antofagasta, Chile.,Laboratorio de Sedimentología y Paleoambientes LASPAL, Universidad de Antofagasta, Antofagasta, Chile
| | - Rodrigo Orrego
- Instituto de Ciencias Naturales Alexander von Humboldt, Universidad de Antofagasta, Antofagasta, Chile
| | - Andrei Tchernitchin
- Laboratorio de Endocrinología Experimental y Patología Ambiental ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile.,Departamento de Medio Ambiente, Colegio Médico de Chile, Santiago, Chile
| | - Cristina Dorador
- Departamento de Biotecnología and Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile.,Centre for Biotechnology and Bioengineering (CeBiB), Antofagasta, Chile
| | - Aliro Bolados
- Departamento de Medio Ambiente, Colegio Médico de Chile, Santiago, Chile
| | - Chris Harrod
- Instituto de Ciencias Naturales Alexander von Humboldt, Universidad de Antofagasta, Antofagasta, Chile.,Núcleo Milenio INVASAL, Concepción, Chile
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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] [What about the content of this article? (0)] [Affiliation(s)] [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
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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Pérez V, Dorador C, Molina V, Yáñez C, Hengst M. Rhodobacter sp. Rb3, an aerobic anoxygenic phototroph which thrives in the polyextreme ecosystem of the Salar de Huasco, in the Chilean Altiplano. Antonie Van Leeuwenhoek 2018; 111:1449-1465. [PMID: 29569108 DOI: 10.1007/s10482-018-1067-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 03/16/2018] [Indexed: 10/17/2022]
Abstract
The Salar de Huasco is an evaporitic basin located in the Chilean Altiplano, which presents extreme environmental conditions for life, i.e. high altitude (3800 m.a.s.l.), negative water balance, a wide salinity range, high daily temperature changes and the occurrence of the highest registered solar radiation on the planet (> 1200 W m-2). This ecosystem is considered as a natural laboratory to understand different adaptations of microorganisms to extreme conditions. Rhodobacter, an anoxygenic aerobic phototrophic bacterial genus, represents one of the most abundant groups reported based on taxonomic diversity surveys in this ecosystem. The bacterial mat isolate Rhodobacter sp. strain Rb3 was used to study adaptation mechanisms to stress-inducing factors potentially explaining its success in a polyextreme ecosystem. We found that the Rhodobacter sp. Rb3 genome was characterized by a high abundance of genes involved in stress tolerance and adaptation strategies, among which DNA repair and oxidative stress were the most conspicuous. Moreover, many other molecular mechanisms associated with oxidative stress, photooxidation and antioxidants; DNA repair and protection; motility, chemotaxis and biofilm synthesis; osmotic stress, metal, metalloid and toxic anions resistance; antimicrobial resistance and multidrug pumps; sporulation; cold shock and heat shock stress; mobile genetic elements and toxin-antitoxin system were detected and identified as potential survival mechanism features in Rhodobacter sp. Rb3. In total, these results reveal a wide set of strategies used by the isolate to adapt and thrive under environmental stress conditions as a model of polyextreme environmental resistome.
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Affiliation(s)
- Vilma Pérez
- Laboratory of Molecular Ecology and Applied Microbiology, Departamento de Ciencias Farmacéuticas, Universidad Católica del Norte, Antofagasta, Chile.,Centre for Biotechnology & Bioengineering (CeBiB), Santiago, Chile
| | - Cristina Dorador
- Centre for Biotechnology & Bioengineering (CeBiB), Santiago, Chile.,Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta & Departamento de Biotecnología, Universidad de Antofagasta, Antofagasta, Chile
| | - Verónica Molina
- Departamento de Biología, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Valparaiso, Chile
| | - Carolina Yáñez
- Laboratorio Microbiología, Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaiso, Chile
| | - Martha Hengst
- Laboratory of Molecular Ecology and Applied Microbiology, Departamento de Ciencias Farmacéuticas, Universidad Católica del Norte, Antofagasta, Chile. .,Centre for Biotechnology & Bioengineering (CeBiB), Santiago, Chile.
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Villalobos AS, Wiese J, Aguilar P, Dorador C, Imhoff JF. Subtercola vilae sp. nov., a novel actinobacterium from an extremely high-altitude cold volcano lake in Chile. Antonie Van Leeuwenhoek 2017; 111:955-963. [PMID: 29214367 PMCID: PMC5945732 DOI: 10.1007/s10482-017-0994-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 12/01/2017] [Indexed: 11/08/2022]
Abstract
A novel actinobacterium, strain DB165T, was isolated from cold waters of Llullaillaco Volcano Lake (6170 m asl) in Chile. Phylogenetic analysis based on 16S rRNA gene sequences identified strain DB165T as belonging to the genus Subtercola in the family Microbacteriaceae, sharing 97.4% of sequence similarity with Subtercola frigoramans DSM 13057T, 96.7% with Subtercola lobariae DSM 103962T, and 96.1% with Subtercola boreus DSM 13056T. The cells were observed to be Gram-positive, form rods with irregular morphology, and to grow best at 10–15 °C, pH 7 and in the absence of NaCl. The cross-linkage between the amino acids in its peptidoglycan is type B2γ; 2,4-diaminobutyric acid is the diagnostic diamino acid; the major respiratory quinones are MK-9 and MK-10; and the polar lipids consist of phosphatidylglycerol, diphosphatidylglycerol, 5 glycolipids, 2 phospholipids and 5 additional polar lipids. The fatty acid profile of DB165T (5% >) contains iso-C14:0, iso-C16:0, anteiso-C15:0, anteiso-C17:0, and the dimethylacetal iso-C16:0 DMA. The genomic DNA G+C content of strain DB165T was determined to be 65 mol%. Based on the phylogenetic, phenotypic, and chemotaxonomic analyses presented in this study, strain DB165T (= DSM 105013T = JCM 32044T) represents a new species in the genus Subtercola, for which the name Subtercola vilae sp. nov. is proposed.
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Affiliation(s)
- Alvaro S Villalobos
- Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105, Kiel, Germany
| | - Jutta Wiese
- Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105, Kiel, Germany
| | - Pablo Aguilar
- Laboratorio de Complejidad Microbiana y Ecología Funcional and Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile.,Lake and Glacier Ecology Research Group, Institute of Ecology, University of Innsbruck, Techniker Str. 25, 6020, Innsbruck, Austria
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional and Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile.,Centre for Biotechnology and Bioengineering (CeBiB), Universidad de Antofagasta, Antofagasta, Chile
| | - Johannes F Imhoff
- Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105, Kiel, Germany.
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Docmac F, Araya M, Hinojosa IA, Dorador C, Harrod C. Habitat coupling writ large: pelagic-derived materials fuel benthivorous macroalgal reef fishes in an upwelling zone. Ecology 2017. [DOI: 10.1002/ecy.1936] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Felipe Docmac
- Facultad de Ciencias del Mar y Recursos Biológicos; Instituto de Ciencias Naturales Alexander von Humboldt; Universidad de Antofagasta; Avenida Angamos 601 Antofagasta Chile
- Universidad de Antofagasta Stable Isotope Facility (UASIF); Universidad de Antofagasta; Avenida Angamos 601 Antofagasta Chile
| | - Miguel Araya
- Facultad de Recursos Naturales Renovables; Universidad Arturo Prat; Avenida Arturo Prat Chacón 2120 Iquique Chile
| | - Ivan A. Hinojosa
- Departamento de Biología Marina; Facultad de Ciencias del Mar; Universidad Católica del Norte; Larrondo 1281 Coquimbo Chile
- Millennium Nucleus for Ecology and Sustainable Management of Oceanic Islands; Larrondo 1281 Coquimbo Chile
- Departamento de Ecología; Facultad de Ciencias; Universidad Católica de la Santísima Concepción; Alonso de Ribera 2850 Concepción Chile
| | - Cristina Dorador
- Instituto Antofagasta; Universidad de Antofagasta; Avenida Angamos 601 Antofagasta Chile
- Centro de Biotecnología y Bioingeniería (CeBiB); Avenida Angamos 601 Antofagasta Chile
- Departamento de Biotecnología; Facultad de Ciencias del Mar y Recursos Biológicos; Universidad de Antofagasta; Avenida Angamos 601 Antofagasta Chile
| | - Chris Harrod
- Facultad de Ciencias del Mar y Recursos Biológicos; Instituto de Ciencias Naturales Alexander von Humboldt; Universidad de Antofagasta; Avenida Angamos 601 Antofagasta Chile
- Universidad de Antofagasta Stable Isotope Facility (UASIF); Universidad de Antofagasta; Avenida Angamos 601 Antofagasta Chile
- School of Biological Sciences; Queen's University; 97 Lisburn Road Belfast UK
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Schmidt SK, Vimercati L, Darcy JL, Arán P, Gendron EM, Solon AJ, Porazinska D, Dorador C. A Naganishia in high places: functioning populations or dormant cells from the atmosphere? Mycology 2017; 8:153-163. [PMID: 30123637 PMCID: PMC6059072 DOI: 10.1080/21501203.2017.1344154] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 06/15/2017] [Indexed: 12/16/2022] Open
Abstract
Here, we review the current state of knowledge concerning high-elevation members of the extremophilic Cryptococcus albidus clade (now classified as the genus Naganishia). These fungi dominate eukaryotic microbial communities across the highest elevation, soil-like material (tephra) on volcanoes such as Llullaillaco, Socompa, and Saírecabur in the Atacama region of Chile, Argentina, and Bolivia. Recent studies indicate that Naganishia species are among the most resistant organisms to UV radiation, and a strain of N. friedmannii from Volcán Llullaillaco is the first organism that is known to grow during the extreme, diurnal freeze-thaw cycles that occur on a continuous basis at elevations above 6000 m.a.s.l. in the Atacama region. These and other extremophilic traits discussed in this review may serve a dual purpose of allowing Naganishia species to survive long-distance transport through the atmosphere and to survive the extreme conditions found at high elevations. Current evidence indicates that there are frequent dispersal events between high-elevation volcanoes of Atacama region and the Dry Valleys of Antarctica via "Rossby Wave" merging of the polar and sub-tropical jet streams. This dispersal hypothesis needs further verification, as does the hypothesis that Naganishia species are flexible "opportunitrophs" that can grow during rare periods of water (from melting snow) and nutrient availability (from Aeolian inputs) in one of the most extreme terrestrial habitats on Earth.
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Affiliation(s)
- Steven K Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Lara Vimercati
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - John L Darcy
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Pablo Arán
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta & Centre for Biotechnology and Bioengineering (CeBiB), Universidad de Antofagasta, Antofagasta, Chile
- Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Eli M.S Gendron
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
- Molecular, Cellular, and Developmental Biology Department, University of Colorado, Boulder, CO, USA
| | - Adam J Solon
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Dorota Porazinska
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta & Centre for Biotechnology and Bioengineering (CeBiB), Universidad de Antofagasta, Antofagasta, Chile
- Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
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Pérez V, Hengst M, Kurte L, Dorador C, Jeffrey WH, Wattiez R, Molina V, Matallana-Surget S. Bacterial Survival under Extreme UV Radiation: A Comparative Proteomics Study of Rhodobacter sp., Isolated from High Altitude Wetlands in Chile. Front Microbiol 2017; 8:1173. [PMID: 28694800 PMCID: PMC5483449 DOI: 10.3389/fmicb.2017.01173] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 06/08/2017] [Indexed: 12/21/2022] Open
Abstract
Salar de Huasco, defined as a polyextreme environment, is a high altitude saline wetland in the Chilean Altiplano (3800 m.a.s.l.), permanently exposed to the highest solar radiation doses registered in the world. We present here the first comparative proteomics study of a photoheterotrophic bacterium, Rhodobacter sp., isolated from this remote and hostile habitat. We developed an innovative experimental approach using different sources of radiation (in situ sunlight and UVB lamps), cut-off filters (Mylar, Lee filters) and a high-throughput, label-free quantitative proteomics method to comprehensively analyze the effect of seven spectral bands on protein regulation. A hierarchical cluster analysis of 40 common proteins revealed that all conditions containing the most damaging UVB radiation induced similar pattern of protein regulation compared with UVA and visible light spectral bands. Moreover, it appeared that the cellular adaptation of Rhodobacter sp. to osmotic stress encountered in the hypersaline environment from which it was originally isolated, might further a higher resistance to damaging UV radiation. Indeed, proteins involved in the synthesis and transport of key osmoprotectants, such as glycine betaine and inositol, were found in very high abundance under UV radiation compared to the dark control, suggesting the function of osmolytes as efficient reactive oxygen scavengers. Our study also revealed a RecA-independent response and a tightly regulated network of protein quality control involving proteases and chaperones to selectively degrade misfolded and/or damaged proteins.
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Affiliation(s)
- Vilma Pérez
- Laboratory of Molecular Ecology and Applied Microbiology, Department of Pharmaceutical Sciences, Universidad Católica del NorteAntofagasta, Chile.,Centre for Biotechnology and BioengineeringSantiago, Chile.,Programa de Doctorado en Ciencias Biológicas, Facultad de Ciencias de la Salud, Universidad de AntofagastaAntofagasta, Chile
| | - Martha Hengst
- Laboratory of Molecular Ecology and Applied Microbiology, Department of Pharmaceutical Sciences, Universidad Católica del NorteAntofagasta, Chile.,Centre for Biotechnology and BioengineeringSantiago, Chile
| | - Lenka Kurte
- Laboratory of Molecular Ecology and Applied Microbiology, Department of Pharmaceutical Sciences, Universidad Católica del NorteAntofagasta, Chile.,Centre for Biotechnology and BioengineeringSantiago, Chile
| | - Cristina Dorador
- Centre for Biotechnology and BioengineeringSantiago, Chile.,Laboratory of Microbial Complexity and Functional Ecology, Institute of Antofagasta and Department of Biotechnology, Universidad de AntofagastaAntofagasta, Chile
| | - Wade H Jeffrey
- Center for Environmental Diagnostics and Bioremediation, University of West Florida, PensacolaFL, United States
| | - Ruddy Wattiez
- Proteomics and Microbiology Laboratory, Research Institute of Biosciences, University of MonsMons, Belgium
| | - Veronica Molina
- Department of Biology, Faculty of Natural and Exact Sciences, Universidad de Playa AnchaValparaíso, Chile
| | - Sabine Matallana-Surget
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of StirlingStirling, United Kingdom
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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.
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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
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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.
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Affiliation(s)
- Verónica Molina
- Programa de Biodiversidad and Departamento de Biología, Facultad de Ciencias Naturales y Exactas, Observatorio de Ecología Microbiana, Universidad de Playa Ancha Valparaíso, Chile
| | - Klaudia Hernández
- Centro de Investigación Marina Quintay, Facultad de Ecología y Recursos Naturales, Universidad Andres Bello Valparaíso, 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 Valparaíso Valparaíso, 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 Antofagasta Antofagasta, Chile
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Filippidou S, Wunderlin T, Junier T, Jeanneret N, Dorador C, Molina V, Johnson DR, Junier P. A Combination of Extreme Environmental Conditions Favor the Prevalence of Endospore-Forming Firmicutes. Front Microbiol 2016; 7:1707. [PMID: 27857706 PMCID: PMC5094177 DOI: 10.3389/fmicb.2016.01707] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 10/12/2016] [Indexed: 12/21/2022] Open
Abstract
Environmental conditions unsuitable for microbial growth are the rule rather than the exception in most habitats. In response to this, microorganisms have developed various strategies to withstand environmental conditions that limit active growth. Endospore-forming Firmicutes (EFF) deploy a myriad of survival strategies in order to resist adverse conditions. Like many bacterial groups, they can form biofilms and detect nutrient scarcity through chemotaxis. Moreover, within this paraphyletic group of Firmicutes, ecophysiological optima are diverse. Nonetheless, a response to adversity that delimits this group is the formation of wet-heat resistant spores. These strategies are energetically demanding and therefore might affect the biological success of EFF. Therefore, we hypothesize that abundance and diversity of EFF should be maximized in those environments in which the benefits of these survival strategies offsets the energetic cost. In order to address this hypothesis, geothermal and mineral springs and drillings were selected because in these environments of steep physicochemical gradients, diversified survival strategies may become a successful strategy.We collected 71 samples from geothermal and mineral environments characterized by none (null), single or multiple limiting environmental factors (temperature, pH, UV radiation, and specific mineral composition). To measure success, we quantified EFF gene copy numbers (GCN; spo0A gene) in relation to total bacterial GCN (16S rRNA gene), as well as the contribution of EFF to community composition. The quantification showed that relative GCN for EFF reached up to 20% at sites characterized by multiple limiting environmental factors, whereas it corresponded to less than 1% at sites with one or no limiting environmental factor. Pyrosequencing of the 16S rRNA gene supports a higher contribution of EFF at sites with multiple limiting factors. Community composition suggested a combination of phylotypes for which active growth could be expected, and phylotypes that are most likely in the state of endospores, in all the sites. In summary, our results suggest that diversified survival strategies, including sporulation and metabolic adaptations, explain the biological success of EFF in geothermal and natural springs, and that multiple extreme environmental factors favor the prevalence of EFF.
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Affiliation(s)
- Sevasti Filippidou
- Laboratory of Microbiology, University of Neuchâtel Neuchâtel, Switzerland
| | - Tina Wunderlin
- Laboratory of Microbiology, University of Neuchâtel Neuchâtel, Switzerland
| | - Thomas Junier
- Laboratory of Microbiology, University of NeuchâtelNeuchâtel, Switzerland; Vital-IT group, Swiss Institute of BioinformaticsLausanne, Switzerland
| | - Nicole Jeanneret
- Laboratory of Microbiology, University of Neuchâtel Neuchâtel, Switzerland
| | - 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; Centre for Biotechnology and Bioengineering, CeBiB, University of ChileSantiago, Chile
| | - Veronica Molina
- Departamento de Biología, Facultad de Ciencias Naturales y Exactas. Universidad de Playa Ancha Valparaíso, Chile
| | - David R Johnson
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag) Dübendorf, Switzerland
| | - Pilar Junier
- Laboratory of Microbiology, University of Neuchâtel Neuchâtel, Switzerland
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Aguilar P, Acosta E, Dorador C, Sommaruga R. Large Differences in Bacterial Community Composition among Three Nearby Extreme Waterbodies of the High Andean Plateau. Front Microbiol 2016; 7:976. [PMID: 27446017 PMCID: PMC4914511 DOI: 10.3389/fmicb.2016.00976] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 06/06/2016] [Indexed: 11/30/2022] Open
Abstract
The high Andean plateau or Altiplano contains different waterbodies that are subjected to extreme fluctuations in abiotic conditions on a daily and an annual scale. The bacterial diversity and community composition of those shallow waterbodies is largely unexplored, particularly, of the ponds embedded within the peatland landscape (i.e., Bofedales). Here we compare the small-scale spatial variability (<1 m) in bacterial diversity and community composition between two of those ponds with contrasting apparent color, using 454 pyrosequencing of the 16S rRNA gene. Further, we compared the results with the nearest (80 m) main lagoon in the system to elucidate the importance of different environmental factors such as salinity and the importance of these ponds as a source of shared diversity. Bacterial diversity was higher in both ponds than in the lagoon and community composition was largely different among them and characterized by very low operational taxonomic unit sharing. Whereas the “green” pond with relatively low dissolved organic carbon (DOC) concentration (33.5 mg L-1) was dominated by Proteobacteria and Bacteroidetes, the one with extreme DOC concentration (424.1 mg L-1) and red hue was dominated by Cyanobacteria. By contrast, the lagoon was largely dominated by Proteobacteria, particularly by Gammaproteobacteria. A large percentage (47%) of all reads was unclassified suggesting the existence of large undiscovered bacterial diversity. Our results suggest that even at the very small-scale spatial range considered, local environmental factors are important in explaining differences in bacterial community composition in those systems. Further, our study highlights that Altiplano peatland ponds represent a hitherto unknown source of microbial diversity.
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Affiliation(s)
- Pablo Aguilar
- Lake and Glacier Ecology Research Group, Institute of Ecology, University of InnsbruckInnsbruck, Austria; Laboratory of Microbial Complexity and Functional Ecology, Antofagasta Institute, University of AntofagastaAntofagasta, Chile; Centre for Biotechnology and Bioengineering, Universidad de ChileSantiago, Chile
| | - Eduardo Acosta
- Laboratory of Microbial Complexity and Functional Ecology, Antofagasta Institute, University of AntofagastaAntofagasta, Chile; Centre for Biotechnology and Bioengineering, Universidad de ChileSantiago, Chile
| | - Cristina Dorador
- Laboratory of Microbial Complexity and Functional Ecology, Antofagasta Institute, University of AntofagastaAntofagasta, Chile; Centre for Biotechnology and Bioengineering, Universidad de ChileSantiago, Chile
| | - Ruben Sommaruga
- Lake and Glacier Ecology Research Group, Institute of Ecology, University of Innsbruck Innsbruck, Austria
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Barahona S, Dorador C, Zhang R, Aguilar P, Sand W, Vera M, Remonsellez F. Isolation and characterization of a novel Acidithiobacillus ferrivorans strain from the Chilean Altiplano: attachment and biofilm formation on pyrite at low temperature. Res Microbiol 2014; 165:782-93. [PMID: 25111023 DOI: 10.1016/j.resmic.2014.07.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 07/28/2014] [Accepted: 07/29/2014] [Indexed: 12/17/2022]
Abstract
Microorganisms are used to aid the extraction of valuable metals from low-grade sulfide ores in mines worldwide, but relatively little is known about this process in cold environments. This study comprises a preliminary analysis of the bacterial diversity of the polyextremophilic acid River Aroma located in the Chilean Altiplano, and revealed that Betaproteobacteria was the most dominant bacterial group (Gallionella-like and Thiobacillus-like). Taxa characteristic of leaching environments, such Acidithiobacillus and Leptospirillum, were detected at low abundances. Also, bacteria not associated with extremely acidic, metal-rich environments were found. After enrichment in iron- and sulfur-oxidizing media, we isolated and identified a novel psychrotolerant Acidithiobacillus ferrivorans strain ACH. This strain can grow using ferrous iron, sulfur, thiosulfate, tetrathionate and pyrite, as energy sources. Optimal growth was observed in the presence of pyrite, where cultures reached a cell number of 6.5 · 10(7) cells mL(-1). Planktonic cells grown with pyrite showed the presence of extracellular polymeric substances (10 °C and 28 °C), and a high density of cells attached to pyrite grains were observed at 10 °C by electron microscopy. The attachment of cells to pyrite coupons and the presence of capsular polysaccharides were visualized by using epifluorescence microscopy, through nucleic acid and lectin staining with Syto(®)9 and TRITC-Con A, respectively. Interestingly, we observed high cell adhesion including the formation of microcolonies within 21 days of incubation at 4 °C, which was correlated with a clear induction of capsular polysaccharides production. Our data suggests that attachment to pyrite is not temperature-dependent in At. ferrivorans ACH. The results of this study highlight the potential of this novel psychrotolerant strain in oxidation and attachment to minerals under low-temperature conditions.
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Affiliation(s)
- Sergio Barahona
- Laboratorio de Tecnología de Membranas, Biotecnología y Medio Ambiente, Departamento de Ingeniería Química, Universidad Católica del Norte, Avenida Angamos 0610, Antofagasta, Chile; Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Centro de Bioinnovación, Facultad de Ciencias del Mar y Recursos Biológicos, Departamento de Biotecnología, Universidad de Antofagasta, Avenida Angamos 0601, Antofagasta, Chile.
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Centro de Bioinnovación, Facultad de Ciencias del Mar y Recursos Biológicos, Departamento de Biotecnología, Universidad de Antofagasta, Avenida Angamos 0601, Antofagasta, Chile.
| | - Ruiyong Zhang
- Biofilm Centre, University of Dusiburg-Essen, 5, 45141 Essen, Germany.
| | - Pablo Aguilar
- Laboratorio de Tecnología de Membranas, Biotecnología y Medio Ambiente, Departamento de Ingeniería Química, Universidad Católica del Norte, Avenida Angamos 0610, Antofagasta, Chile; Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Centro de Bioinnovación, Facultad de Ciencias del Mar y Recursos Biológicos, Departamento de Biotecnología, Universidad de Antofagasta, Avenida Angamos 0601, Antofagasta, Chile.
| | - Wolfgang Sand
- Biofilm Centre, University of Dusiburg-Essen, 5, 45141 Essen, Germany.
| | - Mario Vera
- Biofilm Centre, University of Dusiburg-Essen, 5, 45141 Essen, Germany.
| | - Francisco Remonsellez
- Laboratorio de Tecnología de Membranas, Biotecnología y Medio Ambiente, Departamento de Ingeniería Química, Universidad Católica del Norte, Avenida Angamos 0610, Antofagasta, Chile.
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Schulz D, Beese P, Ohlendorf B, Erhard A, Zinecker H, Dorador C, Imhoff JF. Abenquines A-D: aminoquinone derivatives produced by Streptomyces sp. strain DB634. J Antibiot (Tokyo) 2011; 64:763-8. [PMID: 21952099 DOI: 10.1038/ja.2011.87] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
New bioactive secondary metabolites, called abenquines, were found in the fermentation broth of Streptomyces sp. strain DB634, which was isolated from the soils of the Chilean highland of the Atacama Desert. They are composed of an amino acid linked to an N-acetyl-aminobenzoquinone. Isolation of the abenquines (1-4), their structure elucidation by NMR analysis and MS, as well as the kinetics of their production are presented. The abenquines show inhibitory activity against bacteria, dermatophytic fungi and phosphodiesterase type 4b. The amino acid attached to the quinone is relevant to the enzyme inhibitory activity.
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Affiliation(s)
- Dirk Schulz
- Kieler Wirkstoff-Zentrum at the Leibniz-Institute of Marine Sciences (IFM-GEOMAR), Kiel, Germany
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