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Joshi A, Joshi R, Koradiya P, Vank H. Changes of microbiome in response to supplements with silver nanoparticles in cotton rhizosphere. J Basic Microbiol 2023; 63:1451-1463. [PMID: 37718380 DOI: 10.1002/jobm.202300275] [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: 05/21/2023] [Revised: 07/20/2023] [Accepted: 08/26/2023] [Indexed: 09/19/2023]
Abstract
The current study focuses on analyzing the effects of supplements containing silver nanoparticles (AgNPs) on plant growth and rhizospheric bacterial communities. Specifically, the impact of AgNP supplements was assessed on both plant growth promoting traits and bacterial communities in the soil. To do this, a screening process was conducted to select bacteria capable of synthesizing AgNPs through extracellular biosynthesis. UV-Visible spectrophotometer, Fourier transform infrared, X-ray diffraction, scanning electron microscope, and field emission scanning electron microscopy all confirmed, produced AgNPs is in agglomerates form. The resulting AgNPs were introduced into soil along with various supplements and their effects were evaluated after 10 days using next generation sequencing (Illumina-16S rDNA V3-V4 region dependent) to analyze changes in bacterial communities. Seed germination, root-shoot biomass and chlorophyll content were used to assess the growth of the cotton plant, whereas the bacterial ability to promote growth was evaluated by measuring its culturable diversity including traits like phosphate solubilization and indole acetic acid production. The variance in Bray-Curtis β diversity among six selected combinations including control depends largely on the type of added supplements contributing to 95%-97% of it. Moreover, seed germination improves greatly between 63% and 100% at a concentration range of 1.4 to 2.8 mg/L with different types of supplements. Based on the results obtained through this study, it is evident that using AgNPs along with fructose could be an effective tool for promoting Gossypium hirsutum growth and enhancing plant growth traits like profiling rhizospheric bacteria. The results that have been obtained endorse the idea of boosting the growth of rhizospheric bacteria in a natural way when AgNPs are present. Using these supplements in fields that have been contaminated will lead to a better understanding of how ecological succession occurs among rhizospheric bacteria, and what effect it has on the growth of plants.
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Affiliation(s)
- Abhijeet Joshi
- Department of Microbiology, Atmiya University, Rajkot, Gujarat, India
| | - Radhika Joshi
- Department of Microbiology, Atmiya University, Rajkot, Gujarat, India
| | - Prushti Koradiya
- Department of Microbiology, Atmiya University, Rajkot, Gujarat, India
| | - Hetvi Vank
- Department of Microbiology, Atmiya University, Rajkot, Gujarat, India
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Ruiz-Blas F, Muñoz-Hisado V, Garcia-Lopez E, Moreno A, Bartolomé M, Leunda M, Martinez-Alonso E, Alcázar A, Cid C. The hidden microbial ecosystem in the perennial ice from a Pyrenean ice cave. Front Microbiol 2023; 14:1110091. [PMID: 36778858 PMCID: PMC9909108 DOI: 10.3389/fmicb.2023.1110091] [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: 11/28/2022] [Accepted: 01/03/2023] [Indexed: 01/27/2023] Open
Abstract
Over the last years, perennial ice deposits located within caves have awakened interest as places to study microbial communities since they represent unique cryospheric archives of climate change. Since the beginning of the twentieth century, the temperature has gradually increased, and it is estimated that by the end of this century the increase in average temperature could be around 4.0°C. In this context of global warming the ice deposits of the Pyrenean caves are undergoing a significant regression. Among this type of caves, that on the Cotiella Massif in the Southern Pyrenees is one of the southernmost studied in Europe. These types of caves house microbial communities which have so far been barely explored, and therefore their study is necessary. In this work, the microbial communities of the Pyrenean ice cave A294 were identified using metabarcoding techniques. In addition, research work was carried out to analyze how the age and composition of the ice affect the composition of the bacterial and microeukaryotic populations. Finally, the in vivo effect of climate change on the cellular machinery that allow microorganisms to live with increasing temperatures has been studied using proteomic techniques.
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Affiliation(s)
- Fátima Ruiz-Blas
- Centro de Astrobiología (CAB), CSIC-INTA, Madrid, Spain
- Section Geomicrobiology, GFZ German Research Centre for Geosciences, Potsdam, Germany
| | | | | | - Ana Moreno
- Departamento de Procesos Geoambientales y Cambio Global, Instituto Pirenaico de Ecología - CSIC, Zaragoza, Spain
| | - Miguel Bartolomé
- Departamento de Procesos Geoambientales y Cambio Global, Instituto Pirenaico de Ecología - CSIC, Zaragoza, Spain
- Institut für Geologie und Mineralogie, Universität zu Köln, Köln, Germany
| | - Maria Leunda
- Institute of Plant Sciences and Oeschger Centre for Climate Change Research, University of Bern, Bern, Switzerland
- Swiss Federal Research Institute for Forest, Snow and Landscape Research WSL, Zurich, Switzerland
- Department of Plant Biology and Ecology, University of the Basque Country, Leioa, Spain
| | - Emma Martinez-Alonso
- Department of Investigation, Instituto Ramón y Cajal de Investigación Sanitaria, Hospital Ramón y Cajal, Madrid, Spain
| | - Alberto Alcázar
- Department of Investigation, Instituto Ramón y Cajal de Investigación Sanitaria, Hospital Ramón y Cajal, Madrid, Spain
| | - Cristina Cid
- Centro de Astrobiología (CAB), CSIC-INTA, Madrid, Spain
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Asfour L, Smyth D, Whitchurch CB, Cavaliere R, Roland JT. Fluorescence in situ hybridization and microbial community profiling analysis of explanted cochlear implants. Acta Otolaryngol 2022; 142:395-401. [PMID: 35549817 DOI: 10.1080/00016489.2022.2070931] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
BACKGROUND Cochlear implant (CI) infections affect a small, but significant number of patients. Unremitting infections can lead to explantation. Fluorescence in situ hybridization (FISH) and microbial community profiling (MCP) are methods of studying microbial environments of explanted devices that can provide information to reduce morbidity and costs of infected CIs. AIMS/OBJECTIVES To describe the results and clinical significance of bacterial analyses conducted on explanted CIs. MATERIAL AND METHODS Between 2013 and 2017, 12 explanted devices underwent microbiological analysis in addition to the manufacturer's device failure analysis. Patients' clinical history, infection status and outcome were reviewed and correlated with microbial analysis results. RESULTS From 2013 to 2017, 12 Cochlear™ devices from 11 patients underwent additional MCP or FISH analysis. Five devices were explanted due to suspected implant associated infection, and seven were explanted for other reasons. FISH analysis revealed biofilm presence on all infected devices, only partial correlation of cultures with biofilm composition and confirmation that biofilm formation occurs preferentially at particular device interfaces and geometries. MCP analysis presented challenges in data analysis inherent to its technique but correlated with cultures of infected devices and suggested a diverse microbial composition of explanted devices. CONCLUSIONS AND SIGNIFICANCE Microbial analysis of explanted devices can aid in further elucidating treatment approaches to infected CIs.
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Affiliation(s)
- Leena Asfour
- Department of Otolaryngology—Head & Neck Surgery, New York University School of Medicine, New York City, NY, USA
| | - Daniel Smyth
- Cochlear Limited, 1 University Avenue, Macquarie University, Sydney, Australia
| | | | - Rosalia Cavaliere
- The ithree Institute, University of Technology Sydney, Ultimo, Australia
| | - J. Thomas Roland
- Department of Otolaryngology—Head & Neck Surgery, New York University School of Medicine, New York City, NY, USA
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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] [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: 05/25/2021] [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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Hägglund M, Bäckman S, Macellaro A, Lindgren P, Borgmästars E, Jacobsson K, Dryselius R, Stenberg P, Sjödin A, Forsman M, Ahlinder J. Accounting for Bacterial Overlap Between Raw Water Communities and Contaminating Sources Improves the Accuracy of Signature-Based Microbial Source Tracking. Front Microbiol 2018; 9:2364. [PMID: 30356843 PMCID: PMC6190859 DOI: 10.3389/fmicb.2018.02364] [Citation(s) in RCA: 12] [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: 06/05/2018] [Accepted: 09/14/2018] [Indexed: 11/30/2022] Open
Abstract
Microbial source tracking (MST) analysis is essential to identifying and mitigating the fecal pollution of water resources. The signature-based MST method uses a library of sequences to identify contaminants based on operational taxonomic units (OTUs) that are unique to a certain source. However, no clear guidelines for how to incorporate OTU overlap or natural variation in the raw water bacterial community into MST analyses exist. We investigated how the inclusion of bacterial overlap between sources in the library affects source prediction accuracy. To achieve this, large-scale sampling - including feces from seven species, raw sewage, and raw water samples from water treatment plants - was followed by 16S rRNA amplicon sequencing. The MST library was defined using three settings: (i) no raw water communities represented; (ii) raw water communities selected through clustering analysis; and (iii) local water communities collected across consecutive years. The results suggest that incorporating either the local background or representative bacterial composition improves MST analyses, as the results were positively correlated to measured levels of fecal indicator bacteria and the accuracy at which OTUs were assigned to the correct contamination source increased fourfold. Using the proportion of OTUs with high source origin probability, underpinning a contaminating signal, is a solid foundation in a framework for further deciphering and comparing contaminating signals derived in signature-based MST approaches. In conclusion, incorporating background bacterial composition of water in MST can improve mitigation efforts for minimizing the spread of pathogenic and antibiotic resistant bacteria into essential freshwater resources.
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Affiliation(s)
- Moa Hägglund
- Division of CBRN Security and Defence, FOI, Swedish Defence Research Agency, Umeå, Sweden
| | - Stina Bäckman
- Division of CBRN Security and Defence, FOI, Swedish Defence Research Agency, Umeå, Sweden
| | - Anna Macellaro
- Division of CBRN Security and Defence, FOI, Swedish Defence Research Agency, Umeå, Sweden
| | - Petter Lindgren
- Division of CBRN Security and Defence, FOI, Swedish Defence Research Agency, Umeå, Sweden
| | - Emmy Borgmästars
- Surgery Section, Department of Surgical and Perioperative Sciences, Umeå University, Umeå, Sweden
| | | | | | - Per Stenberg
- Division of CBRN Security and Defence, FOI, Swedish Defence Research Agency, Umeå, Sweden
- Department of Ecology and Environmental Science (EMG), Umeå University, Umeå, Sweden
| | - Andreas Sjödin
- Division of CBRN Security and Defence, FOI, Swedish Defence Research Agency, Umeå, Sweden
- Computational Life Science Cluster (CLiC), Department of Chemistry, Umeå University, Umeå, Sweden
| | - Mats Forsman
- Division of CBRN Security and Defence, FOI, Swedish Defence Research Agency, Umeå, Sweden
| | - Jon Ahlinder
- Division of CBRN Security and Defence, FOI, Swedish Defence Research Agency, Umeå, Sweden
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