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Avendaño R, Muñoz-Montero S, Rojas-Gätjens D, Fuentes-Schweizer P, Vieto S, Montenegro R, Salvador M, Frew R, Kim J, Chavarría M, Jiménez JI. Production of selenium nanoparticles occurs through an interconnected pathway of sulphur metabolism and oxidative stress response in Pseudomonas putida KT2440. Microb Biotechnol 2023; 16:931-946. [PMID: 36682039 PMCID: PMC10128140 DOI: 10.1111/1751-7915.14215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 01/23/2023] Open
Abstract
The soil bacterium Pseudomonas putida KT2440 has been shown to produce selenium nanoparticles aerobically from selenite; however, the molecular actors involved in this process are unknown. Here, through a combination of genetic and analytical techniques, we report the first insights into selenite metabolism in this bacterium. Our results suggest that the reduction of selenite occurs through an interconnected metabolic network involving central metabolic reactions, sulphur metabolism, and the response to oxidative stress. Genes such as sucA, D2HGDH and PP_3148 revealed that the 2-ketoglutarate and glutamate metabolism is important to convert selenite into selenium. On the other hand, mutations affecting the activity of the sulphite reductase decreased the bacteria's ability to transform selenite. Other genes related to sulphur metabolism (ssuEF, sfnCE, sqrR, sqr and pdo2) and stress response (gqr, lsfA, ahpCF and sadI) were also identified as involved in selenite transformation. Interestingly, suppression of genes sqrR, sqr and pdo2 resulted in the production of selenium nanoparticles at a higher rate than the wild-type strain, which is of biotechnological interest. The data provided in this study brings us closer to understanding the metabolism of selenium in bacteria and offers new targets for the development of biotechnological tools for the production of selenium nanoparticles.
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Affiliation(s)
- Roberto Avendaño
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, Costa Rica
| | | | - Diego Rojas-Gätjens
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, Costa Rica
| | - Paola Fuentes-Schweizer
- Escuela de Química, Universidad de Costa Rica, San José, Costa Rica.,Centro de Electroquímica y Energía Química (CELEQ), Universidad de Costa Rica, San José, Costa Rica
| | - Sofía Vieto
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, Costa Rica
| | - Rafael Montenegro
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, Costa Rica
| | - Manuel Salvador
- Biotechnology Applications, IDENER Research & Development, Seville, Spain
| | - Rufus Frew
- Department of Chemistry, University of Leicester, Leicester, UK
| | - Juhyun Kim
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, KNU Institute for Microorganisms, Kyungpook National University, Daegu, Korea
| | - Max Chavarría
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, Costa Rica.,Escuela de Química, Universidad de Costa Rica, San José, Costa Rica.,Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica
| | - Jose I Jiménez
- Department of Life Sciences, Imperial College London, London, UK
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Garcia-Lopez E, Moreno A, Bartolomé M, Leunda M, Sancho C, Cid C. Glacial Ice Age Shapes Microbiome Composition in a Receding Southern European Glacier. Front Microbiol 2021; 12:714537. [PMID: 34867842 PMCID: PMC8636055 DOI: 10.3389/fmicb.2021.714537] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 10/08/2021] [Indexed: 11/13/2022] Open
Abstract
Glaciers and their microbiomes are exceptional witnesses of the environmental conditions from remote times. Climate change is threatening mountain glaciers, and especially those found in southern Europe, such as the Monte Perdido Glacier (northern Spain, Central Pyrenees). This study focuses on the reconstruction of the history of microbial communities over time. The microorganisms that inhabit the Monte Perdido Glacier were identified using high-throughput sequencing, and the microbial communities were compared along an altitudinal transect covering most of the preserved ice sequence in the glacier. The results showed that the glacial ice age gradient did shape the diversity of microbial populations, which presented large differences throughout the last 2000 years. Variations in microbial community diversity were influenced by glacial conditions over time (nutrient concentration, chemical composition, and ice age). Some groups were exclusively identified in the oldest samples as the bacterial phyla Fusobacteria and Calditrichaeota, or the eukaryotic class Rhodophyceae. Among groups only found in modern samples, the green sulfur bacteria (phylum Chlorobi) stood out, as well as the bacterial phylum Gemmatimonadetes and the eukaryotic class Tubulinea. A patent impact of human contamination was also observed on the glacier microbiome. The oldest samples, corresponding to the Roman Empire times, were influenced by the beginning of mining exploitation in the Pyrenean area, with the presence of metal-tolerant microorganisms. The most recent samples comprise 600-year-old ancient ice in which current communities are living.
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Affiliation(s)
- Eva Garcia-Lopez
- Molecular Evolution Department, Centro de Astrobiologia (CSIC-INTA), Madrid, Spain
| | - Ana Moreno
- Departamento de Procesos Geoambientales y Cambio Global, Instituto Pirenaico de Ecología-CSIC, Zaragoza, Spain
| | - Miguel Bartolomé
- Departamento de Geología, Museo de Ciencias Naturales-CSIC, Madrid, Spain
| | - Maria Leunda
- Oeschger Centre for Climate Change Research, Institute of Plant Sciences, University of Bern, Bern, Switzerland.,Swiss Federal Research Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Carlos Sancho
- Departamento de Ciencias de la Tierra, Universidad de Zaragoza, Zaragoza, Spain
| | - Cristina Cid
- Molecular Evolution Department, Centro de Astrobiologia (CSIC-INTA), Madrid, Spain
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Microbial Community Composition Correlates with Metal Sorption in an Ombrotrophic Boreal Bog: Implications for Radionuclide Retention. SOIL SYSTEMS 2021. [DOI: 10.3390/soilsystems5010019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Microbial communities throughout the 6.5 m depth profile of a boreal ombrotrophic bog were characterized using amplicon sequencing of archaeal, fungal, and bacterial marker genes. Microbial populations and their relationship to oxic and anoxic batch sorption of radionuclides (using radioactive tracers of I, Se, Cs, Ni, and Ag) and the prevailing metal concentrations in the natural bog was investigated. The majority of the detected archaea belonged to the Crenarchaeota, Halobacterota, and Thermoplasmatota, whereas the fungal communities consisted of Ascomycota, Basidiomycota, and unclassified fungi. The bacterial communities consisted mostly of Acidobacteriota, Proteobacteria, and Chloroflexi. The occurrence of several microbial genera were found to statistically significantly correlate with metal concentrations as well as with Se, Cs, I, and Ag batch sorption data. We suggest that the metal concentrations of peat, gyttja, and clay layers affect the composition of the microbial populations in these nutrient-low conditions and that particularly parts of the bacterial and archaeal communities tolerate high concentrations of potentially toxic metals and may concurrently contribute to the total retention of metals and radionuclides in this ombrotrophic environment. In addition, the varying metal concentrations together with chemical, mineralogical, and physical factors may contribute to the shape of the total archaeal and bacterial populations and most probably shifts the populations for more metal resistant genera.
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Lusa M, Knuutinen J, Lindgren M, Virkanen J, Bomberg M. Microbial communities in a former pilot-scale uranium mine in Eastern Finland - Association with radium immobilization. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 686:619-640. [PMID: 31185409 DOI: 10.1016/j.scitotenv.2019.05.432] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 05/09/2019] [Accepted: 05/28/2019] [Indexed: 06/09/2023]
Abstract
The bacterial, fungal and archaeal communities were characterized in 17 top soil organic and mineral layer samples and in top sediment samples of the Paukkajanvaara area, a former pilot-scale uranium mine, located in Eno, Eastern Finland, using amplicon sequencing and qPCR. Soil and sediment samples were in addition analyzed for radium (226Ra), sulfate (SO42-), nitrate (NO3-) and phosphate (PO43-) concentrations. New bacterial strains, representing Pseudomonas spp., were isolated from the mine and reference area and used in laboratory experiments on uptake and leaching of radium (Ra). The effect of these strains on the sulfate leaching from the soil samples was also tested in vitro. Between 6 × 106 and 5 × 108 copies g-1 DW (dry weight) of bacterial 16S rRNA genes, 5 × 105-1 × 108 copies g-1 DW archaeal 16S rRNA genes and 1 × 105-1 × 108 copies g-1 DW fungal 5.8S rRNA genes were detected in the samples. A total of 814, 54 and 167 bacterial, archaeal and fungal genera, respectively, were identified. Proteobacteria, Euryarchaeota and Mortiriella were the dominant bacterial, archaeal and fungal phyla, respectively. All tested Pseudomonas spp. strains isolates from Paukkajanvaara removed Ra from the solution, but the amount of removed Ra depended on incubation conditions (temperature, time and nutrient broth). The highest removal of Ra (5320 L/kg DW) was observed by the Pseudomonas sp. strain T5-6-I at 37 °C. All Pseudomonas spp. strains decreased the release of Ra from soil with an average of 23% while simultaneously increasing the concentration of SO42- in the solution by 11%. As Pseudomonas spp. were frequent in both the sequence data and the cultures, these bacteria may play an important role in the immobilization of Ra in the Paukkajanvaara mine area.
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Affiliation(s)
- Merja Lusa
- Department of Chemistry, Radiochemistry, Faculty of Science, University of Helsinki, Finland.
| | - Jenna Knuutinen
- Department of Chemistry, Radiochemistry, Faculty of Science, University of Helsinki, Finland
| | - Marcus Lindgren
- Department of Chemistry, Radiochemistry, Faculty of Science, University of Helsinki, Finland
| | - Juhani Virkanen
- Department of Geosciences and Geography, Faculty of Science, University of Helsinki, Finland
| | - Malin Bomberg
- VTT Technical Research Centre of Finland, Espoo, Finland
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Lusa M, Help H, Honkanen AP, Knuutinen J, Parkkonen J, Kalasová D, Bomberg M. The reduction of selenium(IV) by boreal Pseudomonas sp. strain T5-6-I - Effects on selenium(IV) uptake in Brassica oleracea. ENVIRONMENTAL RESEARCH 2019; 177:108642. [PMID: 31430668 DOI: 10.1016/j.envres.2019.108642] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 08/07/2019] [Accepted: 08/08/2019] [Indexed: 06/10/2023]
Abstract
Selenium (Se) is an essential micronutrient but toxic when taken in excessive amounts. Therefore, understanding the metabolic processes related to selenium uptake and bacteria-plant interactions coupled with selenium metabolism are of high importance. We cultivated Brassica oleracea with the previously isolated heterotrophic aerobic Se(IV)-reducing Pseudomonas sp. T5-6-I strain to better understand the phenomena of bacteria-mediated Se(IV) reduction on selenium availability to the plants. B. oleracea grown on Murashige and Skoog medium (MS-salt agar) with and without of Pseudomonas sp. were amended with Se(IV)/75Se(IV), and selenium transfer into plants was studied using autoradiography and gamma spectroscopy. XANES was in addition used to study the speciation of selenium in the B. oleracea plants. In addition, the effects of Se(IV) on the protein expression in B. oleracea was studied using HPLC-SEC. TEM and confocal microscopy were used to follow the bacterial/Se-aggregate accumulation in plants and the effects of bacterial inoculation on root-hair growth. In the tests using 75Se(IV) on average 130% more selenium was translocated to the B. oleracea plants grown with Pseudomonas sp. compared to the plants grown with selenium, but without Pseudomonas sp.. In addition, these bacteria notably increased root hair density. Changes in the protein expression of B. oleracea were observed on the ∼30-58 kDa regions in the Se(IV) treated samples, probably connected e.g. to the oxidative stress induced by Se(IV) or expression of proteins connected to the Se(IV) metabolism. Based on the XANES measurements, selenium appears to accumulate in B. oleracea mainly in organic C-Se-H and C-Se-C bonds with and without bacteria inoculation. We conclude that the Pseudomonas sp. T5-6-I strain seems to contribute positively to the selenium accumulation in plants, establishing the high potential of Se0-producing bacteria in the use of phytoremediation and biofortification of selenium.
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Affiliation(s)
- Merja Lusa
- Department of Chemistry, Radiochemistry, Faculty of Science, University of Helsinki, Finland.
| | - Hanna Help
- Department of Physics, X-Ray Laboratory, Faculty of Science, University of Helsinki, Finland
| | - Ari-Pekka Honkanen
- Department of Physics, X-Ray Laboratory, Faculty of Science, University of Helsinki, Finland
| | - Jenna Knuutinen
- Department of Chemistry, Radiochemistry, Faculty of Science, University of Helsinki, Finland
| | | | - Dominika Kalasová
- CEITEC - Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Malin Bomberg
- Material Recycling and Geotechnology, VTT, Technical Research Center of Finland, Espoo, Finland
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Honkanen AP, Ollikkala S, Ahopelto T, Kallio AJ, Blomberg M, Huotari S. Johann-type laboratory-scale x-ray absorption spectrometer with versatile detection modes. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2019; 90:033107. [PMID: 30927829 DOI: 10.1063/1.5084049] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 03/01/2019] [Indexed: 06/09/2023]
Abstract
We present a low-cost laboratory X-ray absorption spectrometer that uses a conventional X-ray tube source and bent Johann-type crystal monochromators. The instrument is designed for X-ray absorption spectroscopy studies in the 4-20 keV range which covers most K edges of 3d transition metals and L edges of 5d transition metals and actinides. The energy resolution is typically in the range of 1-5 eV at 10 keV depending on the crystal analyser and the Bragg angle. Measurements can be performed in transmission, fluorescence, and imaging modes. Due to its simple and modular design, the spectrometer can be modified to accommodate additional equipment and complex sample environments required for in situ studies. A showcase of various applications is presented.
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Affiliation(s)
- Ari-Pekka Honkanen
- Department of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Sami Ollikkala
- Department of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Taru Ahopelto
- Department of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Antti-Jussi Kallio
- Department of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Merja Blomberg
- Department of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Simo Huotari
- Department of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
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